Publications

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Currently 1992 publications with reference to de.NBI Cloud are listed.

Recently added publication

Unsupervised anomaly detection in medical imaging using aggregated normative diffusion
A. Frotscher - J. Kapoor, T. Wolfers, C. Baumgartner, et al. - Elsevier BV, 2026

Unsupervised anomaly detection in medical imaging using aggregated normative diffusion
A. Frotscher - J. Kapoor, T. Wolfers, C. Baumgartner, et al. - Elsevier BV, 2026

Complete chloroplast genome assembly of Rubroshorea leprosula wood from Indonesia for phylogenetic and conservation studies
A. Fadilah - A. Hikmat, L. Karlinasari, F. Dwiyanti, et al. - Frontiers Media SA, 2026 usegalaxy.eu

Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults
N. Raethong - P. Patumcharoenpol, W. Vongsangnak, - Springer Science and Business Media LLC, 2026 usegalaxy.eu

Germline fate determination by a single ARGONAUTE protein in Ectocarpus
V. Bukhanets - R. Batista, F. Haas, R. Luthringer, et al. - Proceedings of the National Academy of Sciences, 2026

Germline fate determination by a single ARGONAUTE protein in Ectocarpus
V. Bukhanets - R. Batista, F. Haas, R. Luthringer, et al. - Proceedings of the National Academy of Sciences, 2026

ERGA-BGE Genome of Ailoscolex lacteospumosus Bouché, 1969 – the enigmatic milky worm endemic to the Pyrenees
M. Novo - D. Marchán, S. Gérard, A. Navarro, et al. - F1000 Research Ltd, 2026 usegalaxy.eu

ERGA-BGE genome of Albinaria teres (Olivier, 1801): a rock-dwelling land snail endemic to the island of Crete, Greece
D. Karakasi - K. Vardinoyannis, G. Bolanakis, E. Bitzilekis, et al. - F1000 Research Ltd, 2026 usegalaxy.eu

Platelet Casein Kinase 2α is a pivotal player in arterial thrombotic occlusion and post-ischemic myocardial remodeling
M. Fischer - M. Sigle, M. Manke, J. Marzi, et al. - Oxford University Press (OUP), 2026

Fungal Isolates Enriched Under Anaerobic Conditions from Buffalo Rumen Fluid for Lignocellulosic Rice Straw Conversion and Biogas Production Potential
N. Thongbunrod - P. Chaiprasert, - Springer Science and Business Media LLC, 2026 usegalaxy.eu

Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes
S. Haydar - R. Bednarz, P. Laurette, I. Sobitov, et al. - Springer Science and Business Media LLC, 2026 usegalaxy.eu

Age- and BMI-Dependent Psoas and Gluteus Muscle Mass in 27,805 Participants of the Population-Based German National Cohort (NAKO Gesundheitsstudie): A Deep-Learning 3T MRI Study
L. Kiefer - M. Winter, S. Pappa, M. Fischer, et al. - MDPI AG, 2026

Association between molecular and quantitative variability in a tomato broad cross identified by sequence-specific markers developed from transcriptomic polymorphism for the small Heat Shock Protein (sHSP) cluster in chromosome six
P. Cacchiarelli - V. Goytia Bertero, I. Garcia Labari, D. Arce, et al. - Springer Science and Business Media LLC, 2026 usegalaxy.eu

ERGA-BGE genome of Erebia palarica Chapman, 1905: a montane butterfly endemic to North-West Spain
M. Vila Taboada - L. Torrado-Blanco, N. Ryrholm, D. Romero-Pedreira, et al. - F1000 Research Ltd, 2026 usegalaxy.eu

Foxi1 regulates multipotent mucociliary progenitors and ionocyte specification through transcriptional and epigenetic mechanisms
S. Bowden - M. Brislinger-Engelhardt, M. Hansen, A. Andricek, et al. - Public Library of Science (PLoS), 2026 usegalaxy.eu

No evidence for the putative nitric oxide sensor NsrR as a key regulator of magnetosome formation in Magnetospirillum gryphiswaldense
A. Woller - R. Uebe, D. Schüler, - Oxford University Press (OUP), 2026 usegalaxy.eu

Phylogenetic based dissection of eukaryotic Mo-insertase functionality: From mechanism to complex assembly
T. Schmidt - A. Hassan, B. Pucker, T. Kruse, et al. - bioRxiv - openRxiv, 2026

Evolutionary transcriptomics unveils rapid changes of gene expression patterns in flowering plants
C. Schuster - A. Gabel, H. Drost, I. Grosse, et al. - Elsevier BV, 2026

Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study
A. Nekrutenko - D. Callan, M. Van Den Beek, D. Baker, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

Comparative genomics reveals specialization and divergent virulence potential in Vibrio vulnificus , Vibrio navarrensis , and Vibrio cidicii
K. Lydon - M. Lott, - American Society for Microbiology, 2025 usegalaxy.eu

Immunogenic Streptococcus equi cell surface proteins identified by ORFeome phage display
J. Wan - E. Weldon, G. Ganser, E. Morris, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Benchmarking the PAM compatibility of Cas12a variants for high-throughput yeast genetic variant engineering
W. Xie - Z. Cai, Z. Bao, - American Society for Microbiology, 2025 usegalaxy.eu

Learning diverse and generic representations of the brain with large-scale multi-task pretraining
E. Leonardsen - A. Dahl, M. Holm, A. de Lange, et al. - medRxiv - openRxiv, 2025

Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR
M. Marin-Recinos - B. Pucker, - Springer Science and Business Media LLC, 2025

lncRNA LINC-PINT controls lymphatic function and inflammatory profile in lymphedema
N. Laugero - C. Peghaire, L. Verdu, E. Balzan, et al. - American Association for the Advancement of Science (AAAS), 2025 usegalaxy.eu

First report of mitochondrial genome of Cloeon viridulum (Ephemeroptera: Baetidae) from Hebei, China
M. Lv - T. Zhu, - Informa UK Limited, 2025 usegalaxy.eu

Empowering Healthy Lifestyle Behavior Through Personalized Intervention Portfolios Using a Healthy Lifestyle Recommender System to Prevent and Control Obesity in Young Adults: Pilot Study Protocol from the HealthyW8 Project
S. García - M. Ródenas-Munar, T. Bohn, A. Kemperman, et al. - MDPI AG, 2025 usegalaxy.eu

Detection of disk-jet coprecession in a tidal disruption event
Y. Wang - Z. Lin, L. Wu, W. Lei, et al. - American Association for the Advancement of Science (AAAS), 2025 usegalaxy.eu

BlueEdge neural network approach and its application to automated data type classification in mobile edge computing
N. Elmobark - H. El-ghareeb, S. Elhishi, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Complete genome sequence of Pseudomonas aeruginosa bacteriophage PaFZ4 isolated from Dhaka, Bangladesh
Z. Mahtab - F. Tamanna, I. Jabeen, S. Islam, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Inhibition of Escherichia coli O157:H7 Growth Through Nutrient Competition by Non-O157 E. coli Isolated from Cattle
J. Maki - K. Mou, J. Trachsel, C. Loving, et al. - MDPI AG, 2025 usegalaxy.eu

A Putative Interaction between the Transmembrane Domains of Streptococcus pyogenes Sortase A and Its Endogenous Substrate M Protein Revealed by Molecular Dynamics Simulations
N. Avery - E. Tahti, P. Spiegel, J. Antos, et al. - American Chemical Society (ACS), 2025 usegalaxy.eu

Antagonistic drug interactions protect commensal Bacteroidaceae from macrolides via an RND-type efflux pump
P. Müller - V. Schmidtchen, J. de la Cuesta-Zuluaga, L. Pérez Jiménez, et al. - Informa UK Limited, 2025

eggNOG v7: phylogeny-based orthology predictions and functional annotations
A. Hernández-Plaza - Z. Deng, F. Robledo-Yagüe, D. Szklarczyk, et al. - Oxford University Press (OUP), 2025

Saturation mutagenesis identifies activating and resistance-inducing FGFR kinase domain mutations
C. Tangermann - A. Ghosh, M. Ziegler, F. Facchinetti, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Multi-locus phylogenetic network analysis of Ampelomyces mycoparasites isolated from diverse powdery mildews in Australia and the generation of two de novo genome assemblies
L. Goldspink - A. Sotiropoulos, A. Idnurm, G. Ash, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

SpeckSeq enables high-throughput functional stratification of MEFV variants in autoinflammatory diseases
P. Bronnec - S. Dalmon, C. Briand, O. Allatif, et al. - Rockefeller University Press, 2025 usegalaxy.eu

CRISPR/Cas9 targeted genetic screening in Physcomitrella identifies novel cell division genes
K. Maekawa - N. van Gessel, R. Reski, E. Kozgunova, et al. - Frontiers Media SA, 2025

A smart community interactive art therapy platform based on multimodal computer graphics and resilient artificial intelligence for home-based elderly care
D. Sang - L. Miao, Q. Wu, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Out of sight, but not out of mind: Key issues regarding seafloor macrolitter monitoring
G. Hanke - M. Canals, R. Nakajima, M. Bergmann, et al. - Elsevier BV, 2025

Molecular markers of stress in the sea urchin embryo test: Analysing the effect of climate change and pollutant mixtures on Paracentrotus lividus larvae
J. Bertucci - A. Blanco Osorio, L. Vidal-Liñán, J. Bellas, et al. - Elsevier BV, 2025 usegalaxy.eu

Cladistic Relationships and Landscape Genetics of the Endangered Indian Peacock Softshell Turtle Nilssonia hurum (Gray, 1830): Implications for Strategic Conservation Planning
I. Abedin - A. Putra, H. Kang, A. Singh, et al. - Wiley, 2025 usegalaxy.eu

Assessing the influence of isolation techniques on NK cell transcriptomic profiles
R. ElNouty - A. Moustafa, M. Mostafa, A. Ouf, et al. - Elsevier BV, 2025 usegalaxy.eu

Multi-level expression profiling of cardiac and musculoskeletal Schwann cells in young and old mice
S. Haider - D. Stefanovska, E. Sassu, C. Domisch, et al. - Elsevier BV, 2025 usegalaxy.eu

The complete mitogenome dataset of Hasora Schoenherr (Latreille, 1824) (Lepidoptera: Hesperiidae: Coeliadinae) from Malaysia
L. Hui - M. Miga, C. Siang, A. Rahman, et al. - Elsevier BV, 2025 usegalaxy.eu

Protocol for genomic surveillance of Plasmodium falciparum antigens using amplicon-based PacBio long-read sequencing
D. Plaza - - Elsevier BV, 2025 usegalaxy.eu

Defining the epigenetic toolkit as an evolvable trait
T. Srikant - H. Drost, - Elsevier BV, 2025

A Deep Metagenomic Snapshot as a Proof‐of‐Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food
C. Ueira‐Vieira - A. Santos, T. Araújo, S. Augusto, et al. - Wiley, 2025 usegalaxy.eu

Arp2/3-dependent regulation of ciliogenesis governs adaptive distal tubular epithelial cell states in kidney disease
M. Rogg - L. Weißer, J. Maier, A. Sigle, et al. - American Association for the Advancement of Science (AAAS), 2025 usegalaxy.eu

Lineages to landscapes: mitogenomic insights and climate refugia informing proactive conservation of the endangered Tricarinate Hill Turtle (Melanochelys tricarinata) in the Indian subcontinent
I. Abedin - A. Putra, H. Kang, A. Singh, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

ERGA-BGE reference genome of Leviellus thorelli, a common orb-weaving spider representing the Zygiellidae family
M. Gregorič - E. Bužan, A. Böhne, R. Monteiro, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study
E. Kansou - A. Aubry, E. Brochot, A. Priam, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

ERGA-BGE genome of Xanthium orientale subsp. italicum (Moretti) Greuter. A plant of American origin, now widespread and, in some cases, invasive in Europe
S. Tomasello - E. Manzo, R. Monteiro, A. Böhne, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Hangover regulates gene expression by limiting NSL-mediated H4K16 acetylation
J. Lenz - L. Schmelzer, I. Forné, A. Nist, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

ERGA-BGE reference genome of Lewinskya acuminata, a common epiphytic Mediterranean moss with disjunct populations in California and Ethiopia
P. Aguado-Ramsay - F. Lara, I. Draper, M. Conejero, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Comparative Mitogenomics of Pedetontus and Pedetontinus (Insecta: Archaeognatha) Unveils Phylogeny, Divergence History, and Adaptive Evolution
W. Cen - T. Yang, J. Li, D. Yu, et al. - MDPI AG, 2025 usegalaxy.eu

Vulnerability to memory decline in aging revealed by a mega-analysis of structural brain change
D. Vidal-Piñeiro - Ø. Sørensen, M. Strømstad, I. Amlien, et al. - Springer Science and Business Media LLC, 2025

CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis
M. Rönspies - S. Khosravi, O. Helia, A. Valisi, et al. - American Association for the Advancement of Science (AAAS), 2025 usegalaxy.eu

Transcriptomic, biochemical, and microbiome assessments into drought and salinity tolerance in durum wheat mediated by plant growth-promoting bacteria
M. Yaghoubi Khanghahi - H. AbdElgawad, M. Curci, R. Garrigues, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity
M. Chuvochina - J. Gerken, M. Frentrup, Y. Sandikci, et al. - Oxford University Press (OUP), 2025

Characterization of the Complete Mitogenomes of Four Dacinae Species (Diptera: Tephritidae) with Phylogenetic Analysis
D. Xu - S. Ding, X. Zeng, L. Du, et al. - MDPI AG, 2025 usegalaxy.eu

Fibroblast growth factor signaling induces a chondrocyte-like state of peripheral nerve fibroblast during aging
D. Stefanovska - E. Sassu, M. Tekman, A. Naghsh Nilchi, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Flow Cytometric Challenges in Plasmacytoid Dendritic Cell (pDC) Identification: Limitation of BDCA-4 (CD304)-Based Gating
S. Demeter - T. Fekete, B. Scholtz, Z. Veréb, et al. - MDPI AG, 2025 usegalaxy.eu

Gene expression changes in pancreatic α-cell lines following knock-out Of either CK2α or CK2α’
J. Mayer - M. Pack, M. Montenarh, C. Götz, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family
D. Rothschild-Rodriguez - K. Lambon, S. Kushwaha, S. Garushyants, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Clinical and environmental investigation of six cases of Chryseobacterium arthrosphaerae infections in a Southern Italian hospital
F. Triggiano - G. Caggiano, L. Capozzi, S. Castellana, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Bacillus subtilis as cell factory for enhanced production of the biopolymer precursor pyridine-2,6-dicarboxylic acid
T. Chen - H. Uzunovic, S. Brul, J. Hugenholtz, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

The repressor Capicua is a barrier to lung tumor development driven by Kras/Trp53 mutations
I. Ballesteros-González - I. Hernández-Navas, O. Brehey, C. Lechuga, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Characterisation of Plasmid-Associated Antimicrobial Resistance Genes in Coastal Marine Enterobacterales from the Central Adriatic Sea: De Novo Assembly and Bioinformatic Profiling
I. Šamanić - M. Dželalija, E. Bellulovich, H. Kalinić, et al. - MDPI AG, 2025 usegalaxy.eu

PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single workflow
L. González-Vinceiro - C. Espejo-Serrano, M. Soler-Oliva, E. Soto-Hidalgo, et al. - American Association for the Advancement of Science (AAAS), 2025 usegalaxy.eu

Carotenoid-based immune response in sea cucumbers relies on newly identified coelomocytes—the carotenocytes
N. Wambreuse - E. Bossiroy, F. David, C. Vanwinge, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Disentangling Gut Bacterial Community Patterns in Cryptocercus punctulatus and Comparing Their Metagenomes with Other Xylophagous Dyctioptera Insects
M. Berlanga - D. Miñana-Galbis, R. Guerrero, - MDPI AG, 2025 usegalaxy.eu

Revisiting classical Escherichia coli cell division mutants by whole-genome sequencing
E. Dahdouh - I. García-Pérez, D. Reyes-Zuñagua, J. Mingorance, et al. - Microbiology Society, 2025 usegalaxy.eu

Recombinant Extracellular Factor Protein of Streptococcus suis as Potential Candidate Protein for Antibodies Against S. suis Detection and Subunit Vaccine Development: In Silico and In Vitro Approaches
W. Mitsuwan - P. Saengsawang, R. Boripun, M. Rodríguez-Ortega, et al. - MDPI AG, 2025 usegalaxy.eu

Spatially informed phenotyping by cyclic-in-situ-hybridisation identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis
Y. Li - T. Filla, A. Györfi, M. Liang, et al. - Elsevier BV, 2025

Trichosporon austroamericanum Infections among Hospitalized Patients, France, 2022–2024
E. Burel - C. Sartor, V. Moal, V. Bossi, et al. - Centers for Disease Control and Prevention (CDC), 2025 usegalaxy.eu

The auxin gatekeepers: Evolution and diversification of the YUCCA family
M. Vijayanathan - A. Faryad, T. Abeywickrama, J. Christensen, et al. - Wiley, 2025 usegalaxy.eu

TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity
H. Freese - J. Meier-Kolthoff, J. Sardà Carbasse, A. Afolayan, et al. - Oxford University Press (OUP), 2025

A New Species of Macellicephaloides Uschakov, 1955 (Annelida, Polynoidae) from Cold Seeps in the South China Sea: Insights into the Taxonomy and Phylogeny of Macellicephaloides and Related Genera
J. Li - L. Zhang, M. Wang, X. Wu, et al. - MDPI AG, 2025 usegalaxy.eu

Variations of the Virome in Raw and Treated Water: A One‐Year Follow‐Up at Six Different Drinking Water Treatment Plants
F. Saguti - H. Wang, M. Churqui, T. Tunovic, et al. - Wiley, 2025 usegalaxy.eu

Application of MSB selective enrichment followed by amplicon MinION sequencing for multipathogen detection in smoked salmon
A. Costa-Ribeiro - A. Lamas, M. Prado, A. Garrido-Maestu, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Dissecting lncRNA-mRNA regulatory network in type 2 diabetes as the risk factor of pancreatic cancer
A. Nilchi - F. Dehghanian, S. Vallian, A. Bahreini, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Chaetomium, Chlonostachys, and Pseudogymnoascus isolates from tomato tissues significantly suppress Phytophthora infestans in tomato
P. Orwa - T. Kuhl-Nagel, R. Meinhold-Ernst, A. Seyer, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

Genomic Characterization and Antimicrobial Resistance Profile of Streptococcus uberis Strains Isolated from Cows with Mastitis from Northwestern Spain
E. Quinto - P. Redondo del Río, B. de Mateo Silleras, A. Prieto, et al. - MDPI AG, 2025 usegalaxy.eu

Zoonotic potential of methicillin-resistant Staphylococcus aureus isolated from pets and their owners in Bangladesh
H. Sarker - J. Hassan, A. Rahman, D. Korber, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

ERGA-BGE reference genome of Eunicella cavolini, an IUCN Near Threatened Gorgonian of the Mediterranean Sea
D. Aurelle - D. Guillemain, F. Zuberer, D. Malengros, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Unlocking the Potential of vB_EfaS_LOK1: A Newly Isolated Bacteriophage Against Enterococcus faecalis
L. Plata Suarez - S. Del Valle Balbuena, I. Becerra Mejía, A. Loera Piedra, et al. - MDPI AG, 2025 usegalaxy.eu

Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species
D. McQuarrie - F. Stephens, A. Ferguson, R. Arnold, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

ERGA-BGE reference genome of the lineid heteronemertean Lineus lacteus (Pilidiophora, Nemertea)
A. Verdes - P. Alvarez-Campos, M. Conejero, A. Riesgo, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
Y. Lin - K. Breuer, D. Weichenhan, P. Lafrenz, et al. - Oxford University Press (OUP), 2025

Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor
L. Lestin - R. Villemur, - PeerJ, 2025 usegalaxy.eu

Transforming psychiatry with computational and brain-based methods
T. Akiki - L. Williams, T. Wolfers, Y. Yang, et al. - Springer Science and Business Media LLC, 2025

Immunoinformatic Prediction of HIV-1 Glycoprotein gp120 and Nef Epitopes Conjugated to HBsAg-Binding Protein (SBP) to Induce the Humoral and Cellular Immune Response
A. Habib - X. Xu, J. Xie, N. Zhu, et al. - MDPI AG, 2025 usegalaxy.eu

Complete genome sequences of 34 Arctic marine bacteria
M. Sadler - S. Mino, R. Morris, - American Society for Microbiology, 2025 usegalaxy.eu

Genome-wide CRISPRi screen and proteomic profiling identify key genes related to ferulic acid’s antifungal activity
O. Levi - R. Zuchman, N. Sleman, R. Koren, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Return of the GEDAI: Unsupervised EEG Denoising based on Leadfield Filtering
T. Ros - V. Férat, Y. Huang, C. Colangelo, et al. - bioRxiv - openRxiv, 2025

Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae
N. Choudhary - M. Hagedorn, B. Pucker, - bioRxiv - openRxiv, 2025

Large-scale Phylogenomics Reveals Systematic Loss of Anthocyanin Biosynthesis Genes at the Family Level in Cucurbitaceae
N. Choudhary - M. Hagedorn, B. Pucker, - bioRxiv - openRxiv, 2025

Genetic variability of Shiga toxin-producing Escherichia coli strains isolated from Paraguayan cattle
C. Salinas - F. Rodriguez, A. Muñoz-Barrera, J. Lorenzo Salazar, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Glia Cells Are Selectively Sensitive to Nanosized Titanium Dioxide Mineral Forms
E. Geiszelhardt - E. Tóth, K. Bóka, N. Bencsik, et al. - MDPI AG, 2025 usegalaxy.eu

Arabidopsis thaliana FANCONI ANAEMIA I ( FANCI ) has roles in the repair of interstrand crosslinks and CRISPR ‐Cas9 induced DNA double strand breaks
A. Balobaid - W. Waterworth, S. Vila Nova, B. Causier, et al. - Wiley, 2025 usegalaxy.eu

Mutations in TAC1B drive increased CDR1 and MDR1 expression and azole resistance in Candida auris
K. Barker - D. Santana, Q. Zhang, T. Peters, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Identification of a sex-determining region potentially involved in resolving genetic conflicts over sex ratio
B. Lhéraud - Y. Dussert, M. Chebbi, I. Giraud, et al. - The Royal Society, 2025 usegalaxy.eu

Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025
M. Loach - A. Naghsh Nilchi, D. Chiang, M. Howells, et al. - Elsevier BV, 2025 usegalaxy.eu

Mitochondrial Genomes of Three Species of the Family Camaenidae (Gastropoda: Stylommatophora): Structural Features, Codon Usage Patterns, and Phylogenetic Implications
X. Ran - H. He, L. Yang, J. Long, et al. - Wiley, 2025 usegalaxy.eu

Exploring the Mitogenomes of Acroneuriinae: The First Report of Gene Rearrangements in Plecoptera Species and Phylogenetic Analyses of Perlidae
Y. Wang - Y. Niu, B. Qin, J. Cao, et al. - Wiley, 2025 usegalaxy.eu

Escherichia coli Sequence Type 131-H22 in Parrots from Illegal Pet Trade, Brazil, 2024
V. Rocha - F. Barbosa, J. Ruiz, H. Christensen, et al. - Centers for Disease Control and Prevention (CDC), 2025 usegalaxy.eu

Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin
C. Reyes Loaiciga - W. Li, X. Zhao, J. Li, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow
Z. Zhong - M. Bailey, Y. Kim, N. Afsharyan, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Characterization of the transposable element landscape shaping the Ectocarpus genome
E. Dinatale - R. Craig, C. Martinho, H. Drost, et al. - Springer Science and Business Media LLC, 2025

Characterization of the transposable element landscape shaping the Ectocarpus genome
E. Dinatale - R. Craig, C. Martinho, H. Drost, et al. - Springer Science and Business Media LLC, 2025

Endometriosis-associated infertility alters the microRNA signatures of cumulus cells with a particularly pronounced effect in oocytes that failed fertilization
C. Almiñana - S. Makieva, S. Bauersachs, M. Saenz-de-Juano, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam
M. Hoang - P. Lanh, V. Hien, C. Kao, et al. - MDPI AG, 2025 usegalaxy.eu

The genome sequence of the Common Buzzard, Buteo buteo (Linnaeus, 1758)
E. Blows - . , . , . , et al. - F1000 Research Ltd, 2025 usegalaxy.eu

ERGA-BGE reference genome of Holothuria (Platyperona) sanctori: a sea cucumber from the Mediterranean Sea
K. Vasileiadou - T. Dailianis, G. Skouradakis, E. Vernadou, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

ERGA-BGE reference genome of Hanak's bat (Pipistrellus hanaki), an IUCN Vulnerable species restricted to forest-like biotopes
P. Georgakakis - D. Karakasi, P. Lymberakis, M. Papadimitrakis, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Mapping cerebellar subregional volumes and heterogeneity in schizophrenia spectrum disorders and violence
T. Fischer-Vieler - J. Rokicki, M. Kim, E. Leonardsen, et al. - Springer Science and Business Media LLC, 2025

The early injected genomic region determines sensitivity to Type I restriction-modification defence against Autographiviridae phages
A. Martinez-Cazorla - C. Martinez-Jimenez, P. Elio-Lucas, P. Fineran, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

CoExpPhylo – a novel pipeline for biosynthesis gene discovery
N. Grünig - B. Pucker, - Springer Science and Business Media LLC, 2025

MHCquant2 refines immunopeptidomics tumor antigen discovery
J. Scheid - S. Lemke, N. Hoenisch-Gravel, A. Dengler, et al. - Springer Science and Business Media LLC, 2025

Encouraging reusability of computational research through Data-to-Knowledge Packages - A hydrological use case
M. Konkol - A. Labuce, S. Domisch, M. Buurman, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Comparative genome analysis of human pathogen Parvimonas micra revealed strain JM503A as potential novel species in the genus Parvimonas and high intra-species functional diversity
R. Suresh - S. Jayachandiran, P. Balu, P. Ranganadin, et al. - Microbiology Society, 2025 usegalaxy.eu

Distribution and Genotypic Landscape of Tick-Borne Encephalitis Virus in Ticks from Latvia from 2019 to 2023
L. Chitimia-Dobler - G. Dobler, D. Lang, A. Bormane, et al. - MDPI AG, 2025

Hierarchical Characterization of Brain Dynamics via State Space-Based Vector Quantization
Y. Yang - T. Wolfers, - Springer Nature Switzerland, 2025

Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention
M. Berlanga - A. Martín-García, R. Guerrero, M. Riu-Aumatell, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Downregulation of TCF19 and ATAD2 causes endothelial cell cycle arrest at the transition from cardiac hypertrophy to heart failure
E. Erny - C. Koentges, D. Mukherjee, L. Wirth, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Microcystin-LR aerosol exposure increases inflammatory drivers of asthma, Evidence of an NF-κB amplification mechanism
J. Breidenbach - B. Timalsina, B. French, L. Stanoszek, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

SARS-CoV-2 infection dynamics in a MHCI-mismatched lung transplant recipient
J. Fuchs - V. Karl, I. Hettich, J. Alvarado, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Multi‐Omic Data Analysis Supporting the Plausibility of Human Aging Sperm–Mediated Epigenetic Inheritance
A. Sharma - - Wiley, 2025 usegalaxy.eu

Gene expression alterations in testicular biopsies from males with spermatogenesis arrest identified by transcriptome analysis
O. Batiha - E. Al-Zoubi, R. Almomani, M. Al Smadi, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

Epigenomic profiling of immune cell subtypes reveals H3K27ac-marked stress signatures after long-duration spaceflight
T. Fullstone - L. Fischer, M. Bohmeier, P. Frings-Meuthen, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond
B. Uyar - T. Savchyn, A. Naghsh Nilchi, A. Sarigun, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Cerebellar growth is associated with domain-specific cerebral maturation and socio-linguistic behavioral outcomes
A. Manoli - N. Magielse, F. Hoffstaedter, N. Sağlam, et al. - bioRxiv - openRxiv, 2025

The Influence of Cohesin on the Short-Scale Dynamics of Intact and Damaged Chromatin in Different Phases of the Cell Cycle
V. Viushkov - N. Lomov, P. Kalitina, D. Potashnikova, et al. - MDPI AG, 2025 usegalaxy.eu

Transcriptome Network Biology Reveals the Neuroprotective Potential of Rosmarinic Acid Against Frontotemporal Dementia
A. Arif - P. Garg, P. Srivastava, - bioRxiv - openRxiv, 2025 usegalaxy.eu

Genomic diversity and adaptation in Arctic marine bacteria
M. Sadler - M. Wietz, S. Mino, R. Morris, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities
C. Garrard - K. Heil, M. Aspromonte, B. Batut, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Strain-specific variation in the complement resistome of Pseudomonas aeruginosa
M. Janet-Maitre - M. Robert-Genthon, F. Cretin, S. Elsen, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Genetic parallels in biomineralization of the calcareous sponge Sycon ciliatum and stony corals
O. Voigt - M. Wilde, T. Fröhlich, B. Fradusco, et al. - eLife Sciences Publications, Ltd, 2025 usegalaxy.eu

Single-vessel transcriptome map pathological landscapes and reveal NR2F2-mediated smooth muscle cell phenotype acquisition in capillary malformations
V. Nguyen - I. Mao, S. He, I. Castellanos, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

ERGA-BGE genome of Stigmatoteuthis arcturi Robson, 1948: the jewelled squid
F. Fernández-Álvarez - A. Bernal-Bajo, N. Escudero, M. Conejero, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data
M. Sozzoni - J. Balacco, M. Bellavita, A. Brüniche‐Olsen, et al. - Wiley, 2025 usegalaxy.eu

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
D. Gupta - C. Patinios, H. Bassett, A. Kibe, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences
F. Kolesch - M. Sohn, A. Rempel, P. Hippel, et al. - Springer Science and Business Media LLC, 2025

Microplastic impacts archaeal abundance, microbial communities, and their network connectivity in a Sub-Saharan soil environment
S. Rohrbach - G. Gkoutselis, L. Hink, A. Weig, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Mitogenomic Insights into Orthocladiinae (Diptera: Chironomidae): Structural Diversity and Phylogenetic Implications
H. Xu - X. Xiao, Z. Zhang, Y. Li, et al. - MDPI AG, 2025 usegalaxy.eu

Cellular dynamics and epidermal specialization during Arabidopsis floral development at single-cell resolution
S. Chen - M. Neumann, Z. He, F. Carew, et al. - bioRxiv - openRxiv, 2025

TransFactor—prediction of pro-viral SARS-CoV-2 host factors using a protein language model
Y. An - V. Bergant, S. Firmani, C. Grünke, et al. - Oxford University Press (OUP), 2025

Self-Supervised Feature Learning for Cardiac Cine MR Image Reconstruction
S. Xu - M. Früh, K. Hammernik, A. Lingg, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2025

Exploring the omnigenic architecture of selected complex traits
F. Ratajczak - M. Heinig, P. Falter-Braun, - Elsevier BV, 2025

Predicting Mental and Neurological Illnesses Based on Cerebellar Normative Features
M. Kim - N. Sharma, E. Leonardsen, S. Rutherford, et al. - Elsevier BV, 2025

Large-scale comparative analysis of blowfly mitogenomes, with an emphasis on Calliphorinae (Diptera: Calliphoridae), provides evolutionary insights into mitochondrial DNA structure, gene rearrangements, and inter- and intra-subfamilial relationships among blowflies
D. Parmar - N. Johnston, K. Szpila, - Elsevier BV, 2025 usegalaxy.eu

Genomic insights into a colonization-infection progression by a carbapenemase-producing Klebsiella quasipneumoniae K1 serotype
M. Barroso - B. Oshiro, M. Nogueira, T. Casella, et al. - Elsevier BV, 2025 usegalaxy.eu

Genomic characterization and comparative analysis of antibiotic resistance and virulence in Bangladeshi and global Klebsiella pneumoniae ST48 strains
S. Chaity - M. Hosen, S. Rahman, M. Khan, et al. - Elsevier BV, 2025 usegalaxy.eu

Comparative mitochondrial and phylomitogenomic analyses support the existence of a cryptic species complex in Gonodactylaceus falcatus (Stomatopoda: Gonodactyloidea)
H. Kiser - H. Hwang, J. Jung, J. Baeza, et al. - Elsevier BV, 2025 usegalaxy.eu

Wastewater as a dual indicator of human and environmental exposure to synthetic antioxidants: Occurrence and fate in biological and advanced wastewater treatment
C. Meyer - M. Bär, J. Hollender, - Elsevier BV, 2025 usegalaxy.eu

Comprehensive analysis of Slc15a3 and Myo1f gene expression in renal carcinoma: Insights from RNA-seq data and validation via qRT-PCR
M. Nazari - S. Angaji, B. Beikzadeh, B. Narouie, et al. - Elsevier BV, 2025 usegalaxy.eu

Genetic Diversity and Chromosomal Variations in the Iranian Leishmania major Strain: Insights into Pathogenicity and Drug Resistance
H. Sharifian - A. Khalafiyan, M. Fadaie, H. Khanahmad, et al. - Ovid Technologies (Wolters Kluwer Health), 2025 usegalaxy.eu

OXA-carbapenemases and mutations within PBPs in ST2 carbapenem-resistant A. baumannii: Evaluating the efficacy of cefiderocol and ampicillin-sulbactam combination therapy
C. Tascini - S. Giuliano, L. Martini, N. Carannante, et al. - Elsevier BV, 2025 usegalaxy.eu

Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation
Z. Varga - F. Kagan, S. Maegawa, Á. Nagy, et al. - Elsevier BV, 2025 usegalaxy.eu

Sustainable solution for microplastic removal: Sequential biodegradation and detoxification of polyethylene terephthalate microplastics by two natural microbial consortia
M. Giyahchi - H. Moghimi, - Elsevier BV, 2025 usegalaxy.eu

P16-05 The zebrafish microbiome has the capacity to bioactivate PFOS precursor compounds
S. Gutsfeld - C. Wray, N. Schweiger, A. Röhrig, et al. - Elsevier BV, 2025

The Influence of Maternal Staphylococcus aureus Anti-Hla Neutralizing Antibody on Infant Skin and Soft Tissue Development in the First Year of Life
C. Kao - K. Wylie, M. Boyle, A. Schneider, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Understanding Palladium Ion Induced Bioelectrocatalysis in Shewanella oneidensis MR-1 through Electrochemical and Genetic Interrogations
A. Dantanarayana - K. Beaver, B. Van Devener, N. Chandler, et al. - American Chemical Society (ACS), 2025 usegalaxy.eu

Stabilizing the Baseline: Reference Gene Evaluation in Three Invasive Reynoutria Species
M. Stafiniak - W. Makowski, A. Matkowski, M. Bielecka, et al. - MDPI AG, 2025 usegalaxy.eu

Origin and evolutionary trajectories of brown algal sex chromosomes
J. Barrera-Redondo - A. Lipinska, P. Liu, E. Dinatale, et al. - Springer Science and Business Media LLC, 2025

The genetics of extrinsic postzygotic selection in a migratory divide between subspecies of the Swainson’s thrush
H. Justen - S. Blain, K. Delmore, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Conserved spatial patterning of gene expression in independent lineages of C 4 plants
T. Sun - V. Bonthala, B. Stich, L. Luginbuehl, et al. - Wiley, 2025

In silico expression analysis of germin-like protein genes from rice cultivar Nipponbare
I. Durrani - N. Asim, A. Jan, I. Nissa, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

DNA aptamer AptERA 2 targets ERA from Staphylococcus aureus and limits GTP hydrolysis
K. Peñaranda - N. Pereira, O. Savva, D. Petrelli, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Positive impact of hydroponics and artificial light on yield and quality of wheat
S. Bassu - S. Eichelsbacher, F. Giunta, R. Motzo, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Patient-derived tumoroids from CIC::DUX4 rearranged sarcoma identify MCL1 as a therapeutic target
W. Breunis - E. Brack, A. Ehlers, I. Bechtold, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand
W. Chuchaona - R. Izquierdo-Lara, C. Schapendonk, S. Khongwichit, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Transferability of genomic prediction models across market segments in potato and the effect of selection
K. Thelen - P. Wu, N. Baig, V. Prigge, et al. - Springer Science and Business Media LLC, 2025

First Microbial Survey of a Submerged Petrified Forest in the Black Sea: Culture-Based and Metagenomic Insights
M. Iliev - R. Ilieva, S. Peykov, V. Terziyska, et al. - MDPI AG, 2025 usegalaxy.eu

Targeting invasion-associated proteins PfSUB2 and PfTRAMP in Plasmodium falciparum: identification of potential inhibitors via molecular docking
E. Okafor - M. Bella-Omunagbe, T. Elugbadebo, T. Dokunmu, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
S. He - F. Zhang, - MyJove Corporation, 2025 usegalaxy.eu

Comparison of Functional and Proliferative Activity of hTERT-NK and iCasp9-NK Cells
A. Palamarchuk - M. Ustiuzhanina, E. Kovalenko, M. Streltsova, et al. - Pleiades Publishing Ltd, 2025 usegalaxy.eu

Comparative mitogenomics of the eulipotyphlan species (Mammalia, Eulipotyphla) provides novel insights into the molecular evolution of hibernation
L. Chen - G. Yang, S. Chai, - Informa UK Limited, 2025 usegalaxy.eu

Latent Representations of Early Brain Development: A Multivariate Normative Model of Brain Structure and Behaviour
M. Zabihi - F. Biondo, J. O’Muircheartaigh, T. Wolfers, et al. - bioRxiv - openRxiv, 2025

Distinct myeloid precursors and their interaction with mesenchymal cells orchestrate the spreading of psoriatic disease from the skin to the joints
M. Raimondo - H. Mohammadian, M. Angeli, S. Alivernini, et al. - bioRxiv - openRxiv, 2025

Latent Representations of Early Brain Development: A Multivariate Normative Model of Brain Structure and Behaviour
M. Zabihi - F. Biondo, J. O’Muircheartaigh, T. Wolfers, et al. - bioRxiv - openRxiv, 2025

STRaM: A genetic framework for improved cell product provenance for research and clinical translations
B. Li - C. Le, W. Lei, Y. Zhou, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation
H. Staehle - C. Koellerer, A. Staehle, J. Schulze, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Multiplication of peat moss (Sphagnum L.) species for climate action
J. Parsons - E. Decker, R. Reski, - Oxford University Press (OUP), 2025

FXR adapts hepatic mitochondrial function to increased substrate oxidation in patients with obesity
K. Panzitt - E. Jungwirth, L. Vosko, C. Madreiter-Sokolowski, et al. - American Association for the Advancement of Science (AAAS), 2025 usegalaxy.eu

Genome-wide high-density CRISPR interference screens reveal condition-specific metabolic vulnerabilities in Pseudomonas aeruginosa PAO1
A. Kaczmarczyk - A. Klotz, P. Manfredi, U. Jenal, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

ERGA-BGE genome of Dailognatha quadricollis, an East Mediterranean darkling beetle
G. Bolanakis - D. Karakasi, E. Bitzilekis, M. Stratakis, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

The genomic configurations driving antimicrobial resistance and virulence in colistin resistant Pseudomonas aeruginosa from an Egyptian Tertiary Oncology Hospital
A. AbdulHak - H. Zedan, H. El-Mahallawy, A. Sayed, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

ERGA-BGE Genome of the viperine water snake (Natrix maura): a key species for evolutionary insights of freshwater snakes
S. Carranza - D. Fernández-Guiberteau, L. Blasón, S. Tulloch, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Neural function of Netrin-1 in precancerous lesions of the pancreas
H. Haidar - A. Bellon, K. Sleiman, M. Hocine, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Species Delimitation Methods Facilitate the Identification of Cryptic Species Within the Broadly Distributed Species in Homoeocerus (Tliponius) (Insecta: Hemiptera: Coreidae)
J. Liang - S. Wang, J. Zhang, J. Chen, et al. - MDPI AG, 2025 usegalaxy.eu

ERGA-BGE reference genome of the Azores Bullfinch - Pyrrhula murina Godman, 1866: an IUCN Vulnerable Species endemic to a single island in the Azores Archipelago (Portugal)
R. Lopes - A. Böhne, T. Marcussen, R. Oomen, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

First Assembly of a Draft Genome of the Critically Endangered Northern Muriqui ( Brachyteles hypoxanthus , Primates, Atelidae) Including Non‐Invasive Genotyping Strategies for the Species
A. Melo‐Ximenes - R. Batista, L. Corvalán, T. Marques‐Bonet, et al. - Wiley, 2025 usegalaxy.eu

Rising threat of metallo-β-lactamase-producing Klebsiella oxytoca complex in Taiwan, 2013–2022
Y. Huang - C. Bregente, W. Hsu, C. Liao, et al. - Elsevier BV, 2025 usegalaxy.eu

Thiamine is a vitamin for plant-pathogenic powdery mildew fungi
B. Sabelleck - M. Freh, M. Lammertz, J. Browatzki, et al. - Elsevier BV, 2025 usegalaxy.eu

Mechanisms of Resistance to PARPi in Pancreatic Ductal Adenocarcinoma
J. Stoof - C. Andrieu, F. O'Connell, J. O'Sullivan, et al. - Wiley, 2025 usegalaxy.eu

OXA-1207, a new OXA-48-type carbapenem-hydrolysing class D beta-lactamase from Escherichia coli
J. Sommer - M. Welter, F. Krause, S. Göttig, et al. - bioRxiv - openRxiv, 2025

Discovery of phage CSF, a novel generalist bacteriophage targeting multidrug-resistant and potentially pathogenic Staphylococcus spp. and Mammaliicoccus spp.
F. Ahmad - V. Viana, R. de Rezende, S. Martuchelle, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution
P. Hunold - G. Pizzolato, N. Heramvand, L. Kaiser, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation
N. Aggarwal - J. Schmitz, L. Laufer, S. Rahmann, et al. - bioRxiv - openRxiv, 2025

High-light adaptation in Synechocystis by accumulating NDH proteins and depleting specific phycobilisome linker proteins
W. Chen - E. Abdel-Salam, M. Dann, C. Ott, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

ERGA-BGE genome of Anisus vorticulus (Troschel, 1834): the Lesser Ramshorn Snail, an endangered freshwater snail protected under the EU's Habitats and Species Directive
B. Hausdorf - E. Tapia, R. Monteiro, A. Böhne, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Uncovering the genetic diversity of the malaria parasite antigen MSP2 across Sub-Saharan Africa
J. Zerebinski - I. Broumou, K. Kimenyi, E. Aklilu, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

Characterization of the mitochondrial genomes for Ophiostoma ips and related taxa from various geographic origins and related species: large intron-rich genomes and complex intron arrangements
J. Mukhopadhyay - A. Wai, B. Lang, G. Hausner, et al. - Pensoft Publishers, 2025 usegalaxy.eu

MEGaNorm: Normative Modeling of MEG Brain Oscillations Across the Human Lifespan
M. Zamanzadeh - Y. Verduyn, A. de Boer, T. Ros, et al. - Research Square - Springer Science and Business Media LLC, 2025

Non-rhizobial endophyte recruitment and diversity in Pisum sativum are strongly shaped by phosphorus fertilizer form
S. Thaqi - N. Hensel, N. Vitow, C. Baum, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Predicting Developmental Norms from Baseline Cortical Thickness in Longitudinal Studies
P. Seidel - T. Kaufmann, T. Wolfers, - bioRxiv - openRxiv, 2025

Non-antibiotics disrupt colonization resistance against enteropathogens
A. Grießhammer - J. de la Cuesta-Zuluaga, P. Müller, C. Gekeler, et al. - Springer Science and Business Media LLC, 2025

Comparative mitogenomics analysis of Peltigera species and new insights into the lichen phylogenetics
R. Mamut - G. Yisilam, G. Adil, G. Anwar, et al. - Frontiers Media SA, 2025 usegalaxy.eu

First complete mitogenome assembly of Castanea sativa: structure, comparative genomics, and phylogeny
S. Villa - A. Marchesini, S. Torre, L. Bianco, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Correction: Mapping-based genome size Estimation
S. Natarajan - J. Gehrke, B. Pucker, - Springer Science and Business Media LLC, 2025

Opposing roles of pseudokinases NRBP1 and NRBP2 in regulating L1 retrotransposition
W. Yang - S. Cong, R. Li, J. Schwarz, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Plasmid and chromosomal sequences of Pantoea agglomerans isolated from air in Fort Collins, Colorado
A. Freedman - K. Malmstrom, P. Gruber, B. Borlee, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Bacteriophage infection drives loss of β-lactam resistance in methicillin-resistant Staphylococcus aureus
M. Tran A. Hernandez Viera - P. Tran, E. Nilsen, L. Tran, et al. - eLife Sciences Publications, Ltd, 2025 usegalaxy.eu

Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice
A. Bright - Y. Kotlyarenko, F. Neuhaus, D. Rodrigues, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

sRNA-mediated crosstalk between cell wall stress and galactose metabolism in Staphylococcus aureus
M. Germain - H. Robin, K. Le Huyen, S. Massier, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Coupling tRNAGly gene redundancy with staphylococcal cell wall integrity, antibiotic susceptibility, and virulence potential
A. Kouvela - J. Jaramillo Ponce, N. Giarimoglou, J. Chicher, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation
N. Rahnamae - L. Metzger, L. Hördemann, K. Korfmann, et al. - bioRxiv - openRxiv, 2025

Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction
W. Rojas - Z. Ahmad, J. Jakiela, H. Hecht, et al. - GigaScience Press, 2025 usegalaxy.eu

Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation
P. Belmann - B. Osterholz, N. Kleinbölting, A. Pühler, et al. - Oxford University Press (OUP), 2025

From pollution to reforestation: the hidden microbiome of Alnus glutinosa nodules over 30 years
R. Thompson - M. del Carmen Montero-Calasanz, D. George, E. Fox, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Cohesive data analysis for the identification of prognostic hub genes and significant pathways associated with HER2 + and TN breast cancer types
M. Zakir - A. Saddiqa, M. Sheikh, L. Zakir, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
S. Ouologuem - L. Martens, A. Schaar, M. Shulman, et al. - Oxford University Press (OUP), 2025

Rotifers in space: transcriptomic response of the bdelloid rotifer Adineta vaga aboard the International Space Station
V. Moris - L. Bruneau, J. Berthe, R. Coos, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Mitogenomics of Psorodonotus ebneri Brunner von Wattenwyl, 1861 (Orthoptera: Tettigoniidae): Selection profile and patterns of intraspecific and interspecific divergence
O. Uluar - M. Yartaş, Ö. Yahyaoğlu, B. Çıplak, et al. - Hacettepe University, 2025 usegalaxy.eu

Paedomorphic adaptations in a new Heterostigma species: a novel strategy for ascidians to live in soft-bottom habitats
R. Virgili - V. Tanduo, S. D’Aniello, A. Fontana, et al. - CSIRO Publishing, 2025 usegalaxy.eu

De novo transcriptome assembly and functional annotation supports potential biotechnological applications for the non-model thraustochytrid Ulkenia visurgensis Lng2
P. Contreras - V. Fica-León, J. Navarrete, C. Oviedo, et al. - Elsevier BV, 2025 usegalaxy.eu

Developing Bacillus subtilis as cell factory for the production of the natural biocontrol compound pulcherrimin
T. Chen - H. Uzunovic, S. Brul, J. Hugenholtz, et al. - Elsevier BV, 2025 usegalaxy.eu

Confrontations of the Pathogenic Fungus Colletotrichum graminicola With a Biocontrol Bacterium or a Ubiquitous Fungus Trigger Synthesis of Secondary Metabolites With Lead Structures of Synthetic Fungicides
B. Fernando Devasahayam - H. Uthe, Y. Poeschl, H. Deising, et al. - Wiley, 2025 usegalaxy.eu

The Mitochondrial Genome of the Imperiled Goliath Grouper Epinephelus itajara: Selective Pressures in Protein Coding Genes, Secondary Structure of tRNA Genes, and Phylogenetic Placement
K. Padgett - J. Baeza, - Wiley, 2025 usegalaxy.eu

The draft genome of ‘Candidatus Phytoplasma palmae’ strain LY-C2, the phytoplasma associated with coconut lethal yellowing disease, reveals insights into its biological characteristics
S. Vila-Luna - K. Carreón-Anguiano, I. Córdova-Lara, L. Sáenz-Carbonell, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Experimental evidence on colchicine's mode of action in human carotid artery plaques
A. von Ehr - I. Steenbuck, C. Häfele, F. Remmersmann, et al. - Elsevier BV, 2025 usegalaxy.eu

ERGA-BGE genome of Dendarus foraminosus: an IUCN Least Concern darkling beetle endemic to Crete (Greece)
G. Bolanakis - D. Karakasi, A. Trichas, A. Böhne, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering
J. Sun - K. Biharie, P. Cai, N. Mueller-Boetticher, et al. - bioRxiv - openRxiv, 2025

Uncovering Anti-Melanoma Mechanisms of Bambusa stenostachya Leaf Compounds via Network Pharmacology and Molecular Docking
G. Darilag - H. Liu, C. Hsieh, L. Tayo, et al. - MDPI AG, 2025 usegalaxy.eu

MEGaNorm: Normative Modeling of MEG Brain Oscillations Across the Human Lifespan
M. Zamanzadeh - Y. Verduyn, A. de Boer, T. Ros, et al. - bioRxiv - openRxiv, 2025

Whole genome sequencing of Neolamarckia macrophylla (Roxb.) Bosser and Neolamarckia cadamba (Roxb.) Bosser from Indonesia: a vital resource for completing chloroplast genomes and mining microsatellite markers
F. Dwiyanti - I. Kamal, R. Pratama, D. Syaputra, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Exploring transposons in macroalgae: LTR elements and neighboring genes in red seaweeds
P. Garcia-Jimenez - R. Robaina, - Frontiers Media SA, 2025 usegalaxy.eu

The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1
F. Gather - T. Rauleac, I. Akol, G. Arumugam, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue
O. Sherwood - R. Burke, J. O’Rourke, C. Whelan, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Prevalence and spectrum of germline BRCA1 and BRCA2 mutations in multiethnic cohort of breast cancer patients in Brunei Darussalam
S. Matusin - N. Mumin, H. Zainal Abidin, F. Mohd Jaya, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

PI3Kα inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification
J. Valer A. Deber - M. Wits, C. Pimenta-Lope, M. Goumans, et al. - eLife Sciences Publications, Ltd, 2025 usegalaxy.eu

New Insights into the Sex Chromosome Evolution of the Common Barker Frog Species Complex (Anura, Leptodactylidae) Inferred from Its Satellite DNA Content
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IRF4 expression by NK precursors predetermines exhaustion of NK cells during tumor metastasis
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Depletion of P2X4 receptor alleviates prostate cancer bone metastasis through reduced cancer cell invasiveness and enhanced cell adhesion activities
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Evidence for a CO 2 ‐concentrating mechanism in the model streptophyte green alga Chara braunii
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An emerging Platynota sp. (Lepidoptera: Tortricidae) infesting blueberry (Vaccinium corymbosum) in the central coast of Peru
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The Extremely Low Mechanical Force Generated by Nano‐Pulling Induces Global Changes in the Microtubule Network, Nuclear Morphology, and Chromatin Transcription in Neurons
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Targeting GRPR for sex hormone-dependent cancer after loss of E-cadherin
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Comparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization
S. Salem - D. Osama, N. Abdelsalam, A. Shata, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Exploring the Genetic Networks of HLB Tolerance in Citrus: Insights Across Species and Tissues
R. Machado - S. Moschen, G. Conti, S. González, et al. - MDPI AG, 2025 usegalaxy.eu

In-depth analysis of the first complete mitochondrial genome of the rare shrimp Alpheus euphrosyne, with comparative phylogenetic genomics insights into the Alpheus species
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The complete mitochondrial genome of the snapping shrimp, Alpheus brevicristatus De Haan, 1844 (Crustacea, Decapoda, Alpheidae)
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Cytogenetic and Molecular Characterization of Sphaerophoria rueppellii (Diptera, Syrphidae)
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subMG automates data submission for metagenomics studies
T. Tubbesing - A. Schlüter, A. Sczyrba, - Springer Science and Business Media LLC, 2025

Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila
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C13‐Deacylase from Nocardioides albus Resp. Streptomyces sp., Catalyzing Side Chain Hydrolysis on the Taxane Core
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Resolution of a T1-Like Bacteriophage Outbreak by Receptor Engineering
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Sensitization of Non‐M3 Acute Myeloid Leukemia Blasts to All‐Trans Retinoic Acid by the LSD1 Inhibitor Tranylcypromine: TRANSATRA Phase I Study
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Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation
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SCUBA implements a storage format-agnostic API for single-cell data access in R
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P-346 Endometriosis-associated infertility changes the microRNA profile of cumulus cells with a notably pronounced effect on oocytes that failed fertilisation
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Complete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand
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De novo assembly and annotation of the pantranscriptome of Astyanax lacustris on the liver and pituitary-gonadal axis
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Aurora B and INCENP co-overexpression severely disrupts mitosis and distinctly modifies the global transcriptional landscape
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In silico drug repurposing for potential HPV-induced skin wart treatment − A comparative transcriptome analysis
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Dataset of benthic foraminiferal community structure from sediment eDNA of Sundarbans mangrove ecosystem
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Repeated Low‐Level Inflammatory Challenge Leads to Alterations in the TNF ‐ CXCL10 Signalling Pathway in Mouse Cerebral Endothelial Cells In Vitro
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Expansion of SARS-CoV-2 mutations in patient with B-cell lymphoma and rare combination of ACE2, TLR4, DDX58 and IFIH1 variations: A retrospective analysis of the virus-host interplay
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varVAMP: degenerate primer design for tiled full genome sequencing and qPCR
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Outbreak of NDM-5-Producing Proteus mirabilis During the COVID-19 Pandemic in an Argentine Hospital
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Diversity and Role of Prophages in Pseudomonas aeruginosa: Resistance Genes and Bacterial Interactions
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Alterations in the Expression of a Set of miRNAs in Endometrial Cancer and Their Correlation with Clinical Variables and the p53 Signaling Pathway
J. Zapata García - - MDPI AG, 2025 usegalaxy.eu

Mapping Cerebellar Morphology in 15q11.2 CNV Carriers Using Normative Modeling
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Two distinct host-specialized fungal species cause white-nose disease in bats
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Two Outbreaks of Invasive Pneumococcal Disease in Nursing Homes in Gipuzkoa, Northern Spain
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Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pteronyssinus
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Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis
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Characterisation of Ornithobacterium hominis colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort
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Many transcription factor families have evolutionarily conserved binding motifs in plants
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Longitudinal Immunoprofiling of the CD8+ T-Cell Response in SARS-CoV-2 mRNA Vaccinees and COVID-19 Patients
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Diversity of mobile genetic elements in carbapenem-resistant Enterobacterales isolated from the intensive care units of a tertiary care hospital in Northeast India
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SEOR2 in Arabidopsis mediates Ca2+ dependent defense against phytoplasmas and reduction of plant growth
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Enhanced drought and salt stress tolerance in Arabidopsis via ectopic expression of the PvMLP19 gene
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Exploring effector candidates in Rhynchosporium commune: insights into their expression dynamics during barley infection
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TGF-β signaling redirects Sox11 gene regulatory activity to promote partial EMT and collective invasion of oncogenically transformed intestinal organoids
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Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka
L. Kumari - D. Siriwardhana, V. Liyanapathirana, R. Jinadasa, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Giant mitogenomes in Rhynchospora are a result of nuclear gene and retrotransposon insertions in intergenic spaces
C. Almeida - A. Marques, - Oxford University Press (OUP), 2025 usegalaxy.eu

VEFill: a model for accurate and generalizable deep mutational scanning score imputation across protein domains
P. Polunina - W. Maier, A. Rubin, - bioRxiv - openRxiv, 2025

Mapping-based genome size estimation
S. Natarajan - J. Gehrke, B. Pucker, - Springer Science and Business Media LLC, 2025

Molecular and Genetic Analysis of the Increased Number of Genes for Trypanosoma cruzi Microtubule Associated Proteins in the Class Kinetoplastida
M. Winkler - A. Pan, - MDPI AG, 2025 usegalaxy.eu

Engineering Gypsophila elegans hairy root cultures to produce endosomal escape‐enhancing saponins
E. Lacchini - T. Qu, T. Moses, A. Volkov, et al. - Wiley, 2025 usegalaxy.eu

Comparative Mitochondrial Genomic and Phylogenetic Study of Eight Species of the Family Lonchodidae (Phasmatodea: Euphasmatodea)
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Complete genome sequence of Planococcus koreensis isolated from soil in Fort Collins, Colorado
P. Gruber - A. Freedman, K. Malmstrom, B. Borlee, et al. - American Society for Microbiology, 2025 usegalaxy.eu

Identification of Toxoplasma gondii antigenic proteins using an in vivo approach and in silico investigation of their polymorphism
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Encouraging reusability of computational research through Data-to-Knowledge Packages - A hydrological use case
M. Konkol - A. Labuce, S. Domisch, M. Buurman, et al. - F1000 Research Ltd, 2025 usegalaxy.eu

A proteotranscriptomic approach to dissect the molecular landscape of human retinoblastoma
J. Wolf - R. Hajdu, S. Boneva, I. Godbole, et al. - Frontiers Media SA, 2025 usegalaxy.eu

The oncoprotein DEK controls growth‐regulated gene expression by enhancing the DNA ‐binding activity of basic leucine zipper transcription factors
T. Hashimoto - S. Saito, M. Ohata, M. Okuwaki, et al. - Wiley, 2025 usegalaxy.eu

Unusual Genetic Diversity Within Thereuopoda clunifera (Wood, 1862) (Chilopoda: Scutigeromorpha) Revealed by Phylogeny and Divergence Times Using Mitochondrial Genomes
J. Ji - H. Wu, Y. Gao, C. Shen, et al. - MDPI AG, 2025 usegalaxy.eu

Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition
P. Joshi - R. Bhattacharjee, M. Sahu, D. Gajjar, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Unlocking the Potential of Medicago truncatula A17 Cell Suspension Cultures for Bioproduction of Astaxanthin and Canthaxanthin
S. Gomes - B. Rebelo, R. Abranches, - Wiley, 2025 usegalaxy.eu

A homozygous human WNT11 variant is associated with laterality, heart and renal defects
H. Berns - D. Weber, M. Haas, Z. Bakey, et al. - The Company of Biologists, 2025 usegalaxy.eu

Social Cognition and Functional Connectivity in Early and Chronic Schizophrenia
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Imaging mass cytometry-based characterisation of fibroblast subsets and their cellular niches in systemic sclerosis
A. Rius Rigau - M. Liang, V. Devakumar, R. Neelagar, et al. - Elsevier BV, 2025

A transcriptional atlas of gut-innervating neurons reveals activation of interferon signaling and ferroptosis during intestinal inflammation
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TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors
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Ribonuclease activity undermines immune sensing of naked extracellular RNA
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Characterization of Ribosome inactivating protein genes and their transcripts in Trialeurodes vaporariorum
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Babaco Mosaic Virus (BabMV) Induces Genome‐Wide Transcriptomic Reprogramming in Carica papaya
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Facilitating Reproducibility in Catalysis Research with Managed Workflows and RO‐Crates: A Galaxy Case Study
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Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules
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Coxsackievirus A24: A Causative Agent of Acute Haemorrhagic Conjunctivitis Outbreak in Dar es Salaam, Tanzania, between January and February 2024
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Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities
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Staphylococcus aureus AgrA Modulators From South African Antimicrobial Plants
C. Aruwa - S. Sabiu, - Wiley, 2025 usegalaxy.eu

PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow
L. González-Vinceiro - C. Espejo-Serrano, M. Soler-Oliva, M. Mateos-Martín, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

Transcriptomic profiling of unmethylated full mutation carriers implicates TET3 in FMR1 CGG repeat expansion methylation dynamics in fragile X syndrome
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Morpho-Molecular Discordance and Cryptic Diversity in Jumping Bristletails: A Mitogenomic Analysis of Pedetontus silvestrii (Insecta: Archaeognatha: Machilidae)
W. Cen - J. Li, J. He, X. Chen, et al. - MDPI AG, 2025 usegalaxy.eu

The cytokinesis associated proteins CITK and ASPM-1 regulate neuronal microtubule dynamics and polarity in C. elegans
S. Sharma - K. Ponniah, A. Ghosh-Roy, - bioRxiv - openRxiv, 2025 usegalaxy.eu

Sex-lethal is recruited to chromatin to promote neuronal tRNA synthesis in males through RNA Polymerase III regulation
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Bakta Web – rapid and standardized genome annotation on scalable infrastructures
S. Beyvers - L. Jelonek, A. Goesmann, O. Schwengers, et al. - Oxford University Press (OUP), 2025

Hangover regulates gene expression by limiting NSL-mediated H4K16 acetylation
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Denser Mitogenomic Sampling for Exploring the Phylogeny of Tellinoidea (Mollusca: Bivalvia)
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An Atlas of Thyroid Hormone Responsive Genes in Adult Mouse Hypothalamus
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Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations
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Cross‐Sectional Brain Age Assessments Are Limited in Predicting Future Brain Change
M. Korbmacher - D. Vidal‐Pineiro, M. Wang, D. van der Meer, et al. - Wiley, 2025

Rapid formulation of a genetically diverse phage cocktail targeting uropathogenic Escherichia coli infections using the UTI89 model
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Genome characterization, pathogenicity, and evaluation of therapeutics of Klebsiella aerogenes in Bombyx larvae infection model
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Closed genome sequence of Fretibacterium fastidiosum , a potential contributor to periodontal disease
A. Mori - M. Kudoh, M. Kuboniwa, C. Rückert-Reed, et al. - American Society for Microbiology, 2025

Entamoeba histolytica extracellular vesicles drive pro-inflammatory monocyte signaling
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Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in E. coli using a high-throughput approach
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CoExpPhylo – A Novel Pipeline for Biosynthesis Gene Discovery
N. Grünig - B. Pucker, - bioRxiv - openRxiv, 2025

Transcriptional and epigenomic changes in response to polyethylene glycol-triggered osmotic stress in Brassica napus L.
M. Prasad - P. Shetty, A. Pal, G. Rigó, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer
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Individual-level deviations from normative brain morphology in violence, psychosis, and psychopathy
U. Haukvik - T. Wolfers, N. Tesli, C. Bell, et al. - Springer Science and Business Media LLC, 2025

Targets of the transcription factor Six1 identify previously unreported candidate deafness genes
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PCI-DB: a novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development
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PCI-DB: a novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development
S. Lemke - M. Dubbelaar, P. Zimmermann, J. Bauer, et al. - BMJ, 2025

Multiscale Heterogeneity of White Matter Morphometry in Psychiatric Disorders
A. Segal - R. Smith, S. Chopra, S. Oldham, et al. - Elsevier BV, 2025

Olfactory specialization in the Senegalese sole (Solea senegalensis): CO2 acidified water triggers nostril-specific immune processes
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Case–Control Study of Factors Associated with Hemolytic Uremic Syndrome among Shiga Toxin–Producing Escherichia coli Patients, Ireland, 2017–2020
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Mitochondrial Genomes of Three Melampus Species (Ellobiidae; Gastropoda)
T. Inäbnit - R. Tiedemann, A. Dennis, - Wiley, 2025 usegalaxy.eu

Substrate recognition in Bacillus anthracis sortase B beyond its canonical pentapeptide binding motif and use in sortase-mediated ligation
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The l,d-transpeptidation pathway is inhibited by antibiotics of the β-lactam class in Clostridioides difficile
A. Oliveira Paiva - P. Courtin, G. Charpentier, I. Oueled-Chama, et al. - Elsevier BV, 2025 usegalaxy.eu

Inspired by molecular dynamic simulation, exploring chemical constituents of alcoholic extract of Garuga pinnata computationally as inhibitors of GluN2B-containing NMDA receptors
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Versatile roles of annexin A4 in clear cell renal cell carcinoma: Impact on membrane repair, transcriptional signatures, and composition of the tumor microenvironment
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Comparative Genomic and Mitochondrial Phylogenetic Relationships of Ovulidae (Mollusca: Gastropoda) Along the Chinese Coast
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Developmental pathways underlying sexual differentiation in the U/V sex chromosome system of giant kelp
D. Liesner - G. Cossard, M. Zheng, O. Godfroy, et al. - Elsevier BV, 2025

Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
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Novel tools for genomic modification and heterologous gene expression in the phylum Planctomycetota
T. Haufschild - J. Hammer, N. Rabold, V. Plut, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni
K. Froschauer - S. Svensson, R. Gelhausen, E. Fiore, et al. - Springer Science and Business Media LLC, 2025

Differential Mitochondrial Genome Expression of Four Skink Species Under High-Temperature Stress and Selection Pressure Analyses in Scincidae
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Vulnerability to memory decline in aging. A mega-analysis of structural brain change.
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Accelerated maturation of branched organoids confined in collagen droplets
I. Ruider - A. Pastucha, M. Raich, W. Xu, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

The Quorum Sensing Regulated sRNA Lrs1 Is Involved in the Adaptation to Low Iron in Pseudomonas aeruginosa
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SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences
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Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages
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Genome Skimming of Thysanoptera (Arthropoda, Insecta) and Its Taxonomic and Systematic Applications
E. Wahlberg - - MDPI AG, 2025 usegalaxy.eu

CD38-mediated metabolic reprogramming promotes the stability and suppressive function of regulatory T cells in tumor
I. Sarkar - D. Basak, P. Ghosh, A. Gautam, et al. - American Association for the Advancement of Science (AAAS), 2025

Crossing Wallace’s line: an evolutionarily young gibbon ape leukemia virus like endogenous retrovirus identified from the Philippine flying lemur (Cynocephalus volans)
K. Tsangaras - J. Mayer, A. Greenwood, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Discovery of a human parvovirus B19 analog (Erythroparvovirus) in cats
G. Lanave - F. Pellegrini, G. Diakoudi, C. Catella, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

First report of Moraxella oculi in Brazil in an infectious bovine keratoconjunctivitis outbreak
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Comparative genomics reveals genetic diversity and differential metabolic potentials of the species of Arachnia and suggests reclassification of Arachnia propionica E10012 (=NBRC_14587) as novel species
R. Suresh - S. Jayachandiran, P. Balu, D. Ramasamy, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Characterization of Newly Isolated Rosenblumvirus Phage Infecting Staphylococcus aureus from Different Sources
P. Cunha - P. de Souza, A. Rosseto, I. Rodrigues, et al. - MDPI AG, 2025 usegalaxy.eu

The complete mitochondrial genome of Crocidura rapax Allen, 1923 and its phylogenetic analyses
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Determinants of ascending aortic morphology: cross-sectional deep learning-based analysis on 25 073 non-contrast-enhanced NAKO MRI studies
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The suberin transporter StABCG1 is required for barrier formation in potato leaves
E. Benatto Perino - U. Smolka, K. Gorzolka, R. Grützner, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

QSAR-Based Drug Repurposing and RNA-Seq Metabolic Networks Highlight Treatment Opportunities for Hepatocellular Carcinoma Through Pyrimidine Starvation
N. Talubo - E. Dela Cruz, P. Fowler, P. Tsai, et al. - MDPI AG, 2025 usegalaxy.eu

Isolation and characterization of fMGyn-Pae01, a phiKZ-like jumbo phage infecting Pseudomonas aeruginosa
K. Ranta - M. Skurnik, S. Kiljunen, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

A revision of the hitherto neglected genus Topiris Walker, 1863 (Lepidoptera, Xyloryctidae) with taxonomic notes on the genus Athrypsiastis Meyrick, 1910
M. Sterling - B. Price, D. Lees, - Pensoft Publishers, 2025 usegalaxy.eu

RLB-MALBAC: a rapid, non-transposase method for synthesizing unbiased sequencing libraries from low amount of genomic DNA for Nanopore sequencing
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Attention incorporated network for sharing low-rank, image and k-space information during MR image reconstruction to achieve single breath-hold cardiac Cine imaging
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The role of DNA content in shaping chromatin architecture and gene expression
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Collective oscillatory signaling in Dictyostelium discoideum acts as a developmental timer initiated by weak coupling of a noisy pulsatile signal
C. Brimson - R. Baines, E. Sams-Dodd, I. Stefanescu, et al. - Elsevier BV, 2025 usegalaxy.eu

The effect of thermal stress on the X-organ/sinus gland proteome of the estuarine blue crab Callinectes sapidus during the intermolt and premolt stages
J. Lacerda - D. David, A. Castrucci, - Elsevier BV, 2025 usegalaxy.eu

EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling
C. Schröder - L. Zissel, S. Mersiowsky, M. Tekman, et al. - Elsevier BV, 2025 usegalaxy.eu

Exploring the genomic diversity and breeding applications of the Solanum sessiliflorum transcriptome via phylogenetic analysis
P. Silva - L. Silva, D. Gouveia, P. Rodrigues, et al. - Wiley, 2025 usegalaxy.eu

Morpho-functional characterisation of cœlomocytes in the aquacultivated sea cucumber Holothuria scabra: From cell diversity to transcriptomic immune response
N. Wambreuse - G. Caulier, I. Eeckhaut, L. Borrello, et al. - Elsevier BV, 2025 usegalaxy.eu

Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants
A. Kirbis - N. Rahmatpour, S. Dong, J. Yu, et al. - Springer Science and Business Media LLC, 2025

Comparative analysis using a chromosome-scale genome assembly for Funaria hygrometrica suggests greater collinearity in mosses than in seed plants
A. Kirbis - N. Rahmatpour, S. Dong, J. Yu, et al. - Springer Science and Business Media LLC, 2025

Chronic, Low-Dose Methamphetamine Reveals Sexual Dimorphism of Memory Performance, Histopathology, and Gene Expression Affected by HIV-1 Tat Protein in a Transgenic Model of NeuroHIV
I. Harahap-Carrillo - D. Fok, F. Wong, G. Malik, et al. - MDPI AG, 2025 usegalaxy.eu

Unravelling the complete mitochondrial genomes of Thrips tabaci Lindeman and Thrips parvispinus Karny (Thysanoptera: Thripidae) and their phylogenetic implications
P. Soumia - D. Shirsat, V. Karuppaiah, P. Divekar, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Pseudomonas Species Isolated From Lotus Nodules Are Genetically Diverse and Promote Plant Growth
Y. Yu - J. Kurtenbach, D. Crosbie, A. Brachmann, et al. - Wiley, 2025 usegalaxy.eu

Aquirufa esocilacus sp. nov., Aquirufa originis sp. nov., Aquirufa avitistagni, and Aquirufa echingensis sp. nov. discovered in small freshwater habitats in Austria during a citizen science project
A. Pitt - S. Lienbacher, J. Schmidt, M. Neumann-Schaal, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

A splice donor in E6 influences keratinocyte immortalization by beta-HPV49
T. Rehm - T. Iftner, F. Stubenrauch, - American Society for Microbiology, 2025 usegalaxy.eu

Computer-aided drug repurposing & discovery for Hepatitis B capsid protein
A. Mohebbi - S. Nabavi, M. Naderi, K. Sharifian, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Maternal PRDM10 activates essential genes for oocyte-to-embryo transition
M. Seah - B. Han, Y. Huang, L. Rasmussen, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

SETD1A-dependent EME1 transcription drives PARPi sensitivity in HR deficient tumour cells
E. Sweatman - R. Bayley, R. Selemane, M. Higgs, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Theoretical studies on safety and efficacy of 16 small-molecule MC4R antagonists as therapeutics for obesity
S. Joshi - R. Srivastava, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Revealing the hidden diversity of Chlorella heliozoae-infecting giant viruses
L. Henriques - B. Botelho, R. Carlson, J. Carvalho, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Molecular epidemiology of Neisseria gonorrhoeae isolates in Russia, 2015–2023: current trends and forecasting
I. Kandinov - B. Shaskolskiy, D. Kravtsov, A. Larkin, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Discovering promising drug candidates for Parkinson’s disease: integrating miRNA and DEG analysis with molecular dynamics and MMPBSA
B. Ishtiaq - R. Paracha, M. Nisar, S. Ejaz, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov
A. Pitt - S. Lienbacher, J. Schmidt, M. Neumann-Schaal, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs
A. Ghaffaari - A. Schönhuth, T. Marschall, - bioRxiv - openRxiv, 2025

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
L. Dony - A. Krontira, L. Kaspar, R. Ahmad, et al. - American Association for the Advancement of Science (AAAS), 2025

Direct effects of prolonged TNF-α and IL-6 exposure on neural activity in human iPSC-derived neuron-astrocyte co-cultures
N. Goshi - D. Lam, C. Bogguri, V. George, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Integrative morphological, mitogenomic and phylogenetic analyses reveal new vent-dwelling scallop species
Y. Lin - Y. Peng, C. Chen, T. Xu, et al. - CSIRO Publishing, 2025 usegalaxy.eu

Molecular modelling and experimental validation of mangiferin and its related compounds as quorum sensing modulators of Pseudomonas aeruginosa
N. Nortje - J. Aribisala, C. Pillay, S. Sabiu, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Taxonomic refinement of Bacillus thuringiensis
N. Shiekh Suliman - R. Talaei-Hassanloui, H. Abachi, S. Zarei, et al. - Frontiers Media SA, 2025 usegalaxy.eu

sORFdb – a database for sORFs, small proteins, and small protein families in bacteria
J. Hahnfeld - O. Schwengers, L. Jelonek, S. Diedrich, et al. - Springer Science and Business Media LLC, 2025

Rapid pan-biodiversity lifeform and genomic diversity detection from shotgun sequencing of air eDNA
D. Duffy - M. McCauley, O. Nousias, M. Stammnitz, et al. - Research Square - Springer Science and Business Media LLC, 2025 usegalaxy.eu

TotalSegmentator MRI: Robust Sequence-independent Segmentation of Multiple Anatomic Structures in MRI
T. Akinci D’Antonoli - L. Berger, A. Indrakanti, N. Vishwanathan, et al. - Radiological Society of North America (RSNA), 2025

Coronary artery disease detection using deep learning and ultrahigh-resolution photon-counting coronary CT angiography
J. Brendel - J. Walterspiel, F. Hagen, J. Kübler, et al. - Elsevier BV, 2025

Little influence of DNA quality on the direct sequencing output of non-human primates’ faecal samples
F. Lee - F. Sitam, L. Tan, - Elsevier BV, 2025 usegalaxy.eu

Analysis of meta-transcriptomics and identification of genes linked to bioactive peptides and vitamins in Indonesian tempe
J. Tamang - S. Das, S. Lama, G. Utama, et al. - Elsevier BV, 2025 usegalaxy.eu

Genome and transcriptome analysis of the lignite-degrading Trichoderma cf. simile WF8 strain highlights potential degradation mechanisms
J. Yao - Y. Chen, D. Zhuo, S. Chen, et al. - Elsevier BV, 2025 usegalaxy.eu

Multiple factors contribute to female dominance in migratory bioflows
T. Doyle - O. Poole, J. Barnes, W. Hawkes, et al. - The Royal Society, 2025 usegalaxy.eu

Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome
Y. Chen - X. Wang, X. Wu, Y. Shang, et al. - MDPI AG, 2025 usegalaxy.eu

Meta-analysis of RNA-Seq datasets allows a better understanding of P. tricornutum cellular biology, a requirement to improve the production of Biologics
I. Boulogne - C. Toustou, M. Bardor, - Springer Science and Business Media LLC, 2025 usegalaxy.eu

A One Health approach for the genomic characterization of antibiotic-resistant Campylobacter isolates using Nanopore whole-genome sequencing
A. Hurtado - M. Ocejo, B. Oporto, J. Lavín, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Genome analysis of colistin-resistant Salmonella isolates from human sources in Guizhou of southwestern China, 2019–2023
J. Wu - Y. Wen, L. You, X. Wei, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Carbon monoxide-oxidising Pseudomonadota on volcanic deposits
R. Dawson - N. Fantom, T. Martin-Pozas, P. Aguila, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

De novo transcriptome assembly and analysis during agarwood induction in Gyrinops versteegii Gilg. seedling
D. Hermawaty - T. Setyobudi, H. Nugrahapraja, M. Turjaman, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Mapping cells through time and space with moscot
D. Klein - G. Palla, M. Lange, M. Klein, et al. - Springer Science and Business Media LLC, 2025

In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells
P. de la Cruz-Ojeda - E. Parras-Martínez, R. Rey-Pérez, J. Muntané, et al. - Baishideng Publishing Group Inc., 2025 usegalaxy.eu

PCSK9-antibodies fail to block PCSK9-induced inflammation in macrophages and cannot recapitulate protective effects of PCSK9-deficiency in experimental myocardial infarction
S. Rauterberg - C. Härdtner, J. Hein, P. Schrepf, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Pangeo environment in Galaxy Earth System supported by Fair-Ease
T. Carval - M. Jossé, J. Detoc, - Copernicus GmbH, 2025 usegalaxy.eu

First Detection and Genomic Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolates in Bulgaria
T. Strateva - P. Hristova, T. Stoeva, H. Hitkova, et al. - MDPI AG, 2025 usegalaxy.eu

A Lambda-evo (λevo) phage platform for Zika virus EDIII protein display
H. Negrete-Méndez - G. Valencia-Toxqui, E. Martínez-Peñafiel, O. Medina-Contreras, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

A novel broad-spectrum bacteriophage cocktail against methicillin-resistant Staphylococcus aureus: Isolation, characterization, and therapeutic potential in a mastitis mouse model
M. Banar - H. Kamyab, N. Torkashvand, T. Zahraei Salehi, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

Isolation and Characterization of Colistin-Resistant Enterobacteriaceae from Foods in Two Italian Regions in the South of Italy
R. Fraccalvieri - A. Bianco, L. Difato, L. Capozzi, et al. - MDPI AG, 2025 usegalaxy.eu

Novel Insights into the Nobilamide Family from a Deep-Sea Bacillus: Chemical Diversity, Biosynthesis and Antimicrobial Activity Towards Multidrug-Resistant Bacteria
V. Casella - G. Della Sala, S. Scarpato, C. Buonocore, et al. - MDPI AG, 2025 usegalaxy.eu

Pharmacophore modeling and QSAR analysis of anti-HBV flavonols
B. Baei - P. Askari, F. Askari, S. Kiani, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows
N. Strepis - D. Dollee, D. Vrins, K. Vanneste, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana
Z. Zhong - M. Bailey, Y. Kim, N. Afsharyan, et al. - bioRxiv - openRxiv, 2025 usegalaxy.eu

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
K. Do - S. Mehta, R. Wagner, T. Griffin, et al. - MyJove Corporation, 2025 usegalaxy.eu

Machine learning-guided deconvolution of plasma protein levels
M. Pietzner - C. Beuchel, K. Demircan, J. Anton, et al. - medRxiv - openRxiv, 2025

Galaxy @Sciensano: a comprehensive bioinformatics portal for genomics-based microbial typing, characterization, and outbreak detection
B. Bogaerts - J. Van Braekel, A. Van Uffelen, J. D’aes, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

The zebrafish ( Danio rerio ) snoRNAome
R. Hamar - M. Varga, - Oxford University Press (OUP), 2025 usegalaxy.eu

Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew
L. Kunz - J. Jigisha, F. Menardo, A. Sotiropoulos, et al. - Public Library of Science (PLoS), 2025 usegalaxy.eu

Viral diversity in wild rodents in the regions of Canaã de Carajás and Curionopólis, State of Pará, Brazil
A. Monteiro - F. Silva, A. Cruz, S. Silva, et al. - Frontiers Media SA, 2025 usegalaxy.eu

Enhancing multi-omic analyses through a federated microbiome analysis service
A. Rogers - F. Bäuerle, M. Beracochea, A. Heidari, et al. - Center for Open Science, 2025

Silybin A from Silybum marianum reprograms lipid metabolism to induce a cell fate-dependent class switch from triglycerides to phospholipids
S. Koeberle - M. Thürmer, F. Su, M. Werner, et al. - Ivyspring International Publisher, 2025 usegalaxy.eu

Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer
J. Perez - J. Duda, J. Ryu, M. Shetty, et al. - Springer Science and Business Media LLC, 2025 usegalaxy.eu

Hairpin in a haystack : In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae
A. Wicaksono - K. Meitha, K. Wan, M. Mat Isa, et al. - Walter de Gruyter GmbH, 2025 usegalaxy.eu

Comparative mitogenomics of Leptographium procerum, Leptographium terebrantis, and Leptographium wingfieldii, an invasive fungal species in Canadian forests
A. Zubaer - A. Wai, G. Hausner, - Canadian Science Publishing, 2025 usegalaxy.eu

TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data
W. Xian - I. Bezrukov, Z. Bao, S. Vorbrugg, et al. - Oxford University Press (OUP), 2025

Sero‐Molecular Markers and Genetic Diversity of Hepatitis B Virus Isolated From Hemodialysis Patients From Jenin District, West Bank, Palestine
K. Dumaidi - A. AL-Jawabreh, A. Zraiqi, J. Zaid, et al. - Wiley, 2025 usegalaxy.eu

Microbiota Composition of Buffalo Colostrum and Characterization of Potential Probiotic Bacteria With High Exopolysaccharide Production and Cholesterol Assimilation Capacity
P. Ertürkmen - - Wiley, 2025 usegalaxy.eu

The performance of biochar waste-derived electrodes in different bio-electrochemical applications
A. Goglio - A. Carrara, H. Elboghdady, M. Cucina, et al. - Elsevier BV, 2025 usegalaxy.eu

Surveillance of Escherichia coli From Frozen Chicken Meat in Fiji: Resistance Characteristics and Public Health Concerns
D. Lata - R. Sabala, A. Fukuda, C. Nakajima, et al. - Wiley, 2025 usegalaxy.eu

Functional characterization of Camptotheca acuminata 7-deoxyloganetic acid synthases and 7-deoxyloganetic acid glucosyltransferases involved in camptothecin biosynthesis
Y. Li - X. Wang, H. Jiang, S. Xu, et al. - Elsevier BV, 2025 usegalaxy.eu

Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp
J. Kasmanas - S. Magnúsdóttir, J. Zhang, K. Smalla, et al. - Oxford University Press (OUP), 2025

HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences
A. Al-Najim - S. Hauns, V. Tran, R. Backofen, et al. - Oxford University Press (OUP), 2025

Metagenomic CRISPR Array Analysis Tool: a novel graph-based approach to finding CRISPR arrays in metagenomic datasets
F. Talibli - B. Voß, - Oxford University Press (OUP), 2025

Towards high resolution cardiac T1 mapping utilizing deep learning-based image reconstruction
D. Amsel - J. Wetzl, R. Gebker, C. Tillmanns, et al. - Elsevier BV, 2025

One-shot black-blood late gadolinium enhancement imaging for rapid, motion-free, and diagnostically accurate scar imaging
V. De Villedon de Naide - K. Narceau, B. Durand, T. Kuestner, et al. - Elsevier BV, 2025

De Novo Assembly and Annotation of the Pantranscriptome of Astyanax Lacustris on the Liver and Pituitary-Gonadal Axis
D. Aciole Barbosa - G. Branco, A. Gomes, C. Tolussi, et al. - Elsevier BV, 2025 usegalaxy.eu

A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a Western diet based on NHANES data
E. Pletsch - H. Dawson, L. Cheung, J. Ragonese, et al. - Royal Society of Chemistry (RSC), 2025 usegalaxy.eu

The Complete Mitochondrial Genome Assembly of Bali Cattle (Bos Javanicus) Using Oxford Nanopore Long-Read Sequencing Technology
S. Anwar - F. Shidiq, R. Noor, G. Semiadi, et al. - Elsevier BV, 2025 usegalaxy.eu

Investigating genetic diversity within Cryptosporidium parvum outbreaks using multi-locus variable number tandem repeat analysis
R. Bacchetti - P. McCormack, L. Connelly, D. Brown, et al. - Elsevier BV, 2025 usegalaxy.eu

Integrated Morphological and Genome Redescription of Leidyana Gryllorum in Acheta Domesticus: Uncovering Gregarine Diversity in Gryllidae
E. Bessette - N. Vitt Meyling, B. Williams, - Elsevier BV, 2025 usegalaxy.eu

Microbial Risk and Health Burden Associated with the Domestic Preparation of Lentils in France and Hungary
R. Feliciano - J. Membré, L. Delaunay, - Elsevier BV, 2025 usegalaxy.eu

Using DIMet for Differential Analysis of Labeled Metabolomics Data: A Step-by-step Guide Showcasing the Glioblastoma Metabolism
J. Galvis - J. Guyon, T. Daubon, M. Nikolski, et al. - Bio-Protocol, LLC, 2025 usegalaxy.eu

Exploring the Perturbation of Biological Processes Caused by Gene Upregulation Using Knock-In Transfection, Transcriptomics, and Bioinformatics Analysis
I. Garcia - L. Larcombe, - Springer US, 2025 usegalaxy.eu

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq
C. Goclowski - J. Jakiela, T. Collins, S. Hiltemann, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Enhanced biocompatibility of 3D printed resin parts via wet autoclave postprocessing: implications for stem cell organ-on-a-chip culture
A. Jönsson - A. Iatrou, L. Wildfang, D. Neumann, et al. - Royal Society of Chemistry (RSC), 2025 usegalaxy.eu

Bioinformatics Tools: Insights from Structural Approaches
N. Mahanandia - S. Biswal, C. Nayak, M. Farooqi, et al. - Springer Nature Singapore, 2025 usegalaxy.eu

PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking
E. Nasr - A. Henger, B. Grüning, P. Zierep, et al. - Oxford University Press (OUP), 2025 usegalaxy.eu

Clostridium tetani bacteraemia in the plague area in France: Two cases
M. Boualam - A. Bouri, M. Signoli, M. Drancourt, et al. - Elsevier BV, 2025 usegalaxy.eu

Prevalence and antimicrobial resistance of methicillin-resistant and methicillin-susceptible Staphylococcus in small- to medium-scale and large-scale dairy farms in Thailand
N. Phumthanakorn - J. Thanasak, - Oxford University Press (OUP), 2025 usegalaxy.eu

The Role of Rhodococcus Opacus R7 Laccase-Like Multicopper Oxidase (Lmco1) Enzyme In Biodegradation of Polyethylene Polymer
M. Pishan - S. Sazegari, A. Niazi, M. Majdinasab, et al. - Elsevier BV, 2025 usegalaxy.eu

Deciphering a cryptic minefield: A guide to Cryptosporidium gp60 subtyping
G. Robinson - R. Chalmers, K. Elwin, R. Guy, et al. - Elsevier BV, 2025 usegalaxy.eu

Genomic dataset of eighteen Burkholderia pseudomallei strains isolated from clinical and environmental settings in Malaysia
N. Semail - N. Zuraina, Y. Ismadi, A. Harun, et al. - Elsevier BV, 2025 usegalaxy.eu

DgeaHeatmap: an R package for transcriptomic analysis and heatmap generation
L. Lancelle - P. Potru, B. Spittau, S. Wiemann, et al. - Oxford University Press (OUP), 2024

Bacterial Communities, Pathogens, Resistomes, and Mobilomes Associated with a Wastewater Treatment Plant in Mexico: A Metagenomics Approach
O. Oyedara - C. Ruíz-Amaro, N. Heredia, S. García, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Use of Gain-of-Function Screening to Identify miRNAs Involved in Paclitaxel Resistance in Triple-Negative Breast Cancer
S. Nemours - C. Solé, I. Goicoechea, M. Armesto, et al. - MDPI AG, 2024 usegalaxy.eu

Genome sequence of the ornamental plant Aquilegia vulgaris reveals the flavonoid biosynthesis gene repertoire
R. Friedhoff - K. Wolff, B. Pucker, - bioRxiv - openRxiv, 2024

Canonical androgen response element motifs are tumor suppressive regulatory elements in the prostate
X. Chen - M. Augello, D. Liu, K. Lin, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution
R. Petroll - D. Varshney, S. Hiltemann, H. Finke, et al. - Wiley, 2024 usegalaxy.eu

The complete mitochondrial genome of Phyllobrotica signata (Mannerheim, 1825) (Coleoptera: Chrysomelidae: Galerucinae): characterization and phylogenetic implications
X. Yu - X. Jin, X. Lin, L. Liu, et al. - Informa UK Limited, 2024 usegalaxy.eu

RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex
S. Bloor - N. Wit, P. Lehner, - Oxford University Press (OUP), 2024 usegalaxy.eu

ATP-Gated P2X7-Ion Channel on Kidney-Resident Natural Killer T Cells and Memory T Cells in Intrarenal Inflammation
M. Junge - N. Liaukouskaya, N. Schwarz, C. Pinto-Espinoza, et al. - Ovid Technologies (Wolters Kluwer Health), 2024 usegalaxy.eu

Transcriptional regulation in the absence of inositol trisphosphate receptor calcium signaling
M. Young - D. Booth, D. Smith, M. Tigano, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Interactors and effects of overexpressing YlxR/RnpM, a conserved RNA binding protein in cyanobacteria
L. Hemm - A. Miucci, A. Kraus, M. Riediger, et al. - Informa UK Limited, 2024 usegalaxy.eu

A Comparative Analysis of Mitogenomes in Species of the Tapinoma nigerrimum Complex and Other Species of the Genus Tapinoma (Formicidae, Dolichoderinae)
A. Ruiz-Mena - P. Mora, J. Rico-Porras, B. Kaufmann, et al. - MDPI AG, 2024 usegalaxy.eu

Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases
C. Rempfer - S. Hoernstein, N. van Gessel, A. Graf, et al. - Elsevier BV, 2024

A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor
C. Roessner - S. Griep, A. Becker, - Elsevier BV, 2024

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments
S. Chen - F. Musat, H. Richnow, M. Krüger, et al. - Elsevier BV, 2024

Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases
C. Rempfer - S. Hoernstein, N. van Gessel, A. Graf, et al. - Elsevier BV, 2024

Jumping through hoops: Structural rearrangements and accelerated mutation rates on Dendrodorididae (Mollusca: Nudibranchia) mitogenomes rumble their evolution
C. Galià-Camps - T. Schell, A. Enguídanos, C. Pegueroles, et al. - Elsevier BV, 2024 usegalaxy.eu

Land use intensity differently affects soil microbial functional communities in arable fields
C. Gao - S. Hannula, P. van Bodegom, T. Bezemer, et al. - Elsevier BV, 2024 usegalaxy.eu

Complete mitochondrial genome of the Satanas beetle, Dynastes satanas Moser, 1909 (Coleoptera: Scarabaeidae)
X. He - S. Wei, P. Li, X. Li, et al. - Informa UK Limited, 2024 usegalaxy.eu

Integrated genomic and functional analysis of Streptomyces sp. UP1A-1 for bacterial wilt control and solanaceae yield increase
M. Kaari - R. Manikkam, J. Joseph, S. Krishnan, et al. - Elsevier BV, 2024 usegalaxy.eu

Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries
G. Kumar - P. Bhadury, - Elsevier BV, 2024 usegalaxy.eu

Carbon nanodots as photosensitizer in photodynamic inactivation of Rickettsia slovaca
Y. Peresh - K. Šoltys, Ľ. Kľúčár, G. Beke, et al. - Elsevier BV, 2024 usegalaxy.eu

Hemoglobin targeting potential of aminocarb pesticide: Investigation into dynamics, conformational stability, and energetics in solvent environment
S. Singh - P. Gopi, P. Sharma, M. Rani, et al. - Elsevier BV, 2024 usegalaxy.eu

Rs1347093 regulates microRNA-216/-217 expression and is associated with pancreatic cancer risk
H. Huang - T. Shiu, D. Chan, C. Chang, et al. - Elsevier BV, 2024 usegalaxy.eu

Comparative study of chloroplast genomes across seven Salacca species
A. ARSHAD - R. ADITAMA, M. RAHAYU, A. NATAWIJAYA, et al. - UNS Solo, 2024 usegalaxy.eu

Feasibility, classification and potential clinical impact of non-invasive delineation of abdominal lymphatic vessels in patients following TCPC with T2 weighted MRI
A. Hanser - M. Hofbeck, M. Hofmeister, P. Martirosian, et al. - Springer Science and Business Media LLC, 2024

Panacus: fast and exact pangenome growth and core size estimation
L. Parmigiani - E. Garrison, J. Stoye, T. Marschall, et al. - Oxford University Press (OUP), 2024

Unveiling Genetic Basis Associated With Manganese Content in Turkish Common Bean (Phaseolus vulgaris L.) Germplasm Through a Genome‐Wide Association Study
M. Altaf - M. Nadeem, S. Ayten, E. Aksoy, et al. - Wiley, 2024 usegalaxy.eu

Cyclic electron flow compensates loss of PGDH3 and concomitant stromal NADH reduction
M. Krämer - N. Blanco, J. Penzler, G. Davis, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Cacao genome sequence reveals insights into the flavonoid biosynthesis
M. Marin Recinos - S. Winnier, K. Lagerhausen, B. Ajayi, et al. - bioRxiv - openRxiv, 2024

Plant Thermosensors
J. Casal - G. Murcia, L. Bianchimano, - Annual Reviews, 2024 usegalaxy.eu

Mitogenomics providing new insights into the phylogenetic structure of subfamily Panchaetothripinae (Thripidae: Terebrantia)
A. Ghosh - K. Tyagi, D. Banerjee, V. Kumar, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Genetic characterization and clonal analysis of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae from canine and human origins
N. Khine - A. Shah, T. Chatsuwan, J. Yindee, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Integrative analysis of circulating tumor cells ( CTCs ) and exosomes from small‐cell lung cancer ( SCLC ) patients: a comprehensive approach
D. Papakonstantinou - A. Roumeliotou, E. Pantazaka, A. Shaukat, et al. - Wiley, 2024 usegalaxy.eu

An integrated transcriptomic cell atlas of human neural organoids
Z. He - L. Dony, J. Fleck, A. Szałata, et al. - Springer Science and Business Media LLC, 2024

Pan-flavivirus analysis reveals sfRNA-independent, 3′ UTR-biased siRNA production from an insect-specific flavivirus
B. Besson - G. Overheul, M. Wolfinger, S. Junglen, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Genomics and evolutionary analysis of Chlorella variabilis- infecting viruses demarcate criteria for defining species of giant viruses
J. Carvalho - R. Carlson, J. Ghosh, V. Queiroz, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Advancing Neonatal Care: A Deep Learning Approach for Non-Contact Heart Rate Monitoring
A. Grafton - A. Castelblanco, J. Warnecke, L. Thomson, et al. - IEEE, 2024

Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host
T. Ipoutcha - I. Tsarmpopoulos, G. Gourgues, V. Baby, et al. - Microbiology Society, 2024 usegalaxy.eu

Deciphering the molecular logic of WOX5 function in the root stem cell organizer
N. Zhang - P. Bitterli, P. Oluoch, M. Hermann, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

A homozygous human WNT11 loss-of-function variant associated with laterality, heart and renal defects
H. Berns - M. Haas, Z. Bakey, M. Brislinger-Engelhardt, et al. - bioRxiv - openRxiv, 2024 usegalaxy.eu

The complete mitochondrial DNA of the carnivorous sponge Lycopodina hypogea is putatively complemented by microDNAs
T. de Paula - D. Leite, G. Lobo-Hajdu, J. Vacelet, et al. - PeerJ, 2024 usegalaxy.eu

The multifaceted role of vitreous hyalocytes: Orchestrating inflammation, angiomodulation and erythrophagocytosis in proliferative diabetic retinopathy
S. Boneva - J. Wolf, M. Jung, G. Prinz, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Influenza A virus shedding and reinfection during the post-weaning period in swine: longitudinal study of two nurseries
S. Storms - A. Leonardi-Cattolica, T. Prezioso, C. Varga, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Circularly assembled genome sequences of Asticcacaulis sp. strain MM231 and Brevundimonas subvibrioides MM232, isolated from a pond at Bielefeld University campus
B. Laker - T. Schulze, M. Reis, S. Bormann, et al. - American Society for Microbiology, 2024

Complete genome sequences of Chitinophaga sp. strain MM2321 and Microbacterium sp. strain MM2322, isolated from a sand sample in Harsewinkel, Germany
M. Eisenhut - T. Schulze, F. Matten, A. Sengewald, et al. - American Society for Microbiology, 2024

Benchmarking of T-Cell Receptor - Epitope Predictors with ePytope-TCR
F. Drost - A. Chernysheva, M. Albahah, K. Kocher, et al. - bioRxiv - openRxiv, 2024

Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation
K. Chatti - N. Kmeli, I. Bettaieb, J. Hamdi, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Transcriptomic and de novo proteomic analyses of organotypic entorhino-hippocampal tissue cultures reveal changes in metabolic and signaling regulators in TTX-induced synaptic plasticity
M. Lenz - P. Turko, P. Kruse, A. Eichler, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization
P. Liu - J. Vigneau, R. Craig, J. Barrera-Redondo, et al. - Springer Science and Business Media LLC, 2024

StCDF1: A ‘jack of all trades’ clock output with a central role in regulating potato nitrate reduction activity
M. Shaikh - L. Ramírez‐Gonzales, J. Franco‐Zorrilla, E. Steiner, et al. - Wiley, 2024 usegalaxy.eu

The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation
K. Yu - G. Wang, S. Guo, F. Bassermann, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus
J. Zehr - S. Kosakovsky Pond, S. Shank, H. McQueary, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Genome-wide mapping of RPA1 and RAD9 reveals the management of polycistronic transcription, replication initiation, and responses to replication stress in Leishmania
J. Black - S. Virgilio, M. Bastos, G. Silva, et al. - bioRxiv - openRxiv, 2024 usegalaxy.eu

Smile-to-Bert: a pre-trained Transformer model for molecular property prediction using SMILES representations
M. Barranco-Altirriba - V. Würf, E. Manzini, J. Pauling, et al. - bioRxiv - openRxiv, 2024

Zymogen granule protein 16B (ZG16B) is a druggable epigenetic target to modulate the mammary extracellular matrix
M. Lengyel - Á. Molnár, T. Nagy, S. Jdeed, et al. - Wiley, 2024 usegalaxy.eu

PROSER1 modulates DNA demethylation through dual mechanisms to prevent syndromic developmental malformations
A. Fleming - E. Knatko, X. Li, A. Zoch, et al. - Cold Spring Harbor Laboratory, 2024 usegalaxy.eu

Prostaglandin E2-EP2/EP4 signaling induces immunosuppression in human cancer by impairing bioenergetics and ribosome biogenesis in immune cells
S. Punyawatthananukool - R. Matsuura, T. Wongchang, N. Katsurada, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum
Q. Li - L. Vetter, Y. Veith, E. Christ, et al. - Elsevier BV, 2024 usegalaxy.eu

Cell death induced by Lepeophtheirus salmonis labial gland protein 3 in salmonid fish leukocytes: A mechanism for disabling host immune responses
H. Midtbø - A. Borchel, H. Morton, R. Paley, et al. - Elsevier BV, 2024 usegalaxy.eu

BMS345541 is predicted as a repurposed drug for the treatment of TMZ-resistant Glioblastoma using target gene expression and virtual drug screening
R. Nayak - B. Mallick, - Elsevier BV, 2024 usegalaxy.eu

Distribution and genetic diversity of Bombyx mori nucleopolyhedrovirus in mass-reared silkworms in Thailand
J. Wennmann - S. Senger, B. Ruoff, J. Jehle, et al. - Elsevier BV, 2024 usegalaxy.eu

Mitogenome of a new Ramazzottius species (Tardigrada: Eutardigrada: Ramazzottiidae) discovered in rock pools along with its temperature and desiccation-related proteins repertoire
M. Vecchi - D. Stec, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

A nationwide survey of antimicrobial resistance of Escherichia coli isolated from broiler chickens in Malawi
P. Chisembe - M. Suzuki, D. Dao, G. Njunga, et al. - Oxford University Press (OUP), 2024 usegalaxy.eu

Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides
L. Gorniak - S. Bucka, B. Nasr, J. Cao, et al. - American Society for Microbiology, 2024

Novel hepatocyte-like liver organoids recapitulate crucial mature hepatic functions
A. Ardisasmita - I. Joore, N. Levy, A. Myszczyszyn, et al. - bioRxiv - openRxiv, 2024 usegalaxy.eu

The multifaceted role of mitochondria in cardiac function: insights and approaches
S. Ravindran - C. Rau, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Glut3 promotes cellular O-GlcNAcylation as a distinctive tumor-supportive feature in Treg cells
A. Sharma - G. Sharma, Z. Gao, K. Li, et al. - Springer Science and Business Media LLC, 2024

Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation
P. Belmann - B. Osterholz, N. Kleinboelting, A. Puehler, et al. - bioRxiv - openRxiv, 2024

Suppressive cancer nonstop extension mutations increase C-terminal hydrophobicity and disrupt evolutionarily conserved amino acid patterns
A. Ghosh - M. Riester, J. Pal, K. Lainde, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Epigenetic modulation via the C-terminal tail of H2A.Z
L. Imre - P. Nánási, I. Benhamza, K. Enyedi, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification
F. Padovani - I. Čavka, A. Neves, C. López, et al. - bioRxiv - openRxiv, 2024

Benchmarking Dependence Measures to Prevent Shortcut Learning in Medical Imaging
S. Müller - L. Fay, L. Koch, S. Gatidis, et al. - Springer Nature Switzerland, 2024

Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean
A. Wicaksono - T. Buaboocha, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

A transcriptomic hourglass in brown algae
J. Lotharukpong - M. Zheng, R. Luthringer, D. Liesner, et al. - Springer Science and Business Media LLC, 2024

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery
U. Rocha - J. Kasmanas, R. Toscan, D. Sanches, et al. - Public Library of Science (PLoS), 2024

In-Silico Perspectives on the Potential Therapeutic Aids of Hesperetin Derivatives for Lung Cancer
A. Asiri - - The Running Line, 2024 usegalaxy.eu

Oviduct epithelial spheroids during in vitro culture of bovine embryos mitigate oxidative stress, improve blastocyst quality and change the embryonic transcriptome
T. Pranomphon - Á. López-Valiñas, C. Almiñana, C. Mahé, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome
L. Pyöriä - D. Pratas, M. Toppinen, P. Simmonds, et al. - Oxford University Press (OUP), 2024 usegalaxy.eu

Unravelling the complexity of bovine milk microbiome: insights into mastitis through enterotyping using full-length 16S-metabarcoding
L. Urrutia-Angulo - M. Ocejo, B. Oporto, G. Aduriz, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Immunoinformatics Design of a Multiepitope Vaccine (MEV) Targeting Streptococcus mutans: A Novel Computational Approach
R. Naorem - B. Pangabam, S. Bora, C. Fekete, et al. - MDPI AG, 2024 usegalaxy.eu

Mapping lineage-traced cells across time points with moslin
M. Lange - Z. Piran, M. Klein, B. Spanjaard, et al. - Springer Science and Business Media LLC, 2024

JunB is required for CD8+ T cell responses to acute infections
S. Sarkar - N. Taira, T. Hsieh, H. Chien, et al. - Oxford University Press (OUP), 2024 usegalaxy.eu

Pertussis Outbreak During 2023 in Gipuzkoa, North Spain
J. Marimón - M. Montes, N. Vizuete, L. Alvarez Guerrico, et al. - MDPI AG, 2024 usegalaxy.eu

Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus
S. Richter - S. Kind, T. Oberhänsli, M. Schneider, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations
V. Pham - C. Rödel, M. Valentino, M. Malinverno, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Rbm3 deficiency leads to transcriptome-wide splicing alterations
S. Erkelenz - M. Grzonka, A. Papadakis, H. Schaal, et al. - Informa UK Limited, 2024 usegalaxy.eu

Laminin-α2 chain deficiency in skeletal muscle causes dysregulation of multiple cellular mechanisms
S. Martins - V. Ribeiro, C. Melo, C. Paulino-Cavaco, et al. - Life Science Alliance, LLC, 2024 usegalaxy.eu

Artificial intelligence-enhanced detection of subclinical coronary artery disease in athletes: diagnostic performance and limitations
J. Kübler - J. Brendel, T. Küstner, J. Walterspiel, et al. - Springer Science and Business Media LLC, 2024

Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions
M. Tufail - B. Jordan, L. Hadjeras, R. Gelhausen, et al. - Springer Science and Business Media LLC, 2024

Comparison of Mitochondrial Genome Expression Differences among Four Skink Species Distributed at Different Latitudes under Low-Temperature Stress
L. Zhan - J. He, L. Ding, K. Storey, et al. - MDPI AG, 2024 usegalaxy.eu

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets
L. Hemm - D. Rabsch, H. Ropp, V. Reimann, et al. - bioRxiv - openRxiv, 2024

The haplotype-resolved assembly of COL40 a cassava ( Manihot esculenta ) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12
C. Thoben - B. Pucker, S. Winter, B. Econopouly, et al. - bioRxiv - openRxiv, 2024

A snapshot of the Physcomitrella N-terminome reveals N-terminal methylation of organellar proteins
S. Hoernstein - A. Schlosser, K. Fiedler, N. van Gessel, et al. - Springer Science and Business Media LLC, 2024

Identification of Pathogenic Copy Number Variants in Mexican Patients With Inherited Retinal Dystrophies Applying an Exome Sequencing Data‐Based Read‐Depth Approach
G. Fabian‐Morales - V. Ordoñez‐Labastida, F. Garcia‐Martínez, L. Montes‐Almanza, et al. - Wiley, 2024 usegalaxy.eu

Astrocytes originated from neural stem cells drive the regenerative remodeling of pathologic CSPGs in spinal cord injury
S. Hosseini - S. Nemati, S. Karimi-Abdolrezaee, - Elsevier BV, 2024 usegalaxy.eu

Sorafenib induces cachexia by impeding transcriptional signaling of the SET1/MLL complex on muscle-specific genes
B. Khan - C. Lanzuolo, V. Rosti, P. Santarelli, et al. - Elsevier BV, 2024 usegalaxy.eu

Impact of vaccination with the Anaplasma phagocytophilum MSP4 chimeric antigen on gene expression in the rabbit host
A. Moraga-Fernández - M. de Sousa-Blanco, J. Marques, J. Queirós, et al. - Elsevier BV, 2024 usegalaxy.eu

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis
S. Hakim - N. Choudhary, K. Malhotra, J. Peng, et al. - bioRxiv - openRxiv, 2024

Mitogenome-Based Phylogeny with Divergence Time Estimates Revealed the Presence of Cryptic Species within Heptageniidae (Insecta, Ephemeroptera)
Z. Guo - C. Shen, H. Cheng, Y. Chen, et al. - MDPI AG, 2024 usegalaxy.eu

In vivo evolution to hypermucoviscosity and ceftazidime/avibactam resistance in a liver abscess caused by Klebsiella pneumoniae sequence type 512
V. Capitani - G. Arcari, C. Ambrosi, D. Scribano, et al. - American Society for Microbiology, 2024 usegalaxy.eu

miRNA-mediated gene silencing in Drosophila larval development involves GW182-dependent and independent mechanisms
E. Matsuura-Suzuki - K. Kiyokawa, S. Iwasaki, Y. Tomari, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

EXCRETE workflow enables deep proteomics of the microbial extracellular environment
D. Russo - D. Oliinyk, G. Pohnert, F. Meier, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Unravelling the main genomic features of Mycoplasma equirhinis
M. Martineau - C. Ambroset, S. Lefebvre, É. Kokabi, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
Y. Lin - K. Breuer, D. Weichenhan, P. Lafrenz, et al. - bioRxiv - openRxiv, 2024

Genus-wide analysis of Trichoderma antagonism toward Pythium and Globisporangium plant pathogens and the contribution of cellulases to the antagonism
S. Chen - P. Daly, W. Anjago, R. Wang, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Characterization of the angiomodulatory effects of Interleukin 11 cis- and trans-signaling in the retina
P. Liang - J. Ness, J. Rapp, S. Boneva, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Evidence for phosphate-dependent control of symbiont cell division in the model anemone Exaiptasia diaphana
N. Faulstich - A. Deloach, Y. Ksor, G. Mesa, et al. - American Society for Microbiology, 2024 usegalaxy.eu

DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing
M. Kristen - M. Lander, L. Kilz, L. Gleue, et al. - Oxford University Press (OUP), 2024 usegalaxy.eu

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
R. Rebollo - P. Gerenton, E. Cumunel, A. Mary, et al. - Peer Community In, 2024 usegalaxy.eu

Nanopore sequencing of IPNV vp2 gene in Peruvian Andean trout ( Oncorhynchus mykiss ) cultures
S. Tapia - J. Orellana, Y. Duran, J. Rodriguez, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Reducing energy consumption in musculoskeletal MRI using shorter scan protocols, optimized magnet cooling patterns, and deep learning sequences
S. Afat - J. Wohlers, J. Herrmann, A. Brendlin, et al. - Springer Science and Business Media LLC, 2024

Dark Mystery Solved: A Captive Black Leopard from South Africa is of Asian Descent
L. Tensen - G. Camacho, - Southern African Wildlife Management Association, 2024 usegalaxy.eu

The Diversity of Seed-Borne Fungi Associated with Soybean Grown in Southern Poland
H. Olszak-Przybyś - G. Korbecka-Glinka, - MDPI AG, 2024 usegalaxy.eu

On discovery of novel hub genes for ER+ and TN breast cancer types through RNA seq data analyses and classification models
A. Saddiqa - M. Zakir, M. Sheikh, Z. Muneer, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Biphasic response of human iPSC-derived neural network activity following exposure to a sarin-surrogate nerve agent
C. Bogguri - V. George, B. Amiri, A. Ladd, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Harnessing Lignocellulolytic and Electrogenic Potential: Insights from Shewanella oneidensis MR-1 and Cellulomonas Strains on Lignocellulosic Biomass
A. Molla - V. Mishyn, N. Bernet, T. Bouchez, et al. - The Electrochemical Society, 2024 usegalaxy.eu

Mesenchymal Osr1+ cells regulate embryonic lymphatic vessel formation
P. Vallecillo-García - M. Kühnlein, M. Orgeur, N. Hansmeier, et al. - The Company of Biologists, 2024 usegalaxy.eu

Gene expression networks in endothelial cells from failing human hearts
L. Wirth - E. Erny, M. Krane, H. Lahm, et al. - American Physiological Society, 2024 usegalaxy.eu

The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface
B. Ramos - M. Cunha, - Elsevier BV, 2024 usegalaxy.eu

The fork protection complex promotes parental histone recycling and epigenetic memory
S. Charlton - V. Flury, Y. Kanoh, A. Genzor, et al. - Elsevier BV, 2024 usegalaxy.eu

Molecular similarities between the genes for Trypanosoma cruzi microtubule-associated proteins, mammalian interferons, and TRIMs
M. Winkler - A. Pan, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties
J. Gavalda-Garcia - A. Díaz, W. Vranken, - Oxford University Press (OUP), 2024 usegalaxy.eu

Identification of effector candidates in Bipolaris sorokiniana and their expression profile analysis during pathogen-wheat interactions
M. Kamajian - A. Soorni, R. Mehrabi, - Elsevier BV, 2024 usegalaxy.eu

PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation
Z. Liang - T. Zhu, Y. Yu, C. Wu, et al. - Elsevier BV, 2024 usegalaxy.eu

Viral hijacking of hnRNPH1 unveils a G-quadruplex-driven mechanism of stress control
P. Schult - B. Kümmerer, M. Hafner, K. Paeschke, et al. - Elsevier BV, 2024 usegalaxy.eu

Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12 . 1C
D. Nguyen - Q. Tran, L. Le, H. Nguyen, et al. - Wiley, 2024 usegalaxy.eu

Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system
V. Tiwari - B. Prajapati, Y. Asare, A. Damkou, et al. - Elsevier BV, 2024 usegalaxy.eu

In Silico Prediction of Antibacterial Activity of Quinolone Derivatives
T. Karim - M. Almatarneh, S. Rahman, A. Alodhayb, et al. - Wiley, 2024 usegalaxy.eu

Characteristics and phylogenetic implications of the mitochondrial genome of a rare species, Libellula melli
B. Lin - H. Chen, J. Li, J. Liao, et al. - Elsevier BV, 2024 usegalaxy.eu

Correlation of Immunomodulatory Cytokines with Tumor Volume and Cerebrospinal Fluid in Vestibular Schwannoma Patients
A. Becker - L. Scholle, C. Klause, M. Staege, et al. - MDPI AG, 2024 usegalaxy.eu

Multitask perturbation modeling for single-cell omics
M. van Baardwijk - G. Gavriilidis, N. Ishaque, O. Lazareva, et al. - F1000 Research Ltd, 2024

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR
N. Choudhary - B. Pucker, - Public Library of Science (PLoS), 2024

Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches
A. Hashempour - N. Khodadad, S. Akbarinia, F. Ghasabi, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species
A. Uncu - A. Patat, A. Uncu, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Genomic Insights into Vietnamese Extended-Spectrum β-Lactamase-9-Producing Extensively Drug-Resistant Pseudomonas aeruginosa Isolates Belonging to the High-Risk Clone ST357 Obtained from Bulgarian Intensive Care Unit Patients
T. Strateva - A. Stratev, S. Peykov, - MDPI AG, 2024 usegalaxy.eu

Genetic Polymorphisms of Angiotensin-Converting Enzyme 1 (ACE1) and ACE2 Associated With Severe Acute Respiratory Syndrome COVID-19 in the Palestinian Population
L. AbuSaleh - S. Ereqat, A. Al-Jawabreh, A. Nasereddin, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Coordinated metabolic adaptation of Arabidopsis thaliana to high light
G. Balcke - K. Vahabi, J. Giese, I. Finkemeier, et al. - Wiley, 2024 usegalaxy.eu

Research topic displacement and the lack of interdisciplinarity: lessons from the scientific response to COVID-19
E. Seidlmayer - T. Melnychuk, L. Galke, L. Kühnel, et al. - Springer Science and Business Media LLC, 2024

Inference of Host–Pathogen Interaction Matrices from Genome-Wide Polymorphism Data
H. Märkle - S. John, L. Metzger, . , et al. - Oxford University Press (OUP), 2024

Three feminizing Wolbachia strains in a single host species: comparative genomics paves the way for identifying sex reversal factors
P. Grève - B. Moumen, D. Bouchon, - Frontiers Media SA, 2024 usegalaxy.eu

InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata
M. Elhossary - K. Förstner, - SAGE Publications, 2024

Disseminated Echovirus 11 infection in a newborn in the Province of Bolzano, Italy
I. Bianconi - L. Battisti, A. Staffler, E. Giacobazzi, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
M. Hoshino - G. Cossard, F. Haas, E. Kane, et al. - Springer Science and Business Media LLC, 2024

Identification of epigenetic modifiers essential for growth and survival of AML1/ETO‐positive leukemia
J. Duque‐Afonso - P. Veratti, U. Rehman, H. Herzog, et al. - Wiley, 2024 usegalaxy.eu

Genomic characterization of prophage elements in Clostridium clostridioforme: an understudied component of the intestinal microbiome
S. Humphrey - A. Marouli, K. Thümmler, M. Mullin, et al. - Microbiology Society, 2024 usegalaxy.eu

Potential Ancestral Conoidean Toxins in the Venom Cocktail of the Carnivorous Snail Raphitoma purpurea (Montagu, 1803) (Neogastropoda: Raphitomidae)
G. Chiappa - G. Fassio, M. Modica, M. Oliverio, et al. - MDPI AG, 2024 usegalaxy.eu

In silico studies of benzothiazole derivatives as potential inhibitors of Anopheles funestus and Anopheles gambiae trehalase
T. Ogunnupebi - G. Oduselu, O. Elebiju, O. Ajani, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Nonlinear latent representations of high-dimensional task-fMRI data: Unveiling cognitive and behavioral insights in heterogeneous spatial maps
M. Zabihi - S. Kia, T. Wolfers, S. de Boer, et al. - Public Library of Science (PLoS), 2024

Genomic Evaluation of Multidrug-Resistant Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli from Irrigation Water and Fresh Produce in South Africa: A Cross-Sectional Analysis
L. Richter - S. Duvenage, E. du Plessis, T. Msimango, et al. - American Chemical Society (ACS), 2024 usegalaxy.eu

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing
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Attention-Aware Non-Rigid Image Registration for Accelerated MR Imaging
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Biofoams with untapped enzymatic potential produced from beer bagasse by indigenous fungal strains
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Acute Hypoxia Does Not Alter Tumor Sensitivity to FLASH Radiation Therapy
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Differences in activity and stability drive transposable element variation in tropical and temperate maize
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Bioelectrochemical protein production valorising NH3-rich pig manure-derived wastewater and CO2 from anaerobic digestion
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Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks
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Prostaglandin D2 receptor 2 downstream signaling and modulation of type 2 innate lymphoid cells from patients with asthma
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Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
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An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease
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Trusted Research Environments: Analysis of Characteristics and Data Availability
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FAIRsoft—a practical implementation of FAIR principles for research software
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Complete genome sequence of the Exiguobacterium bacteriophage
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Sulcation in children with autism spectrum disorders
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Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations
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Transcription Factor 23 is an Essential Determinant of Murine Term Parturition
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Spotlight on Secondary Metabolites Produced by an Early-Flowering Apulian Artichoke Ecotype Sanitized from Virus Infection by Meristem-Tip-Culture and Thermotherapy
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Cytochrome P450 2J2 is required for the natural compound austocystin D to elicit cancer cell toxicity
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A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis
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Bioinformatic Prediction and High Throughput In Vivo Screening to Identify Cis-Regulatory Elements for the Development of Algal Synthetic Promoters
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ProSwats: A Proxy-based Scientific Workflow Retrieval Approach by Bridging the Gap between Textual and Structural Semantics
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A 10-Year Longitudinal Study of Brain Cortical Thickness in People with First-Episode Psychosis Using Normative Models
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Decoding the language of chromatin modifications with MARCS
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Biodiversity and potential functionality of biofilm-sediment biotope in La Muerte lagoon, Monegros Desert, Spain
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Identification and Characterization of ATOH7-Regulated Target Genes and Pathways in Human Neuroretinal Development
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Amazonian Bacteria from River Sediments as a Biocontrol Solution against Ralstonia solanacearum
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ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists
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Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle
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The effect of successive summer drought periods on bacterial diversity along a plant species richness gradient
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Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil
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Complete mitochondrial genomes of Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua (Diptera: Tephritidae) and their phylogenetic relationships with other congeners
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Pangenome graph layout by Path-Guided Stochastic Gradient Descent
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Genomic prediction in Brassica napus: evaluating the benefit of imputed whole-genome sequencing data
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Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417
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Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms
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Deciphering the Key Players of the Bacterial Microbiota Associated with Aerial Crown Gall Tumors on Rhododendron: Insights into the Gallobiome
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Characterization of a highly thermostable recombinant xylanase from Anoxybacillus ayderensis
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Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient
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A reproducible workflow for assembling the mitochondrial genome of Acheta domesticus (Orthoptera: Gryllidae)
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Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation
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Motion-Compensated MR CINE Reconstruction With Reconstruction-Driven Motion Estimation
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Meiotic maturation failure in primary ovarian insufficiency: insights from a bovine model
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Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java
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Overview of transcriptome changes and phenomic profile of sanitized artichoke vis‐à‐vis non‐sanitized plants
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First Indonesian report of WGS-based MTBC L3 discovery
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Iron Chelation in Soil: Scalable Biotechnology for Accelerating Carbon Dioxide Removal by Enhanced Rock Weathering
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Generation of functionally active resident macrophages from adipose tissue by 3D cultures
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Wall-Associated Kinase (WAK) and WAK-like Kinase Gene Family in Sugar Beet: Genome-Wide Characterization and In Silico Expression Analysis in Response to Beet Cyst Nematode (Heterodera schachtii Schmidt) Infection
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Exploring the biotechnological potential of novel soil-derived Klebsiella sp. and Chryseobacterium sp. strains using phytate as sole carbon source
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Path-based reasoning for biomedical knowledge graphs with BioPathNet
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Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily Victoria cruziana
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SETD1A-dependent EME1 transcription drives PARPi sensitivity in HR deficient tumour cells
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Nodulating Aeschynomene indica without Nod Factor Synthesis Genes: In Silico Analysis of Evolutionary Relationship
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DeepNeo: Deep Learning for neointimal tissue characterization using optical coherence tomography
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CellRank 2: unified fate mapping in multiview single-cell data
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The genomic and phylogenetic analysis of Marseillevirus cajuinensis raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization
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Panacus: fast and exact pangenome growth and core size estimation
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Complete genome sequence of the Microbacterium enclense bacteriophage phiMiGM15
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Examining Transcriptomic Alterations in Rat Models of Intracerebral Hemorrhage and Severe Intracerebral Hemorrhage
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Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation: a novel adjuvant option?
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Partial hepatectomy accelerates colorectal metastasis by priming an inflammatory premetastatic niche in the liver
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Genetic influence on vascular smooth muscle cell apoptosis
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De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders
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Nuclear position and local acetyl-CoA production regulate chromatin state
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Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study
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Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies
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SmCYP71D373 of Salvia miltiorrhiza catalyzes the methyl oxidation reaction of tanshinone IIA-19 position
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Carbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain
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Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique Fusarium oxysporum f. sp. cubense Isolate in Hawaii
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From genes to toxins: Profiling Prymnesium parvum during a riverine harmful algal bloom
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Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons
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Detection of KPC-216, a Novel KPC-3 Variant, in a Clinical Isolate of Klebsiella pneumoniae ST101 Co-Resistant to Ceftazidime-Avibactam and Cefiderocol
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Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency
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JAK-2 V617F Mutation in Endothelial Cells of Patients with Atherosclerotic Carotid Disease
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Robust Graph Pruning for Efficient Segmentation and Cluster Splitting of Cell Nuclei Using Deformable Shape Models
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Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae
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Elucidating the impact of Y chromosome microdeletions and altered gene expression on male fertility in assisted reproduction
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Mitigating candidiasis with acarbose by targeting Candida albicans α-glucosidase: in-silico, in-vitro and transcriptomic approaches
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The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
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Unveiling soil bacterial ecosystems in andean citrus orchards of Santander, Colombia
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Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs
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The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
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Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast
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Divergence within the Taxon ‘Candidatus Phytoplasma asteris’ Confirmed by Comparative Genome Analysis of Carrot Strains
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Apoplastomes of contrasting cacao genotypes to witches’ broom disease reveals differential accumulation of PR proteins
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Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
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Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response
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Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca)
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A practical guide to bioimaging research data management in core facilities
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First Isolation of the Heteropathotype Shiga Toxin-Producing and Extra-Intestinal Pathogenic (STEC-ExPEC) E. coli O80:H2 in French Healthy Cattle: Genomic Characterization and Phylogenetic Position
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Cluster efficient pangenome graph construction with nf-core/pangenome
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Modeling brain sex in the limbic system as phenotype for female-prevalent mental disorders
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Rab7 deficiency induces lysosome formation from recycling endosomes leading to an increased degradation of cell surface proteins
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Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression
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Reduction of APOE accounts for neurobehavioral deficits in fetal alcohol spectrum disorders
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Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp
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Assessment and Partial Characterization of Candidate Genes in Dihydrochalcone and Arbutin Biosynthesis in an Apple–Pear Hybrid by De Novo Transcriptome Assembly
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Tolperisone hydrochloride improves motor functions in Parkinson’s disease via MMP-9 inhibition and by downregulating p38 MAPK and ERK1/2 signaling cascade
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Removing scanner effects with a multivariate latent approach: A RELIEF for the ABCD imaging data?
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Metagenomic Study of Bacteria Diversity and Functional Profile in Bulk and Rhizosphere Soils of Fusarium-Wilt Infected Plantain (Musa paradisiaca)
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Evaluation of novel pyridoxal isonicotinoyl hydrazone (PIH) derivatives as potential anti‐tuberculosis agents: An in silico investigation
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Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer
S. Joshi - R. Srivastava, - Wiley, 2024 usegalaxy.eu

The Damietta Server: a comprehensive protein design toolkit
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Contrasting microbial communities drive iron cycling across global biomes
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BTR: a bioinformatics tool recommendation system
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DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
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Revisiting pangenome openness with k-mers
L. Parmigiani - R. Wittler, J. Stoye, - Peer Community In, 2024

Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue
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Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells
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The Celiac‐Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model
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A Transcriptomic Hourglass In Brown Algae
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Nicheformer: a foundation model for single-cell and spatial omics
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A Minimal Metadata Schema and Its Tool to Improve the Searchableness of Research Data in Bioinformatics
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Deep learning–assisted biodiversity assessment in deep-sea benthic megafauna communities: a case study in the context of polymetallic nodule mining
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Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice
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In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae
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Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
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StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
V. Bonthala - B. Stich, - Springer Science and Business Media LLC, 2024

Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients
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Deep Regression for Biological Age Estimation in Multiple Organs: Investigations on 40,000 Subjects of the UK Biobank
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Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets
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Complete genome sequence of Pseudomonas aeruginosa phage Knedl
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Complete genome sequence of Escherichia coli MP1
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Comparative Transcriptomics of Fat Bodies between Symbiotic and Quasi-Aposymbiotic Adult Females of Blattella germanica with Emphasis on the Metabolic Integration with Its Endosymbiont Blattabacterium and Its Immune System
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Enhancing the image analysis community in Galaxy
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Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships
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The Intellectual Disability Risk GeneKdm5bRegulates Long-Term Memory Consolidation in the Hippocampus
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RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats
M. Choudalakis - P. Bashtrykov, A. Jeltsch, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Genomic epidemiology of the primary methicillin-resistant Staphylococcus aureus clones causing invasive infections in Paraguayan children
R. Guillén - C. Salinas, A. Mendoza-Álvarez, L. Rubio Rodríguez, et al. - American Society for Microbiology, 2024 usegalaxy.eu

GENTRAIN – genomisch-gestützte Infektionskettenanalyse zur Steigerung des digitalen Reifegrads im ÖGD
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Dataset from RNAseq analysis of differential gene expression among developmental stages of two non-marine ostracodes
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ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3
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Molecular characteristics of Cryptosporidium spp. in human cases in five Finnish hospital districts during 2021: first findings of Cryptosporidium mortiferum (Cryptosporidium chipmunk genotype I) in Finland
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The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis
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Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation
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EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
J. Schmitz - N. Aggarwal, L. Laufer, J. Walter, et al. - Oxford University Press (OUP), 2024

Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria
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Menarche, pubertal timing and the brain: female-specific patterns of brain maturation beyond age-related development
N. Gottschewsky - D. Kraft, T. Kaufmann, - Springer Science and Business Media LLC, 2024

First detection of a cefiderocol-resistant and extensively drug-resistant Acinetobacter baumannii clinical isolate in Bulgaria
T. Strateva - S. Peykov, - Akademiai Kiado Zrt., 2024 usegalaxy.eu

The mitochondrial genome sequence of Syagrus coronata (Mart.) Becc. (Arecaceae) is characterized by gene insertion within intergenic spaces
S. de Melo - A. Marques, C. Almeida, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Quantum chemistry based prediction of electron ionization mass spectra for environmental chemicals
H. Hecht - W. Rojas, Z. Ahmad, A. Křenek, et al. - American Chemical Society (ACS), 2024 usegalaxy.eu

Leverage the Explainability of Transformer Models to Improve the DNA 5-Methylcytosine Identification (Student Abstract)
W. Zeng - D. Huson, - Association for the Advancement of Artificial Intelligence (AAAI), 2024

DNA sequence data, multispecies coalescent and morphometrics shed new light on the systematics of Iberian islamiinae springsnails (Caenogastropoda: Hydrobiidae)
D. Delicado - J. Miller, F. García-Guerrero, B. Arconada, et al. - Oxford University Press (OUP), 2024

SpatialData: an open and universal data framework for spatial omics
L. Marconato - G. Palla, K. Yamauchi, I. Virshup, et al. - Springer Science and Business Media LLC, 2024

An RRM domain protein SOE suppresses transgene silencing in rice
R. Zhao - W. Wu, Y. Huang, X. Li, et al. - Wiley, 2024 usegalaxy.eu

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress
S. Hosseinzadeh - K. Hasanpur, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Private and well drinking water are reservoirs for antimicrobial resistant bacteria
M. Alawi - C. Smyth, D. Drissner, A. Zimmerer, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes
G. Zhang - T. Xu, Y. Chen, W. Xu, et al. - MDPI AG, 2024 usegalaxy.eu

Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
Ö. Kahraman-Ilıkkan - - Springer Science and Business Media LLC, 2024 usegalaxy.eu

The altered TBI fecal microbiome is stable and functionally distinct
R. Pyles - A. Miller, R. Urban, M. Sheffield-Moore, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Draft genome sequences of two Micromonospora strains isolated from the root nodules of Alnus glutinosa
R. Thompson - E. Fox, M. Montero-Calasanz, - American Society for Microbiology, 2024 usegalaxy.eu

CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications
S. Alessandri - M. Ratto, S. Rabellino, G. Piacenti, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Characterization of the major autolysin (AtlC) of Staphylococcus carnosus
M. Merz - C. Schiffer, A. Klingl, M. Ehrmann, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression
L. Deng - L. Pollmeier, R. Bednarz, C. Cao, et al. - American Association for the Advancement of Science (AAAS), 2024 usegalaxy.eu

Human Metagenome Analysis with COVID-19 Infectious Disease
K. Jain - R. Yadav, - Manuscript Technomedia LLP, 2024 usegalaxy.eu

Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany
C. Wurzbacher - T. Haufschild, J. Hammer, M. van Teeseling, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

CD38–RyR2 axis–mediated signaling impedes CD8 + T cell response to anti-PD1 therapy in cancer
A. Kar - P. Ghosh, A. Gautam, S. Chowdhury, et al. - Proceedings of the National Academy of Sciences, 2024

The contribution of BvgR, RisA, and RisS to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation in Bordetella bronchiseptica
T. Nicholson - U. Waack, D. Fleming, Q. Chen, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Decoding chromatin states by proteomic profiling of nucleosome readers
S. Lukauskas - A. Tvardovskiy, N. Nguyen, M. Stadler, et al. - Springer Science and Business Media LLC, 2024

Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans
F. Candeliere - E. Musmeci, L. Sola, A. Amaretti, et al. - Frontiers Media SA, 2024 usegalaxy.eu

A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages
T. Ipoutcha - R. Racharaks, S. Huttelmaier, C. Wilson, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Identification of genetic determinants of bedaquiline resistance in Mycobacterium tuberculosis in Ural region, Russia
T. Umpeleva - E. Chetverikova, D. Belyaev, N. Eremeeva, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Targeted RNAseq Revealed the Gene Expression Signature of Ferroptosis-Related Processes Associated with Disease Severity in Patients with Multiple Sclerosis
L. Stojkovic - I. Jovanovic, E. Dincic, A. Djordjevic, et al. - MDPI AG, 2024 usegalaxy.eu

Misidentification of neural cell identity in liver-derived organoid systems
I. Schene - A. Ardisasmita, S. Fuchs, - Elsevier BV, 2024 usegalaxy.eu

The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins
H. Bastide - H. Legout, N. Dogbo, D. Ogereau, et al. - Elsevier BV, 2024 usegalaxy.eu

PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency
R. Crespo - E. Ne, J. Reinders, J. Meier, et al. - Elsevier BV, 2024 usegalaxy.eu

Nonpreferential but Detrimental Accumulation of Macrophages With Clonal Hematopoiesis-Driver Mutations in Cardiovascular Tissues—Brief Report
T. Dederichs - A. Yerdenova, H. Horstmann, T. Vico, et al. - Ovid Technologies (Wolters Kluwer Health), 2024 usegalaxy.eu

Characterisation of prophages in Clostridium clostridioforme : an understudied component of the intestinal microbiome
S. Humphrey - A. Marouli, K. Thümmler, M. Mullin, et al. - bioRxiv - openRxiv, 2024 usegalaxy.eu

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances
A. Rain-Franco - H. Peter, G. Pavan de Moraes, S. Beier, et al. - American Society for Microbiology, 2024

Identification of the odorant binding proteins of Western Flower Thrips ( Frankliniella occidentalis ), characterization and binding analysis of FoccOBP3 with molecular modelling, molecular dynamics simulations and a confirmatory field trial
Z. Zafar - M. Wood, S. Fatima, M. Bhatti, et al. - Informa UK Limited, 2024 usegalaxy.eu

Identification and functional characterisation of a locus for target site integration in Fusarium graminearum
M. Darino - M. Urban, N. Kaur, A. Machado Wood, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits
D. Beerling - D. Epihov, I. Kantola, M. Masters, et al. - Proceedings of the National Academy of Sciences, 2024 usegalaxy.eu

Changes in the Expression of Proteins Associated with Neurodegeneration in the Brains of Mice after Infection with Influenza A Virus with Wild Type and Truncated NS1
K. Donátová - M. Mladá, K. Lopušná, F. Baran, et al. - MDPI AG, 2024 usegalaxy.eu

Whole-genome resequencing identifies exonic single-nucleotide variations in terpenoid biosynthesis genes of the medicinal and aromatic plant common sage (Salvia officinalis L.)
F. Ceylan - A. Uncu, A. Soyturk Patat, A. Uncu, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda
G. Zhang - M. Gao, Y. Chen, Y. Wang, et al. - MDPI AG, 2024 usegalaxy.eu

Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications
P. Singh - P. Gopi, M. Rani, S. Singh, et al. - Wiley, 2024 usegalaxy.eu

Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes
S. Tetzlaff - A. Hillebrand, N. Drakoulis, Z. Gluhic, et al. - eLife Sciences Publications, Ltd, 2024 usegalaxy.eu

Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation
J. Horz - K. Wolff, R. Friedhoff, B. Pucker, et al. - bioRxiv - openRxiv, 2024

Dynamics of cardiomyocyte gene expression and reversibility of catecholamine-induced heart injury
C. Bode - S. Preissl, L. Hein, A. Lother, et al. - Research Square - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
N. Rahman - C. O'Cathail, A. Zyoud, A. Sokolov, et al. - Microbiology Society, 2024 usegalaxy.eu

Draft genome sequence of Streptomyces poriferorum RTGN2, a bacterial endophyte isolated from Alnus glutinosa root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - American Society for Microbiology, 2024 usegalaxy.eu

Draft genome sequences of five Mycobacterium strains, isolated from Alnus glutinosa root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - American Society for Microbiology, 2024 usegalaxy.eu

Effect of Anti‐S100A4 Monoclonal Antibody Treatment on Experimental Skin Fibrosis and Systemic Sclerosis–Specific Transcriptional Signatures in Human Skin
T. Trinh‐Minh - A. Györfi, M. Tomcik, C. Tran‐Manh, et al. - Wiley, 2024 usegalaxy.eu

Neoadjuvant chemo‐ or chemo‐radiation‐therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass
M. Stillger - K. Kurowski, P. Bronsert, E. Brombacher, et al. - Wiley, 2024 usegalaxy.eu

Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes
J. Wight - A. Byrne, K. Tahlan, A. Lang, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Molecular Phylogenetics and Light Microscopy Reveal “True” and “False” Calacarines and Novel Genital Structures in Gall Mites (Acariformes, Eriophyoidea)
P. Chetverikov - C. Craemer, V. Gankevich, N. Le, et al. - MDPI AG, 2024 usegalaxy.eu

Genome‐wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses
K. Mostafa - B. Yerlikaya, M. Abdulla, A. Aydin, et al. - Wiley, 2024 usegalaxy.eu

Restraining Wnt activation and intestinal tumorigenesis by a Rab35 dependent GTPase relay
S. Redhai - T. Wang, K. Boonekamp, S. Reuter, et al. - bioRxiv - openRxiv, 2024

Whole-genome long-read sequencing to unveil Enterococcus antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of Enterococcus lactis
M. Ocejo - M. Mugica, B. Oporto, J. Lavín, et al. - American Society for Microbiology, 2024 usegalaxy.eu

Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos
V. Pilliol - M. Morsli, L. Terlier, Y. Hassani, et al. - American Society for Microbiology, 2024 usegalaxy.eu

The Genome of Arsenophonus sp. and Its Potential Contribution in the Corn Planthopper, Peregrinus maidis
Y. Wang - A. Mikaelyan, B. Coates, M. Lorenzen, et al. - MDPI AG, 2024 usegalaxy.eu

The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient
Y. de Souza - M. Schloter, W. Weisser, Y. Huang, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

From Complexity to Precision—Charting Decision-Making Through Normative Modeling
P. Kumar - P. Dayan, T. Wolfers, - American Medical Association (AMA), 2024

Predicting the Identities of su(met-2) and met-3 in Neurospora crassa by Genome Resequencing
K. McCluskey - D. Brown, E. Bredeweg, S. Baker, et al. - New Prairie Press, 2024 usegalaxy.eu

A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides
L. Ostenfeld - A. Sørensen, H. Neve, A. Vitt, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Cocoa Apoplastome Contains Defense Proteins Against Pathogens
I. de Oliveira - I. Moura, J. Santana, K. Gramacho, et al. - Scientific Societies, 2024 usegalaxy.eu

Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing
A. Nugroho - I. Siregar, D. Matra, U. Siregar, et al. - Elsevier BV, 2024 usegalaxy.eu

Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation
P. Volkova - A. Prazyan, M. Podlutskii, V. Saburov, et al. - Elsevier BV, 2024 usegalaxy.eu

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
M. Shankar - M. Rani, P. Gopi, A. P, et al. - Elsevier BV, 2024 usegalaxy.eu

Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification
O. Delandre - O. Lamer, J. Loreau, N. Papa Mze, et al. - MDPI AG, 2024 usegalaxy.eu

Integrated Analysis of Transcriptome and Epigenome Reveals ENSR00000272060 as a Potential Biomarker in Gastric Cancer
B. Bahrami - M. Wolfien, P. Nikpour, - Informa UK Limited, 2024 usegalaxy.eu

Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing Escherichia coli Isolates Collected over a 16-Year Period in Bolzano (Northern Italy)
I. Bianconi - M. Spath, R. Aschbacher, R. Pedron, et al. - SAGE Publications, 2024 usegalaxy.eu

TcSERPIN, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens
M. Ferreira - K. Farias, M. Zugaib, A. Alves, et al. - Frontiers Media SA, 2024 usegalaxy.eu

Predictive uncertainty in deep learning–based MR image reconstruction using deep ensembles: Evaluation on the fastMRI data set
T. Küstner - K. Hammernik, D. Rueckert, T. Hepp, et al. - Wiley, 2024

Rat1 promotes premature transcription termination at R-loops
J. Mérida-Cerro - P. Maraver-Cárdenas, A. Rondón, A. Aguilera, et al. - Oxford University Press (OUP), 2024 usegalaxy.eu

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
D. Larivière - L. Abueg, N. Brajuka, C. Gallardo-Alba, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

A 14-Day Double-Blind, Randomized, Controlled Crossover Intervention Study with Anti-Bacterial Benzyl Isothiocyanate from Nasturtium (Tropaeolum majus) on Human Gut Microbiome and Host Defense
S. Pfäffle - C. Herz, E. Brombacher, M. Proietti, et al. - MDPI AG, 2024 usegalaxy.eu

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models
O. Ishola - S. Kublik, A. Durai Raj, C. Ohnmacht, et al. - MDPI AG, 2024 usegalaxy.eu

Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga
V. Moris - L. Bruneau, J. Berthe, A. Heuskin, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Challenges and perspectives for naming lipids in the context of lipidomics
M. Witting - A. Malik, A. Leach, A. Bridge, et al. - Springer Science and Business Media LLC, 2024

Growth, Enzymatic, and Transcriptomic Analysis of xyr1 Deletion Reveals a Major Regulator of Plant Biomass-Degrading Enzymes in Trichoderma harzianum
L. Wang - Y. Zhao, S. Chen, X. Wen, et al. - MDPI AG, 2024 usegalaxy.eu

Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity
T. Oliveira - J. Freitas, V. de Medeiros, T. Xavier, et al. - Life Science Alliance, LLC, 2024 usegalaxy.eu

Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates
T. Vieira - C. Dos Santos, A. de Jesus Bertani, G. Costa, et al. - MDPI AG, 2024 usegalaxy.eu

SimLivA–Modeling ischemia‐reperfusion injury in the liver: A first step towards a clinical decision support tool
H. Tautenhahn - T. Ricken, U. Dahmen, L. Mandl, et al. - Wiley, 2024

Genetic variability of New Caledonian Boeckella De Guerne & Richard, 1889 (Copepoda: Calanoida), with the description of a new species
C. Royaux - N. Charpin, N. Rabet, - Oxford University Press (OUP), 2024 usegalaxy.eu

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
L. Dony - A. Krontira, L. Kaspar, R. Ahmad, et al. - bioRxiv - openRxiv, 2024

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis
V. Pilliol - M. Beye, L. Terlier, J. Balmelle, et al. - MDPI AG, 2024 usegalaxy.eu

Transcriptomic characterization of the human segmental endotoxin challenge model
C. Gress - T. Litzenburger, R. Schmid, K. Xiao, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

In Vivo Silencing of Regulatory Elements Using a Single AAV-CRISPRi Vector
P. Laurette - C. Cao, D. Ramanujam, M. Schwaderer, et al. - Ovid Technologies (Wolters Kluwer Health), 2024 usegalaxy.eu

Mitochondrial genome of Hancornia speciosa gomes: intergenic regions containing retrotransposons and predicted genes
F. de Souza - A. Marques, C. Almeida, - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Draft genome sequence of Amycolatopsis camponoti RTGN1, a bacterial endophyte isolated from Alnus glutinosa root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - American Society for Microbiology, 2024 usegalaxy.eu

Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice
B. Herwibawa - C. Lekklar, S. Chadchawan, T. Buaboocha, et al. - MDPI AG, 2024 usegalaxy.eu

Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools
S. Joshi - R. Srivastava, - Frontiers Media SA, 2024 usegalaxy.eu

Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis
T. Lapp - P. Kammrath Betancor, G. Schlunck, C. Auw-Hädrich, et al. - Frontiers Media SA, 2024 usegalaxy.eu

EHMT2 LOSS-OF-FUNCTION ALTERATIONS CAUSE A KLEEFSTRA-LIKE SYNDROME
B. Martinez-Delgado - E. Lopez-Martin, J. Kerkhof, B. Baladron, et al. - medRxiv - openRxiv, 2024 usegalaxy.eu

A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies
L. Schäfer - J. Jehle, R. Kleespies, J. Wennmann, et al. - Microbiology Society, 2024 usegalaxy.eu

Oncostatin M Reduces Pathological Neovascularization in the Retina Through Müller Cell Activation
J. Rapp - A. Hospach, P. Liang, M. Schwämmle, et al. - Association for Research in Vision and Ophthalmology (ARVO), 2024 usegalaxy.eu

Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy
A. Garcia-Fernandez - A. Janowicz, F. Marotta, M. Napoleoni, et al. - Frontiers Media SA, 2024 usegalaxy.eu

hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS)
H. Salapa - P. Thibault, C. Libner, Y. Ding, et al. - Springer Science and Business Media LLC, 2024 usegalaxy.eu

Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses
P. Kruse - G. Brandes, H. Hemeling, Z. Huang, et al. - MDPI AG, 2024 usegalaxy.eu

Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk
P. Andriyanov - D. Kashina, A. Menshikova, - Frontiers Media SA, 2024 usegalaxy.eu

More May Not be Better: Enhanced Spacecraft Shielding May Exacerbate Cognitive Decrements by Increasing Pion Exposures during Deep Space Exploration
M. Vozenin - Y. Alaghband, O. Drayson, F. Piaget, et al. - Radiation Research Society, 2024 usegalaxy.eu

American lobster (Homarus americanus) hepatopancreas transcriptome reveals the significance of chitin-related genes during impoundment shell disease
N. Argenta - M. Rampaul, K. Clark, - Canadian Science Publishing, 2024 usegalaxy.eu

Postnatal persistence of hippocampal Cajal-Retzius cells has a crucial role in the establishment of the hippocampal circuit
I. Glærum - K. Dunville, K. Moan, M. Krause, et al. - The Company of Biologists, 2024 usegalaxy.eu

Two male-killing Wolbachia from Drosophila birauraia that are closely related but distinct in genome structure
H. Arai - M. Watada, D. Kageyama, - The Royal Society, 2024 usegalaxy.eu

Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin
F. Bruno - C. Coronel-Guisado, C. González-Aguilera, - Elsevier BV, 2024 usegalaxy.eu

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells
O. Kalnytska - P. Qvist, S. Kunz, T. Conrad, et al. - Elsevier BV, 2024 usegalaxy.eu

CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
T. Müller - S. Mautner, P. Videm, F. Eggenhofer, et al. - Oxford University Press (OUP), 2024

DISENTANGLING OCCUPANCY FROM SAMPLING BIASES TO INFER THE EXTINCTION DYNAMICS IN PHANEROZOIC MARINE BIVALVES
. T. Hauffe - J. Cantalapiedra, D. Delicado, D. Silvestro, et al. - Geological Society of America, 2024

Fungani, a Blast-Based Program for Analyzing Average Nucleotide Identity (Ani) between Two Fungal Genomes, Enables Easy Fungal Species Delimitation
P. Silar - C. Lalanne, - Elsevier BV, 2024 usegalaxy.eu

Normative modeling for clinical neuroscience
A. Marquand - S. Rutherford, T. Wolfers, - Elsevier, 2024

Development of Similarity Measures From Graph-Structured Bibliographic Metadata: An Application to Identify Scientific Convergence
T. Melnychuk - L. Galke, E. Seidlmayer, S. Bröring, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2024

Towards Trustworthy AI in Cardiology: A Comparative Analysis of Explainable AI Methods for Electrocardiogram Interpretation
N. Gumpfer - B. Dinov, S. Sossalla, M. Guckert, et al. - Springer Nature Switzerland, 2024

Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol
C. Albrecht - P. Bashtrykov, A. Jeltsch, - Springer US, 2024 usegalaxy.eu

Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19
S. Bihani - A. Gupta, S. Mehta, A. Rajczewski, et al. - Springer US, 2024 usegalaxy.eu

The Unique Specialization of Olfaction in the Senegalese Sole (Solea Senegalensis). Smelling in Co2 Acidified Water Triggers Nostril Specific Immune Processes
R. Costa - P. Hubbard, M. Manchado, D. Power, et al. - Elsevier BV, 2024 usegalaxy.eu

Evolutionary Structure Conservation and Covariance Scores
F. Eggenhofer - C. Höner zu Siederdissen, - Springer US, 2024 usegalaxy.eu

Genetic Evidence of Methicillin Resistant Staphylococcus Aureus Transmission between Pets and Their Owners
H. Sarker - J. Hassan, A. Rahman, D. Korber, et al. - Elsevier BV, 2024 usegalaxy.eu

CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
T. Müller - S. Mautner, P. Videm, F. Eggenhofer, et al. - Oxford University Press (OUP), 2024 usegalaxy.eu

Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases
B. Raubenolt - D. Blankenberg, - Oxford University Press (OUP), 2024 usegalaxy.eu

Deepdefense: annotation of immune systems in prokaryotes using deep learning
S. Hauns - O. Alkhnbashi, R. Backofen, - Oxford University Press (OUP), 2024

Bioinformatics and Computational Biology
M. Ali - A. Zahoor, Z. Niaz, M. Jabran, et al. - Springer Nature Singapore, 2024 usegalaxy.eu

Salmonella phylogenomics
C. Jia - H. Zhou, Z. Wang, Y. Liu, et al. - Elsevier, 2024 usegalaxy.eu

In-silico transcriptome analysis of antibiotic-treated Mycobacterium tuberculosis identifies novel antibiotic resistance factors
S. Sundar - - Elsevier BV, 2024 usegalaxy.eu

Description of eight new mitochondrial genomes for the genus Neoarius and phylogenetic considerations for the family Ariidae (Siluriformes)
L. Pimentel - I. da Silva, I. Rodrigues-Oliveira, R. Pasa, et al. - Korea Genome Organization, 2023 usegalaxy.eu

Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistron
M. Cedeño-Sanchez - T. Cheng, C. Lambert, M. Kolarík, et al. - Springer Science and Business Media LLC, 2023

Cross-Species Variability in Lobular Geometry and Cytochrome P450 Hepatic Zonation: Insights into CYP1A2, CYP2E1, CYP2D6 and CYP3A4
M. Albadry - J. Küttner, J. Grzegorzewski, O. Dirsch, et al. - bioRxiv - openRxiv, 2023

Detailing Early Shoot Growth Arrest in Kro-0 x BG-5 Hybrids of Arabidopsis thaliana
K. Sageman-Furnas - G. Duarte, R. Laitinen, - Oxford University Press (OUP), 2023 usegalaxy.eu

Transcriptional Comparison of Human and Murine Retinal Neovascularization
L. Pauleikhoff - S. Boneva, M. Boeck, A. Schlecht, et al. - Association for Research in Vision and Ophthalmology (ARVO), 2023 usegalaxy.eu

A systematic review of the Iberian springsnail subgenus Alzoniella (Navarriella) (Caenogastropoda: Hydrobiidae), with the description of a new potentially relict subfamily
F. García-Guerrero - J. Miller, D. Delicado, M. Novo, et al. - Oxford University Press (OUP), 2023

Genome-wide identification and characterization of the plant defensins (Pdfs) gene family in selected Leguminous crops and their expression profiles in response to biotic and abiotic stresses
Z. Hassan - A. Abbas, I. Shafique, - Journal of Global Innovations in Agricultural and Social Sciences (JGIASS), 2023 usegalaxy.eu

Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress
K. Schumacher - R. Gelhausen, W. Kion-Crosby, L. Barquist, et al. - American Society for Microbiology, 2023

USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder
J. Cheron - L. Beccari, P. Hagué, R. Icick, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae
A. Vieira Da Cruz - J. Jiménez-Castellanos, C. Börnsen, L. Van Maele, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs
P. Klemm - P. Stadler, M. Lechner, - Frontiers Media SA, 2023 usegalaxy.eu

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities
P. Müller - J. de la Cuesta-Zuluaga, M. Kuhn, M. Baghai Arassi, et al. - Springer Science and Business Media LLC, 2023

Rapid evolution of pre-zygotic reproductive barriers in allopatric populations
A. Mahilkar - P. Nagendra, P. Venkataraman, S. Deshmukh, et al. - American Society for Microbiology, 2023 usegalaxy.eu

Construction and analysis of pseudogene-related ceRNA network in breast cancer
H. Mohebifar - A. Sabbaghian, T. Farazmandfar, M. Golalipour, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Resin acids play key roles in shaping microbial communities during degradation of spruce bark
A. Ristinmaa - A. Tafur Rangel, A. Idström, S. Valenzuela, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

The millennial dynamics of malaria in the mediterranean basin: documenting Plasmodium spp. on the medieval island of Corsica
M. Boualam - A. Corbara, G. Aboudharam, D. Istria, et al. - Frontiers Media SA, 2023 usegalaxy.eu

A reappraisal of transcriptional regulation by NR5A1 and beta-catenin in adrenocortical carcinoma
E. Lalli - - Frontiers Media SA, 2023 usegalaxy.eu

Environmental regulation of male fertility is mediated through Arabidopsis transcription factors bHLH89, 91, and 10
J. Robson - A. Tidy, S. Thomas, Z. Wilson, et al. - Oxford University Press (OUP), 2023 usegalaxy.eu

Oncogene-induced MALT1 protease activity drives posttranscriptional gene expression in malignant lymphomas
N. Wimberger - F. Ober, G. Avar, M. Grau, et al. - American Society of Hematology, 2023

Association of Reproductive Phenology with Air Temperature in Almond (Prunus dulcis [Mill.] D.A. Webb) Cultivars Under Northwestern Himalayan Conditions
K. Kumawat - S. Raina, D. Kumar, M. Verma, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families
S. Mathura - F. Sutton, V. Bowrin, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Reusability Challenges of Scientific Workflows: A Case Study for Galaxy
K. Alam - B. Roy, A. Serebrenik, - IEEE, 2023 usegalaxy.eu

A global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
V. Bonthala - B. Stich, - Research Square - Research Square Platform LLC, 2023

Tigecycline causes loss of cell viability mediated by mitochondrial OXPHOS and RAC1 in hepatocellular carcinoma cells
D. Koch - H. Yu, I. Beirith, M. Schirren, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Glycation Interferes with the Expression of Sialyltransferases and Leads to Increased Polysialylation in Glioblastoma Cells
P. Schildhauer - P. Selke, M. Staege, A. Harder, et al. - MDPI AG, 2023 usegalaxy.eu

Investigating the patterns of simple sequence repeats (SSRs) inferred from the whole genome of a critically endangered species Cassine koordersii kosterm
I. Husaini - D. Rinandio, I. Martiansyah, M. Magandhi, et al. - IOP Publishing, 2023 usegalaxy.eu

Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification
A. Lamas - A. Garrido-Maestu, A. Prieto, A. Cepeda, et al. - Frontiers Media SA, 2023 usegalaxy.eu

Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis
A. Bafna - P. Lau, G. Banks, P. Nolan, et al. - Elsevier BV, 2023 usegalaxy.eu

Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring blaCMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal
P. Braga - C. dos Santos, A. Bertani, T. Vieira, et al. - Elsevier BV, 2023 usegalaxy.eu

PIM kinases regulate early human Th17 cell differentiation
T. Buchacher - A. Shetty, S. Koskela, J. Smolander, et al. - Elsevier BV, 2023 usegalaxy.eu

Acemannan ameliorates STZ-activated diabetes by attenuating high glucose via inhibiting inflammatory cytokines and apoptosis pathway
A. Omer - H. Altayb, F. Al-Abbasi, G. Gupta, et al. - Elsevier BV, 2023 usegalaxy.eu

Low prevalence of germline TP53 and PALB2 mutations in unselected cohort of breast cancer patients from Brunei Darussalam
S. Matusin - Z. Lu, M. Haji Abdul Hamid, - F1000 Research Ltd, 2023 usegalaxy.eu

ELIXIR’s List of indicators, and other evidence, for monitoring performance and impact in a distributed data research infrastructure for the life sciences
C. Martin - D. Sousoni, E. Balsyte, - F1000 Research Ltd, 2023 usegalaxy.eu

Mouse models of pediatric high-grade gliomas with MYCN amplification reveal intratumoral heterogeneity and lineage signatures
M. Schoof - S. Godbole, T. Albert, M. Dottermusch, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy
U. Rocha - J. Coelho Kasmanas, R. Kallies, J. Saraiva, et al. - Wiley, 2023

Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach
B. Mallol - J. Grzegorzewski, H. Tautenhahn, M. König, et al. - bioRxiv - openRxiv, 2023

A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response
B. Ben-Oz - F. Machour, M. Nicola, A. Argoetti, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants
D. Wulf - A. Bräutigam, - bioRxiv - openRxiv, 2023

Dual targeting of MAPK and PI3K pathways unlocks redifferentiation of Braf-mutated thyroid cancer organoids
H. Lasolle - A. Schiavo, A. Tourneur, P. Gillotay, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy
D. Jhinjharia - A. Kaushik, S. Sahi, - Informa UK Limited, 2023 usegalaxy.eu

Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020–2021
A. Gladkikh - T. Cao, E. Klyuchnikova, M. Dao, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Phage DNA Extraction, Genome Assembly, and Genome Closure
J. Boeckman - M. Liu, J. Ramsey, J. Gill, et al. - Springer US, 2023 usegalaxy.eu

Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana
P. Goossens - J. Spooren, K. Baremans, A. Andel, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Exploring the influences of geographical variation on sequence signatures in the human gut microbiome
G. Kumar - P. Bhadury, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

A rabies-related lyssavirus from a Nycticeinops schlieffeni bat with neurological signs, South Africa
N. Viljoen - A. Ismail, J. Weyer, W. Markotter, et al. - American Society for Microbiology, 2023 usegalaxy.eu

Exploring the potential of fluoro‐flavonoid derivatives as anti‐lung cancer agents: DFT, molecular docking, and molecular dynamics techniques
N. Esha - S. Quayum, M. Saif, M. Almatarneh, et al. - Wiley, 2023 usegalaxy.eu

Fast proliferating and slowly migrating non‐small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment
G. Pelos - M. Riester, J. Pal, K. Myacheva, et al. - Wiley, 2023 usegalaxy.eu

Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins
S. Palecanda - E. Madrid, M. Porter, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases
F. Ratajczak - M. Joblin, M. Hildebrandt, M. Ringsquandl, et al. - Springer Science and Business Media LLC, 2023

Genome-Level Investigation of WRKY Transcription Factors and Their Potential Roles in Fruit Peel Ripening and Coloration in the Common Fig (Ficus carica L.)
N. Kmeli - I. Bettaieb, J. Hamdi, R. Mlouka, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Non-antibiotic drugs break colonization resistance against pathogenic Gammaproteobacteria
A. Grießhammer - J. de la Cuesta-Zuluaga, T. Zahir, P. Müller, et al. - bioRxiv - openRxiv, 2023

Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species
N. Ahmed - R. Khattab, Y. Ragab, M. Hassan, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR
N. Choudhary - B. Pucker, - bioRxiv - openRxiv, 2023

Characterization and expression analysis of SnRK2, PYL, and ABF/ AREB/ ABI5 gene families in sweet potato
S. Mathura - F. Sutton, V. Bowrin, - Public Library of Science (PLoS), 2023 usegalaxy.eu

MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice
C. Göbel - S. Godbole, M. Schoof, D. Holdhof, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

RNA interaction format: a general data format for RNA interactions
R. Schäfer - D. Rabsch, G. Scholz, P. Stadler, et al. - Oxford University Press (OUP), 2023

Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease
B. Mairhörmann - A. Castelblanco, F. Häfner, V. Koliogiannis, et al. - Radiological Society of North America (RSNA), 2023

SIGNed explanations: Unveiling relevant features by reducing bias
N. Gumpfer - J. Prim, T. Keller, B. Seeger, et al. - Elsevier BV, 2023

Genotypic Evolution of Klebsiella pneumoniae Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy
G. Arcari - F. Cecilia, A. Oliva, R. Polani, et al. - Centers for Disease Control and Prevention (CDC), 2023 usegalaxy.eu

SWORTS: A Scientific Workflow Retrieval Approach by Learning Textual and Structural Semantics
Y. Gu - J. Cao, S. Qian, W. Guan, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2023 usegalaxy.eu

The impact of salt stress on the physiology and the transcriptome of the model streptophyte green alga Chara braunii
D. Heß - C. Heise, H. Schubert, W. Hess, et al. - Wiley, 2023 usegalaxy.eu

Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction
M. Javed - B. Reddy, N. Sheoran, P. Ganesan, et al. - Elsevier BV, 2023 usegalaxy.eu

Toxic effects and molecular mechanisms of estuarian crustaceans (Scylla paramamosain) exposed to five commonly used benzophenones
Y. Zhou - W. Dong, M. Shu, - Elsevier BV, 2023 usegalaxy.eu

Multiple transcription factors mediate acclimation of Chlamydomonas to light stress
D. Wulf - F. Krüger, L. Klages, P. Viehöver, et al. - bioRxiv - openRxiv, 2023

Genetic background of neomycin resistance in clinical Escherichia coli isolated from Danish pig farms
P. Subramani - G. Menichincheri, M. Pirolo, G. Arcari, et al. - American Society for Microbiology, 2023 usegalaxy.eu

Individual-level deviations from normative brain morphology in violence, psychosis, and psychopathy
U. Haukvik - T. Wolfers, N. Tesli, C. Bell, et al. - medRxiv - openRxiv, 2023

A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications
P. Gautam - P. Bisht, A. Gautam, G. Gupta, et al. - Informa UK Limited, 2023

Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism
M. Cosenza-Contreras - A. Schäfer, J. Sing, L. Cook, et al. - Oxford University Press (OUP), 2023 usegalaxy.eu

Domain adapted brain network fusion captures variance related to pubertal brain development and mental health
D. Kraft - D. Alnæs, T. Kaufmann, - Springer Science and Business Media LLC, 2023

Accurate prediction of quantitative traits with failed SNP calls in canola and maize
S. Weber - H. Chawla, L. Ehrig, L. Hickey, et al. - Frontiers Media SA, 2023

Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR
R. Ioos - A. Puertolas, C. Renault, A. Ndiaye, et al. - PeerJ, 2023 usegalaxy.eu

Accurate prediction of quantitative traits with failed SNP calls in canola and maize
S. Weber - H. Chawla, L. Ehrig, L. Hickey, et al. - Frontiers Media SA, 2023

Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma
D. Biswas - A. Halder, A. Barpanda, S. Ghosh, et al. - MDPI AG, 2023 usegalaxy.eu

Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins
G. Farmiloe - E. van Bree, S. Robben, L. Janssen, et al. - Oxford University Press (OUP), 2023 usegalaxy.eu

Spitting in the wind?—The challenges of RNA sequencing for biomarker discovery from saliva
A. Gosch - R. Banemann, G. Dørum, C. Haas, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast
G. Guesdon - G. Gourgues, F. Rideau, T. Ipoutcha, et al. - American Chemical Society (ACS), 2023 usegalaxy.eu

Interaction of Mesonivirus and Negevirus with arboviruses and the RNAi response in Culex tarsalis-derived cells
E. Agboli - J. Schulze, S. Jansen, D. Cadar, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Scaling cross-tissue single-cell annotation models
F. Fischer - D. Fischer, E. Biederstedt, A. Villani, et al. - bioRxiv - openRxiv, 2023

SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
M. Yousif - S. Rachida, S. Taukobong, N. Ndlovu, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Whole-genome sequence and mass spectrometry study of the snow blight fungus Phacidium infestans (Karsten) DSM 5139 growing at freezing temperatures
C. Zerouki - K. Chakraborty, S. Kuittinen, A. Pappinen, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

A Galaxy of informatics resources for MS-based proteomics
S. Mehta - M. Bernt, M. Chambers, M. Fahrner, et al. - Informa UK Limited, 2023 usegalaxy.eu

An integrated transcriptomic cell atlas of human neural organoids
Z. He - L. Dony, J. Fleck, A. Szałata, et al. - bioRxiv - openRxiv, 2023

The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
A. Avila Santos - M. Kabiru Nata’ala, J. Kasmanas, A. Bartholomäus, et al. - Springer Science and Business Media LLC, 2023

LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies
D. Kopczynski - N. Hoffmann, N. Troppmair, C. Coman, et al. - American Chemical Society (ACS), 2023

Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in Tetrahymena
C. Lee - W. Maier, Y. Jiang, K. Nakano, et al. - The Company of Biologists, 2023 usegalaxy.eu

FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress
A. Brunner - Q. Li, S. Fisicaro, A. Kourtesakis, et al. - Elsevier BV, 2023 usegalaxy.eu

Changes in rice rhizosphere and bulk soil bacterial communities in the Doñana wetlands at different growth stages
M. Iniesta-Pallarés - M. Brenes-Álvarez, A. Lasa, M. Fernández-López, et al. - Elsevier BV, 2023 usegalaxy.eu

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics
A. Mc Cartney - G. Formenti, A. Mouton, D. De Panis, et al. - bioRxiv - openRxiv, 2023 usegalaxy.eu

Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics
J. Hassa - T. Tubbesing, I. Maus, R. Heyer, et al. - MDPI AG, 2023

Pangenome graph layout by Path-Guided Stochastic Gradient Descent
S. Heumos - A. Guarracino, J. Schmelzle, J. Li, et al. - bioRxiv - openRxiv, 2023

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification
A. Gautam - D. Bhowmik, S. Basu, W. Zeng, et al. - Oxford University Press (OUP), 2023

Genotypic and phenotypic insights into virulence factors of nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria (2011–2022)
T. Strateva - A. Trifonova, A. Stratev, S. Peykov, et al. - Akademiai Kiado Zrt., 2023 usegalaxy.eu

Complete genome sequence of a human bacteremia isolate of Kalamiella piersonii
M. Howard - J. Maki, S. Connelly, D. Hardy, et al. - American Society for Microbiology, 2023 usegalaxy.eu

Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia
N. Mathlouthi - H. Oumarou Hama, I. Belguith, S. Charfi, et al. - MDPI AG, 2023 usegalaxy.eu

Translating genomic tools to Raman spectroscopy analysis enables high-dimensional tissue characterization on molecular resolution
M. Sigle - A. Rohlfing, M. Kenny, S. Scheuermann, et al. - Springer Science and Business Media LLC, 2023

The de novo transcriptome assembly of Agave angustifolia Haw, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development
E. Valadez-Moctezuma - S. Samah, J. Mascorro-Gallardo, J. Reynoso, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae)
D. Delicado - T. Hauffe, T. Wilke, - Wiley, 2023

Cuscuta campestrisfine-tunes gene expression during haustoriogenesis as an adaptation to different hosts
T. Bawin - A. Didriksen, C. Faehn, S. Olsen, et al. - Oxford University Press (OUP), 2023 usegalaxy.eu

Identification and Pathogenicity of Fusarium Isolated from Soybean in Poland
H. Olszak-Przybyś - G. Korbecka-Glinka, E. Patkowska, - MDPI AG, 2023 usegalaxy.eu

Activator-blocker model of transcriptional regulation by pioneer-like factors
A. Riesle - M. Gao, M. Rosenblatt, J. Hermes, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Parallel loss of sex in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
M. Hoshino - G. Cossard, F. Haas, E. Kane, et al. - bioRxiv - openRxiv, 2023

Natural diversity of lactococci in γ-aminobutyric acid (GABA) production and genetic and phenotypic determinants
V. Laroute - N. Aubry, M. Audonnet, M. Mercier-Bonin, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep’s Milk
I. Apostolakos - T. Skarlatoudi, K. Vatavali, A. Giannouli, et al. - MDPI AG, 2023 usegalaxy.eu

Distribution, inducibility, and characteristics of Latilactobacillus curvatus temperate phages
C. Ambros - M. Ehrmann, - OAE Publishing Inc., 2023 usegalaxy.eu

Shigella induces epigenetic reprogramming of zebrafish neutrophils
M. Gomes - D. Brokatzky, M. Bielecka, F. Wardle, et al. - American Association for the Advancement of Science (AAAS), 2023 usegalaxy.eu

German Human Genome-Phenome Archive in an International Context: Toward a Federated Infrastructure for Managing and Analyzing Genomics and Health Data
L. Gadelha - J. Eufinger, - TIB Open Publishing, 2023

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities
N. Hoffmann - I. Maus, S. Beier, P. Belmann, et al. - TIB Open Publishing, 2023 usegalaxy.eu

Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets
S. Weber - M. Frisch, R. Snowdon, K. Voss-Fels, et al. - Frontiers Media SA, 2023

Genomic analysis and antimicrobial activity of β-lactam/β-lactamase inhibitors and other agents against KPC-producing Klebsiella pneumoniae clinical isolates from Brazilian hospitals
C. Camargo - A. Yamada, A. de Souza, M. Cunha, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland
L. Andrade - M. P Ryan, L. P Burke, P. Hynds, et al. - Elsevier BV, 2023 usegalaxy.eu

Whole genome sequencing of Bacillus anthracis isolated from animal in the 1960s, Brazil, belonging to the South America subclade
T. de Andrade - C. Camargo, K. Campos, A. Reis, et al. - Elsevier BV, 2023 usegalaxy.eu

DNA-directed termination of RNA polymerase II transcription
Z. Han - G. Moore, R. Mitter, D. Lopez Martinez, et al. - Elsevier BV, 2023 usegalaxy.eu

Eomes restricts Brachyury functions at the onset of mouse gastrulation
K. Schüle - J. Weckerle, S. Probst, A. Wehmeyer, et al. - Elsevier BV, 2023 usegalaxy.eu

A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing
D. Plaza - J. Zerebinski, I. Broumou, M. Lautenbach, et al. - Elsevier BV, 2023 usegalaxy.eu

Bridging the gap in African biodiversity genomics and bioinformatics
A. Sharaf - C. Ndiribe, T. Omotoriogun, L. Abueg, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
S. Meckoni - B. Nass, B. Pucker, - Springer Science and Business Media LLC, 2023

Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
S. Meckoni - B. Nass, B. Pucker, - Springer Science and Business Media LLC, 2023

CRISPR-Cas9 Library Screening Identifies Novel Molecular Vulnerabilities in KMT2A-Rearranged Acute Lymphoblastic Leukemia
P. Schneider - P. Wander, S. Arentsen-Peters, K. Vrenken, et al. - MDPI AG, 2023 usegalaxy.eu

Integrated signaling and transcriptome analysis reveals Src family kinase individualities and novel pathways controlled by their constitutive activity
N. Koutras - V. Morfos, K. Konnaris, A. Kouvela, et al. - Frontiers Media SA, 2023 usegalaxy.eu

Identification and functional characterisation of a locus for target site integration in Fusarium graminearum
M. Darino - M. Urban, N. Kaur, A. Machado-Wood, et al. - bioRxiv - openRxiv, 2023 usegalaxy.eu

Precision Genome Engineering in Streptococcus suis Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
A. Gussak - M. Ferrando, M. Schrama, P. van Baarlen, et al. - American Chemical Society (ACS), 2023 usegalaxy.eu

The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication
K. Pannhorst - J. Carlson, J. Hölper, F. Grey, et al. - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Volatile Organic Compounds Emitted by the Biocontrol Agent Pythium oligandrum Contribute to Ginger Plant Growth and Disease Resistance
T. Sheikh - D. Zhou, H. Ali, S. Hussain, et al. - American Society for Microbiology, 2023 usegalaxy.eu

Multiplicity of bla KPC Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307
G. Arcari - R. Polani, S. Santilli, V. Capitani, et al. - American Society for Microbiology, 2023 usegalaxy.eu

kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species
M. Podobnik - A. Singh, Z. Fu, C. Dooley, et al. - The Company of Biologists, 2023

Regional, circuit and network heterogeneity of brain abnormalities in psychiatric disorders
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Efficient assembly of plant genomes: A case study with evolutionary implications in Ranunculus (Ranunculaceae)
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DOT1L deletion impairs the development of cortical parvalbumin-expressing interneurons
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A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome
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The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns
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Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches
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Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study
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Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning
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A translational regulator MHZ9 modulates ethylene signaling in rice
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An Empirical Approach to Derive Water T1 from Multiparametric MR Images Using an Automated Pipeline and Comparison With Liver Stiffness
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A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell
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Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa
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A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird
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The design of functional proteins using tensorized energy calculations
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Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet
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Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic Jeongeupia species
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Insight into the nodal cells transcriptome of the streptophyte green alga Chara braunii S276
D. Heß - A. Holzhausen, W. Hess, - Wiley, 2023 usegalaxy.eu

Proteogenomic data and resources for pan-cancer analysis
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Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications
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Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage
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Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide
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Fine-grained topographic organization within somatosensory cortex during resting-state and emotional face-matching task and its association with ASD traits
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Combination of two rare mutations in the SARS-CoV-2 M gene in patients with severe and prolonged COVID-19
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Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae)
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Unified fate mapping in multiview single-cell data
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BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa
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Viruses participate in the organomineralization of travertines
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Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids
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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
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Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients
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Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes
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CRISPR library screening to develop HEK293-derived cell lines with improved lentiviral vector titers
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Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans
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Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil
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Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies
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Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil
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Integrative meta-omics in Galaxy and beyond
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A YAP/TAZ–ARHGAP29–RhoA Signaling Axis Regulates Podocyte Protrusions and Integrin Adhesions
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WHIRLY proteins maintain seed longevity by effects on seed oxygen signalling during imbibition
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The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species
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EODIE — Earth Observation Data Information Extractor
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Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells
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Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
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Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
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Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of Escherichia coli towards interventive antibacterial therapy
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The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses
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Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48
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A biologist’s guide to planning and performing quantitative bioimaging experiments
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Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
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Genome-wide identification and comparative in-silico characterization of β-galactosidase (GH-35) in ascomycetes and its role in germ tube development of Aspergillus fumigatus via RNA-seq analysis
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Genome-wide Identification of the Auxin Transporter Gene Families in Sweet Potato (Ipomoea batatas) and their Expression During Tuberization
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Identification of annotation artifacts concerning the chalcone synthase (CHS)
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Towards the discovery of novel molecular clocks in Prokaryotes
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MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
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The autoPET challenge: Towards fully automated lesion segmentation in oncologic PET/CT imaging
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Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone
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Two-million-year-old microbial communities from the Kap København Formation in North Greenland
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In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut
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Su(Hw) interacts with Combgap to establish long-range chromatin contacts
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Genetic factors explaining anthocyanin pigmentation differences
M. Recinos - B. Pucker, - bioRxiv - openRxiv, 2023

A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin
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Enhanced 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification and a Domain-specific Loss Function
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Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress
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Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması
Ö. ILIKKAN - - Igdir University, 2023 usegalaxy.eu

Proline and Silver Nitrate Promotes Multiple Shoot Induction from Mature Embryo and Shoot Tip Explants of Sorghum
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SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
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A Roadmap for the Human Gut Cell Atlas
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Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
M. Chanama - P. Prombutara, S. Chanama, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

CpG DNA methylation changes during epididymal sperm maturation in bulls
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SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022
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Species Delineation and Comparative Genomics within theCampylobacter ureolyticusComplex
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Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
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β-Cell–Specific E2f1 Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
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Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
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De Novo Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte - Alternaria burnsii NCIM 1409
S. Natarajan - B. Pucker, S. Srivastava, - bioRxiv - openRxiv, 2023

Single‐heartbeat cardiac cine imaging via jointly regularized nonrigid motion‐corrected reconstruction
G. Cruz - K. Hammernik, T. Kuestner, C. Velasco, et al. - Wiley, 2023

APOE expression and secretion are modulated by mitochondrial dysfunction
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MpoxRadar: a worldwide MPXV genomic surveillance dashboard
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Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
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Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge
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Mapping cells through time and space with moscot
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A draft human pangenome reference
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - Springer Science and Business Media LLC, 2023

Genetic architecture of brain age and its causal relations with brain and mental disorders
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Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
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Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
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Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia
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Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition
L. Le Corre - D. Padovani, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum
J. Jesudoss Chelladurai - A. Abraham, T. Quintana, D. Ritchie, et al. - MDPI AG, 2023 usegalaxy.eu

Automatic annotation of the bHLH gene family in plants
C. Thoben - B. Pucker, - bioRxiv - openRxiv, 2023

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
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Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress
S. Hosseinzadeh - K. Hasanpur, - Frontiers Media SA, 2023 usegalaxy.eu

Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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ODNA: identification of organellar DNA by machine learning
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Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
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Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
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Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
A. Boutigny - B. Remenant, B. Legendre, V. Beven, et al. - Elsevier BV, 2023 usegalaxy.eu

Building on Communities to Further Software Sustainability
A. Fouilloux - J. Iaquinta, A. Gupta, H. Struthers, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2023 usegalaxy.eu

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
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Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium
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Increasing complexity of opsin expression across stomatopod development
S. Palecanda - M. Steck, M. Porter, - Wiley, 2023 usegalaxy.eu

How does particulate matter affect plant transcriptome and microbiome?
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DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate
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Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
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Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
J. Miller - D. Delicado, F. García-Guerrero, N. Khalloufi, et al. - Museum National D'Histoire Naturelle, 2023

Galaxy for open-source computational drug discovery solutions
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Mapping lineage-traced cells across time points with moslin
M. Lange - Z. Piran, M. Klein, B. Spanjaard, et al. - bioRxiv - openRxiv, 2023

A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
J. Küttner - J. Grzegorzewski, H. Tautenhahn, M. König, et al. - bioRxiv - openRxiv, 2023

Aircraft surveys for air eDNA: probing biodiversity in the sky
K. Métris - J. Métris, - PeerJ, 2023 usegalaxy.eu

Epidemiological Description and Detection of Antimicrobial Resistance in Various Aquatic Sites in Marseille, France
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Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion
M. Lenz - A. Eichler, P. Kruse, P. Stöhr, et al. - Frontiers Media SA, 2023 usegalaxy.eu

Comparison of transformations for single-cell RNA-seq data
C. Ahlmann-Eltze - W. Huber, - Springer Science and Business Media LLC, 2023

Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient
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Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections
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Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification
A. Gautam - D. Bhowmik, S. Basu, W. Zeng, et al. - bioRxiv - openRxiv, 2023

Building pangenome graphs
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The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops
J. Voelker - R. Mauleon, M. Shepherd, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
L. Schwab - L. Prinsen, G. Nowack, D. Popp, et al. - Frontiers Media SA, 2023

Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
L. Schwab - L. Prinsen, G. Nowack, D. Popp, et al. - Frontiers Media SA, 2023

Proteome alterations in human autopsy tissues in relation to time after death
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The complete reference genome for grapevine (Vitis viniferaL.) genetics and breeding
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mlf-core: a framework for deterministic machine learning
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Mapping Normative Trajectories of Cognitive Function and Its Relation to Psychopathology Symptoms and Genetic Risk in Youth
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Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)
M. Warabieda - N. Kuzmanović, P. Trzciński, J. Puławska, et al. - Elsevier BV, 2023

Premature termination of transcription is shaped by Rho and translated uORFS in Mycobacterium tuberculosis
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Identification of a Czc-like operon of the periodontal pathobiont Porphyromonas gingivalis involved in metal ion efflux
A. Gains - D. Lambert, G. Stafford, - Elsevier BV, 2023 usegalaxy.eu

A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages
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DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
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Genomics of the “tumorigenes” clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.
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Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
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Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
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Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin
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Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
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Experience of Klebsiella pneumoniae genome sequencing using the short read method on the Illumina platform
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Phenotypic and Molecular Characteristics of Carbapenem-Resistant Acinetobacter baumannii Isolates from Bulgarian Intensive Care Unit Patients
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External DNA contamination and efficiency of bleach decontamination for arthropod diet analysis
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An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
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Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes
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Rapid evolution of pre-zygotic reproductive barriers in allopatric populations
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Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model
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Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses
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The giant diploid faba genome unlocks variation in a global protein crop
M. Jayakodi - A. Golicz, J. Kreplak, L. Fechete, et al. - Springer Science and Business Media LLC, 2023

IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides
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Sex-biased gene expression in nutrient-sensing pathways
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Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
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Identification of Radiomic Biomarkers in a Set of Four Skeletal Muscle Groups on Dixon MRI of the NAKO MR study
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Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness
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Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L.
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Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022)
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Evaluating Tuning Strategies for Sequence Generation with Protein Language Models
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Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43
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Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region
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A comprehensive review of bioinformatics tools for chromatin loop calling
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Embryogenesis of a calanoid copepod analyzed by transcriptomics
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Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease
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Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint
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MeganServer: facilitating interactive access to metagenomic data on a server
A. Gautam - W. Zeng, D. Huson, - Oxford University Press (OUP), 2023

Co‐action of COP1, SPA and cryptochrome in light signal transduction and photomorphogenesis of the moss Physcomitrium patens
M. Kreiss - F. Haas, M. Hansen, S. Rensing, et al. - Wiley, 2023

Pilot Study on the Action of Thymus vulgaris Essential Oil in Treating the Most Common Bacterial Contaminants and Salmonella enterica subsp. enterica Serovar Derby in Poultry Litter
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A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin
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Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru
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S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
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Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
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Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples
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Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution
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Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources
D. Becker - D. Popp, F. Bonk, S. Kleinsteuber, et al. - MDPI AG, 2023

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage
M. Welzel - P. Schwarz, H. Löchel, T. Kabdullayeva, et al. - Springer Science and Business Media LLC, 2023

MpoxRadar: a worldwide Mpox genomic surveillance dashboard
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Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera
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Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach
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Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression
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Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients
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Biodegradable microplastic increases CO2 emission and alters microbial biomass and bacterial community composition in different soil types
A. Rauscher - N. Meyer, A. Jakobs, R. Bartnick, et al. - Elsevier BV, 2023

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
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Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents
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Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling
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A Physcomitrella PIN protein acts in spermatogenesis and sporophyte retention
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Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
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The Full Genome Sequences of Pseudomonas sp. Strain MM221 and Pseudoarthrobacter sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
M. Eisenhut - M. Hawrylo, K. Trevlopoulou, H. Fingerhut, et al. - American Society for Microbiology, 2023

Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue
M. Sulyok - J. Luibrand, J. Strohäker, P. Karacsonyi, et al. - Springer Science and Business Media LLC, 2023

Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine
C. Nielsen - J. Barrett, C. Davis, J. Fallon, et al. - American Society for Clinical Investigation, 2023 usegalaxy.eu

Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study
S. Phillip - M. Mushi, A. Decano, J. Seni, et al. - MDPI AG, 2023 usegalaxy.eu

The Full Genome Sequences of Pseudomonas sp. Strain MM221 and Pseudoarthrobacter sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
M. Eisenhut - M. Hawrylo, K. Trevlopoulou, H. Fingerhut, et al. - American Society for Microbiology, 2023

Complete Genome Sequences of Pseudomonas sp. Strains MM223 and MM227 and Rheinheimera sp. Strain MM224, Isolated from a Pond Edge in Bielefeld, Germany
B. Frommer - T. Folchert, A. Witschel, M. Reddeker, et al. - American Society for Microbiology, 2023

Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat
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Apiaceae FNS I originated from F3H through tandem gene duplication
B. Pucker - M. Iorizzo, - Public Library of Science (PLoS), 2023

nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plant root tissue
J. Wanner - L. Cuellar, L. Rausch, K. Berendzen, et al. - bioRxiv - openRxiv, 2023

New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors
S. Cherrad - B. Gillet, J. Dellinger, L. Bellaton, et al. - Public Library of Science (PLoS), 2023 usegalaxy.eu

Book of Abstracts of the 1st Colloquium for Bioinformatics Learning, Education, and Training
A. Fatima - M. Khan, - F1000 Research Ltd, 2023 usegalaxy.eu

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis
S. Hoernstein - B. Özdemir, N. van Gessel, A. Miniera, et al. - Springer Science and Business Media LLC, 2023

Genome-wide characterization of Ficus carica MADS-box transcription factors with a focus on their roles during fruit development
N. Kmeli - J. Hamdi, D. Bouktila, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Endosomal vesicle fusion machinery is involved with the contractile vacuole in Dictyostelium discoideum
P. Manna - L. Barlow, I. Ramirez-Macias, E. Herman, et al. - The Company of Biologists, 2023 usegalaxy.eu

Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia
T. Wallach - M. Raden, L. Hinkelmann, M. Brehm, et al. - Frontiers Media SA, 2023

Azithromycin Susceptibility Testing and Molecular Investigation of Neisseria gonorrhoeae Isolates Collected in Russia, 2020–2021
I. Kandinov - B. Shaskolskiy, D. Kravtsov, A. Vinokurova, et al. - MDPI AG, 2023 usegalaxy.eu

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
E. Deutsch - J. Vizcaíno, A. Jones, P. Binz, et al. - American Chemical Society (ACS), 2023

A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
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Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge
N. Abdulkadir - J. Saraiva, F. Schattenberg, R. Toscan, et al. - MDPI AG, 2023

Galaxy Training: A powerful framework for teaching!
S. Hiltemann - H. Rasche, S. Gladman, H. Hotz, et al. - Public Library of Science (PLoS), 2023 usegalaxy.eu

MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments
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Transcription factors mediating regulation of photosynthesis
W. Halpape - D. Wulf, B. Verwaaijen, A. Stasche, et al. - bioRxiv - openRxiv, 2023

Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma
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MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
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Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome
I. Akol - A. Izzo, F. Gather, S. Strack, et al. - Proceedings of the National Academy of Sciences, 2023 usegalaxy.eu

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
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Physics-Driven Deep Learning for Computational Magnetic Resonance Imaging: Combining physics and machine learning for improved medical imaging
K. Hammernik - T. Kustner, B. Yaman, Z. Huang, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2023

CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway
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RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.
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The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves
B. Seckin Dinler - H. Cetinkaya, Z. Secgin, - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation
M. Zirngibl - G. Araguirang, A. Kitashova, K. Jahnke, et al. - Elsevier BV, 2023 usegalaxy.eu

Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
A. Andersson - A. Behanova, C. Wählby, F. Malmberg, et al. - Springer Nature Switzerland, 2023

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - Oxford University Press (OUP), 2023

Characterization of mercury species and microbial communities in sediments and suspended particulate matter from historically contaminated river systems
J. Wiederhold - L. Gfeller, N. Marquardt, A. Alten, et al. - European Association of Geochemistry, 2023

Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
V. Atanasova - C. de Jesus Cardona, V. Hejret, A. Tiefenbacher, et al. - Elsevier BV, 2023

DIAMOND +  MEGAN Microbiome Analysis
A. Gautam - W. Zeng, D. Huson, - Springer US, 2023

Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions
N. Ruiz-Molina - J. Parsons, E. Decker, R. Reski, et al. - Elsevier BV, 2023

Revealing the small proteome ofHaloferax volcaniiby combining ribosome profiling and small-protein optimized mass spectrometry
L. Hadjeras - J. Bartel, L. Maier, S. Maaß, et al. - Oxford University Press (OUP), 2023

A bibliometric analysis and visualization of spatially resolved transcriptomics
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Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland
L. Andrade - M. Ryan, L. Burke, P. Hynds, et al. - Elsevier BV, 2023 usegalaxy.eu

Analysis of RNA Sequences and Modifications Using NASE
S. Wein - - Springer US, 2023 usegalaxy.eu

SWARM: A Scientific Workflow Fragments Recommendation Approach via Contrastive Learning and Semantic Matching
Y. Gu - J. Cao, J. Tang, S. Qian, et al. - Springer Nature Switzerland, 2023 usegalaxy.eu

Hybrid Genome Assembly of Short and Long Reads in Galaxy
T. Ohta - Y. Shiwa, - Springer US, 2023 usegalaxy.eu

Identification of Taxa and Functional Pathway Information of Mycobacterium tuberculosis Microbiome and High Throughput Simulation Studies with Mycobacteriophage
D. Verma - I. Murthy, P. Bagchi, - Atlantis Press International BV, 2023 usegalaxy.eu

Exploring Scutellaria baicalensis bioactives as EGFR tyrosine kinase inhibitors: Cheminformatics and molecular docking studies
A. Yusuf - A. Adegboyega, A. Yakubu, G. Johnson, et al. - Elsevier BV, 2023 usegalaxy.eu

NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming
Z. Zhang - X. Wang, F. Hamdan, A. Likhobabina, et al. - Elsevier BV, 2023 usegalaxy.eu

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - Oxford University Press (OUP), 2023

The first cavefish in the Dinaric Karst? Cave colonization made possible by phenotypic plasticity in <i>Telestes karsticus</i>
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Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan
H. SAKAMOTO - G. ITO, Y. GOTO-KOSHINO, M. SAKAMOTO, et al. - Japanese Society of Veterinary Science, 2023 usegalaxy.eu

Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
M. Suzuki - Y. Hashimoto, A. Hirabayashi, K. Yahara, et al. - Springer US, 2023 usegalaxy.eu

Morpho-functional Characterisation of Cœlomocytes in the Aquacultivated Sea Cucumber Holothuria Scabra: From Cell Diversity to Transcriptomic Immune Response
N. Wambreuse - G. Caulier, I. Eeckhaut, L. Borrello, et al. - Elsevier BV, 2023 usegalaxy.eu

Avoiding Shortcut-Learning by Mutual Information Minimization in Deep Learning-Based Image Processing
L. Fay - E. Cobos, B. Yang, S. Gatidis, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2023

Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
S. Bordel - D. Martín-González, R. Muñoz, F. Santos-Beneit, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates
D. Lagman - H. Haines, X. Abalo, D. Larhammar, et al. - Public Library of Science (PLoS), 2022 usegalaxy.eu

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
A. Kumar - G. Cuccuru, B. Grüning, R. Backofen, et al. - Oxford University Press (OUP), 2022 usegalaxy.eu

Training Infrastructure as a Service
H. Rasche - C. Hyde, J. Davis, S. Gladman, et al. - Oxford University Press (OUP), 2022 usegalaxy.eu

Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea
D. Lee - J. Kim, A. Park, D. Kim, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Comparative Genome Analysis of 19 Trueperella pyogenes Strains Originating from Different Animal Species Reveal a Genetically Diverse Open Pan-Genome
Z. Thakur - R. Vaid, T. Anand, B. Tripathi, et al. - MDPI AG, 2022 usegalaxy.eu

Guiding the choice of informatics software and tools for lipidomics research applications
Z. Ni - M. Wölk, G. Jukes, K. Mendivelso Espinosa, et al. - Springer Science and Business Media LLC, 2022

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
L. Weber - Y. Jia, B. Stielow, S. Gisselbrecht, et al. - Oxford University Press (OUP), 2022 usegalaxy.eu

Better Together
S. Gatidis - T. Kart, M. Fischer, S. Winzeck, et al. - Ovid Technologies (Wolters Kluwer Health), 2022

Better Together
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Molecular identification of SARS-CoV-2 variants of concern at urban wastewater treatment plants across South Africa
M. Yousif - S. Rachida, S. Taukobong, N. Ndlovu, et al. - medRxiv - openRxiv, 2022 usegalaxy.eu

Whole-Genome Sequences of Human Monkeypox Virus Strains from Two 2022 Global Outbreak Cases in Western New York State
M. Howard - J. Maki, S. Connelly, D. Hardy, et al. - American Society for Microbiology, 2022 usegalaxy.eu

Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
S. Tajuddin - A. Khan, L. Chong, C. Wong, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium
M. Dziuba - A. Paulus, L. Schramm, R. Awal, et al. - Oxford University Press (OUP), 2022 usegalaxy.eu

Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein 1 (LRP1) as crucial cellular receptor
J. Schoellkopf - T. Mueller, L. Hippchen, T. Mueller, et al. - Public Library of Science (PLoS), 2022 usegalaxy.eu

A temperature-tolerant CRISPR base editor mediates highly efficient and precise gene inactivation in vivo
R. Doll - M. Boutros, F. Port, - bioRxiv - openRxiv, 2022

Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
A. Andersson - A. Behanova, C. Avenel, J. Windhager, et al. - bioRxiv - openRxiv, 2022

Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips
D. Feng - Z. Liang, Y. Wang, J. Yao, et al. - Springer Science and Business Media LLC, 2022

MGnify: the microbiome sequence data analysis resource in 2023
L. Richardson - B. Allen, G. Baldi, M. Beracochea, et al. - Oxford University Press (OUP), 2022

STAT3 signaling induced by IL-6 family cytokines modulates angiogenesis
J. Rapp - M. Jung, R. Klar, J. Wolf, et al. - The Company of Biologists, 2022 usegalaxy.eu

Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21–15 from marine sediments in comparison with other Aeromonas spp.
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A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data
A. Atxaerandio-Landa - A. Arrieta-Gisasola, L. Laorden, J. Bikandi, et al. - MDPI AG, 2022 usegalaxy.eu

Rapid detection and online analysis of microbial changes through flow cytometry
J. Kupschus - S. Janssen, A. Hoek, J. Kuska, et al. - Wiley, 2022

Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov
K. Gašić - N. Zlatković, N. Kuzmanović, - Frontiers Media SA, 2022

Transcriptomic Landscape and Functional Characterization of Human Induced Pluripotent Stem Cell-Derived Limbal Epithelial Progenitor Cells
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Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome
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Transcriptional Profiling Provides New Insights into Organ Culture-Induced Changes in Human Donor Corneas
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Renewal of planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction by benthic colonizers
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Discovery and biosynthetic assessment of Streptomyces ortus sp nov. isolated from a deep-sea sponge
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IMA genome‑F17
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MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
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Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
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Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink
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Complete Genome Sequence of Terrisporobacter glycolicus Strain WW3900, Isolated from Influent Wastewater at a Research Center with Multiple-Species Research Animal Facilities
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Revisiting pangenome openness with k-mers
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Comparative Genomic Hybridization and Transcriptome Sequencing Reveal Genes with Gain in Acute Lymphoblastic Leukemia: JUP Expression Emerges as a Survival-Related Gene
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Replication collisions induced by de-repressed S-phase transcription are connected with malignant transformation of adult stem cells
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Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics
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Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti
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Functional and Safety Characterization of Weissella paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics
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Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni
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Further Extension of Lifespan by Unc-43/CaMKII and Egl-8/PLCβ Mutations in Germline-Deficient Caenorhabditis elegans
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Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei
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Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
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Shigella induces epigenetic reprogramming of zebrafish neutrophils
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RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis
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The complete mitochondrial genome of the zebra seabream Diplodus cervinus (Perciformes, Sparidae) from the Mediterranean Sea
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Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
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Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium
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A South American Mouse Morbillivirus Provides Insight into a Clade of Rodent-Borne Morbilliviruses
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Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis
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Two New Rhizobiales Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies
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Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism
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Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan
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Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche
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Multi-histone ChIP-Seq Analysis with DecoDen
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Multi-histone ChIP-Seq Analysis with DecoDen
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Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
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Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower
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Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds
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Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
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Draft Genome Sequences of 25 Mycobacterium marinum Strains Isolated from Animals and Environmental Components in Aquaria and an Aquaculture Farm
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Semi-automated assembly of high-quality diploid human reference genomes
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LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
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Thin‐Plate Superstructures of the Immunogenic 33‐mer Gliadin Peptide
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Cheminformatics Bioprospection of Broad Spectrum Plant Secondary Metabolites Targeting the Spike Proteins of Omicron Variant and Wild-Type SARS-CoV-2
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A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use
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Nutritional composition, heavy metal content and in vitro effect on the human gut microbiota of Talitrus saltator, an underutilized crustacean from the Atlantic coast
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Arnold tongue entrainment reveals dynamical principles of the embryonic segmentation clock
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Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
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The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia
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Epigenetic nature of Arabidopsis thaliana telomeres
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Multivalent binding kinetics resolved by fluorescence proximity sensing
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Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations
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Transcriptome-wide modulation bySargassum vulgareandAcanthophora spiciferaextracts results in a prime-triggered plant signalling cascade in tomato and sweet pepper
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A whole-body FDG-PET/CT Dataset with manually annotated Tumor Lesions
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The mitochondrial RNA granule modulates manganese-dependent cell toxicity
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Self-supervised learning for automated anatomical tracking in medical image data with minimal human labeling effort
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Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France
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Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent
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Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica
M. Tabarelli - M. Malnoy, K. Janik, - MDPI AG, 2022 usegalaxy.eu

Impaired immune response drives age-dependent severity of COVID-19
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Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time
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Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A
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Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids
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On the way to plant data commons – a genotyping use case
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Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
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miR-106b is a novel target to promote muscle regeneration and restore satellite stem cell function in injured Duchenne dystrophic muscle
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Genome‐wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae
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In silico drug repurposing against SARS-CoV-2 using an integrative transcriptomic profiling approach: Hydrocortisone and Benzhydrocodone as potential drug candidates against COVID-19
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Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens
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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
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Investigation of the Defective Growth Pattern and Multidrug Resistance in a Clinical Isolate of Candida glabrata Using Whole-Genome Sequencing and Computational Biology Applications
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Development of a Hybrid-Imaging-Based Prognostic Index for Metastasized-Melanoma Patients in Whole-Body 18F-FDG PET/CT and PET/MRI Data
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Cheminformatics Identification of Phenolics as Modulators of Penicillin-Binding Protein 2a of Staphylococcus aureus: A Structure–Activity-Relationship-Based Study
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DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
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Redistribution of the SWI/SNF Complex Dictates Coordinated Transcriptional Control over Epithelial–Mesenchymal Transition of Normal Breast Cells through TGF-β Signaling
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The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation
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E. faecalis acquires resistance to antimicrobials and insect immunity via common mechanisms
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Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease
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Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures
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The Effects of Hypoxic Preconditioned Murine Mesenchymal Stem Cells on Post-Infarct Arrhythmias in the Mouse Model
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Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
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Fused inverse-normal method for integrated differential expression analysis of RNA-seq data
B. Prasad - X. Li, - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Pre-Synaptic GABAA in NaV1.8+ Primary Afferents Is Required for the Development of Punctate but Not Dynamic Mechanical Allodynia following CFA Inflammation
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Delineating genome-wide alternative splicing landscapes and their functional significance in orchids
A. Hazra - P. Mahadani, - Elsevier BV, 2022

An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
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Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydrobiidae)
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Genetic and genomic diversity in the sorghum gene bank collection of Uganda
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Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges
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TRIM28-dependent SUMOylation protects the adult ovary from activation of the testicular pathway
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Potential of enriched and stabilized anaerobic lignocellulolytic fungi coexisting with bacteria and methanogens for enhanced methane production from rice straw
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Robertsonian Fusion and Centromere Repositioning Contributed to the Formation of Satellite-free Centromeres During the Evolution of Zebras
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Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
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Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
H. Bokharaie - W. Kolch, A. Krstic, - MDPI AG, 2022 usegalaxy.eu

Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint
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Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat
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A Draft Human Pangenome Reference
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A fully phased interspecific grapevine rootstock genome sequence representing V. riparia and V. cinerea and allele-aware annotation of the phylloxera resistance locus Rdv1
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MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
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DBC1 is a key positive regulator of enhancer epigenomic writers KMT2D and p300
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Custos Secrets: a Service for Managing User-Provided Resource Credential Secrets for Science Gateways
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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
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Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
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Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
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KIPEs3: Automatic annotation of biosynthesis pathways
A. Rempel - N. Choudhary, B. Pucker, - bioRxiv - openRxiv, 2022

Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response
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Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
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Tracking of SARS-CoV-2 Alpha variant (B.1.1.7) in Palestine
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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
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Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny
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Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses
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LRF Promotes Indirectly Advantageous Chromatin Conformation via BGLT3-lncRNA Expression and Switch from Fetal to Adult Hemoglobin
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A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
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Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)
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MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
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Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
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An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
L. Fancello - T. Burger, - Springer Science and Business Media LLC, 2022 usegalaxy.eu

A Comprehensive Study of the WRKY Transcription Factor Family in Strawberry
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SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues
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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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Galaxy Training: A Powerful Framework for Teaching!
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Conditional termination of transcription is shaped by Rho and translated uORFS in Mycobacterium tuberculosis
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GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis
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Genomic Analyses of Rose Crown Gall-Associated Bacteria Revealed Two New Agrobacterium Species: Agrobacterium burrii sp. nov. and Agrobacterium shirazense sp. nov.
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Sequence-based pangenomic core detection
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Structural analysis of microbiomes from salt caverns used for underground gas storage
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AB12PHYLO: An Integrated Pipeline for Maximum Likelihood Phylogenetic Inference from ABI Trace Data
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P989: DYNAMIC CHANGES IN THE HISTONE H3 LYSINE 27 TRIMETHYLATION EPIGENETIC LANDSCAPE FOLLOWING RUXOLITINIB ADMINISTRATION
G. Greenfield - M. McMullin, K. Mills, - Wiley, 2022 usegalaxy.eu

Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
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Association of DNA methylation and genetic variations of the APOE gene with the risk of diabetic dyslipidemia
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A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
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Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
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A novel membrane complex is required for docking and regulated exocytosis of lysosome-related organelles in Tetrahymena thermophila
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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
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Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
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Single-Cell Protein and Transcriptional Characterization of Epiretinal Membranes From Patients With Proliferative Vitreoretinopathy
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Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
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Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation
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ODGI: understanding pangenome graphs
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Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
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Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
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Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes
V. Bonthala - B. Stich, - Frontiers Media SA, 2022

Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021
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MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
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The potential of bacterial key species as a tool for monitoring peatland quality
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Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau
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Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum)
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Tissue remodeling by an opportunistic pathogen triggers allergic inflammation
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Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds
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Computational identification and characterization of vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici) CAZymes in tomato xylem sap
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Age-related brain deviations and aggression
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Impaired immune response drives age-dependent severity of COVID-19
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Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water
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A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
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Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
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Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2
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Hidden Talents: Silent Gene Clusters Encoding Magnetic Organelle Biosynthesis in a Non-Magnetotactic Phototrophic Bacterium
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Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework
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PEGR: a flexible management platform for reproducible epigenomic and genomic research
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Integrative Gene Expression and Metabolic Analysis Tool IgemRNA
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
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Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
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Identification and annotation of peptide allergens in Prunus dulcis
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Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
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NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
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Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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Critical Assessment of Metagenome Interpretation: the second round of challenges
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Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration
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Unifying the known and unknown microbial coding sequence space
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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
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Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture
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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function
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A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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Transcriptional and Distributional Profiling of Microglia in Retinal Angiomatous Proliferation
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In-Depth Molecular Profiling Specifies Human Retinal Microglia Identity
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Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation
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Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
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Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
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Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist
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Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
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ECO: An Integrated Gene Expression Omnibus for Mouse Endothelial Cells In Vivo
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β-Glucuronidase Pattern Predicted From Gut Metagenomes Indicates Potentially Diversified Pharmacomicrobiomics
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Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen
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Antibody escape and global spread of SARS-CoV-2 lineage A.27
T. Kaleta - L. Kern, S. Hong, M. Hölzer, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis)
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In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue
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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
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Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
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Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
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Shell features and anatomy of the springsnail genus Radomaniola (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years
D. Delicado - T. Hauffe, - Oxford University Press (OUP), 2022

Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
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Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
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Onset of Late Cretaceous diversification in Europe’s freshwater gastropod fauna links to global climatic and biotic events
T. Neubauer - M. Harzhauser, - Springer Science and Business Media LLC, 2022

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
K. Sielemann - B. Pucker, N. Schmidt, P. Viehöver, et al. - Springer Science and Business Media LLC, 2022

Pluripotency factors determine gene expression repertoire at zygotic genome activation
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Unsupervised encoding selection through ensemble pruning for biomedical classification
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STENCIL: A web templating engine for visualizing and sharing life science datasets
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The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family
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Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage
D. Verma - P. Bagchi, S. IA, - Research Square - Research Square Platform LLC, 2022 usegalaxy.eu

Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
C. Bamford - L. Broadbent, E. Aranday-Cortes, M. McCabe, et al. - MDPI AG, 2022 usegalaxy.eu

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate
D. Katsanos - M. Barkoulas, - American Association for the Advancement of Science (AAAS), 2022 usegalaxy.eu

Drivers of diversification in freshwater gastropods vary over deep time
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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
D. Aggarwal - R. Myers, W. Hamilton, T. Bharucha, et al. - Elsevier BV, 2022 usegalaxy.eu

Characterization of the Cellular Microenvironment and Novel Specific Biomarkers in Pterygia Using RNA Sequencing
J. Wolf - R. Hajdu, S. Boneva, A. Schlecht, et al. - Frontiers Media SA, 2022 usegalaxy.eu

Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
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sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
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Spread of hypervirulent multidrug-resistant ST147 Klebsiella pneumoniae in patients with severe COVID-19: an observational study from Italy, 2020–21
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RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
A. Lucaci - J. Zehr, S. Shank, D. Bouvier, et al. - bioRxiv - openRxiv, 2022 usegalaxy.eu

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
D. Martin - S. Lytras, A. Lucaci, W. Maier, et al. - bioRxiv - openRxiv, 2022 usegalaxy.eu

Ultraviolet vision in larval Neogonodactylus oerstedii
M. McDonald - S. Palecanda, J. Cohen, M. Porter, et al. - The Company of Biologists, 2022 usegalaxy.eu

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning
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TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens
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What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach
L. Colin - D. Abed-Navandi, D. Conde, J. Craggs, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
K. Koeppel - A. Mendes, A. Strydom, L. Rotherham, et al. - MDPI AG, 2022 usegalaxy.eu

Experimental Evolution of Anticipatory Regulation in Escherichia coli
A. Mahilkar - P. Venkataraman, A. Mall, S. Saini, et al. - Frontiers Media SA, 2022 usegalaxy.eu

Saccharomyces boulardii CNCM I‐745 supplementation modifies the fecal resistome during Helicobacter pylori eradication therapy
S. Cifuentes - M. Prado, M. Fornasini, H. Cohen, et al. - Wiley, 2022

Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
G. Arcari - A. Oliva, F. Sacco, F. Di Lella, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
H. Mack - J. Kremer, E. Albertini, E. Mack, et al. - Springer Science and Business Media LLC, 2022 usegalaxy.eu

Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles
S. Ramnarine - J. Jayaraman, A. Ramsubhag, - PeerJ, 2022 usegalaxy.eu

LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus (Nelumbo nucifera) Rhizomes
S. Deng - X. Ma, Y. Chen, H. Feng, et al. - Scientific Societies, 2022 usegalaxy.eu

Expanding the Galaxy’s reference data
N. VijayKrishna - J. Joshi, N. Coraor, J. Hillman-Jackson, et al. - Oxford University Press (OUP), 2022 usegalaxy.eu

In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer
X. Jiang - Y. Zhang, H. Wang, Z. Wang, et al. - American Association for the Advancement of Science (AAAS), 2022 usegalaxy.eu

A new insight into sex-specific non-coding RNAs and networks in response to SARS-CoV-2
N. Askari - M. Hadizadeh, M. Rashidifar, - Elsevier BV, 2022 usegalaxy.eu

Multi-label classification for multi-drug resistance prediction of Escherichia coli
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Elsevier BV, 2022

Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets ofAcinetobacter baumannii
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Canonical Workflows to Make Data FAIR
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A Tetragenococcus halophilus human gut isolate
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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
M. Gaïa - L. Meng, E. Pelletier, P. Forterre, et al. - bioRxiv - openRxiv, 2021

ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data
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Phylogenetic Distribution of csp1 Types in Aspergillus fumigatus and Their Correlates to Azole Antifungal Drug Resistance
O. Bader - - American Society for Microbiology, 2021 usegalaxy.eu

Taxonomic transfer of two species of hydrobiid snails from western Anatolia (Caenogastropoda, Truncatelloidea) to two new genera, based on molecular and morphological evidence
D. Delicado - M. Gürlek, - Schweizerbart, 2021

CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences
A. Fasemore - A. Helbich, M. Walter, T. Dandekar, et al. - American Society for Microbiology, 2021

Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
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Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis
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Whole-genome based strain identification of fowlpox virus directly from cutaneous tissue and propagated virus
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PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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COVID-19++: A Citation-Aware Covid-19 Dataset for the Analysis of Research Dynamics
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Natural Coinfection between Novel Species of Baculoviruses in Spodoptera ornithogalli Larvae
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Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
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Plant Viruses Can Alter Aphid-Triggered Calcium Elevations in Infected Leaves
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Case Series: Convalescent Plasma Therapy for Patients with COVID-19 and Primary Antibody Deficiency
J. Lang-Meli - J. Fuchs, P. Mathé, H. Ho, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Immunosenescence in Choroidal Neovascularization (CNV)—Transcriptional Profiling of Naïve and CNV-Associated Retinal Myeloid Cells during Aging
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Microencapsulation of a Pseudomonas Strain (VUPF506) in Alginate–Whey Protein–Carbon Nanotubes and Next-Generation Sequencing Identification of This Strain
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Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition
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An ecological perspective on microbial genes of unknown function in soil
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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence
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Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
J. Bartoszewicz - F. Nasri, M. Nowicka, B. Renard, et al. - bioRxiv - openRxiv, 2021

Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides
M. Achom - P. Roy, B. Lagunas, E. Picot, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
T. Kustner - J. Pan, H. Qi, G. Cruz, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2021

Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N
A. Al-Jawabreh - S. Ereqat, K. Dumaidi, H. Al-Jawabreh, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
S. Gilbertson - A. Weinmann, - Elsevier BV, 2021 usegalaxy.eu

Current Trends and Future Directions of Large Scale Image and Video Annotation: Observations From Four Years of BIIGLE 2.0
M. Zurowietz - T. Nattkemper, - Frontiers Media SA, 2021

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
A. Gautam - H. Felderhoff, C. Bağci, D. Huson, et al. - bioRxiv - openRxiv, 2021

Expression Atlas update: gene and protein expression in multiple species
P. Moreno - S. Fexova, N. George, J. Manning, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

First complete mitochondrial genome of Antheraea pernyi Guérin-Méneville 1855 (Lepidoptera: Saturniidae) from North Korea
S. Sun - E. Tan, Y. Liu, - Informa UK Limited, 2021 usegalaxy.eu

The diversity among the species Tetragenococcus halophilus including new isolates from a lupine seed fermentation
T. Link - R. Vogel, M. Ehrmann, - Springer Science and Business Media LLC, 2021 usegalaxy.eu

High-quality whole-genome sequence analysis of Lactobacillus paragasseri UBLG-36 reveals oxalate-degrading potential of the strain
Y. Mehra - P. Viswanathan, - Public Library of Science (PLoS), 2021 usegalaxy.eu

Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
P. Vollrath - H. Chawla, D. Alnajar, I. Gabur, et al. - Frontiers Media SA, 2021

New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
D. Barbosa - A. Simeone, A. Humberto, Y. de Maria, et al. - Research Square - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Dual-Transcriptomic, Microscopic, and Biocontrol Analyses of the Interaction Between the Bioeffector Pythium oligandrum and the Pythium Soft-Rot of Ginger Pathogen Pythium myriotylum
P. Daly - S. Chen, T. Xue, J. Li, et al. - Frontiers Media SA, 2021 usegalaxy.eu

An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis
C. O'Neill - R. Skilton, J. Forster, D. Cleary, et al. - F1000 Research Ltd, 2021 usegalaxy.eu

Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
G. da Silva - A. Gautam, I. Silveira Duarte, T. Delforno, et al. - bioRxiv - openRxiv, 2021

The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
I. Phan - C. Rice, J. Craig, R. Noorai, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants
S. Weigang - J. Fuchs, G. Zimmer, D. Schnepf, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Peakhood: individual site context extraction for CLIP-seq peak regions
M. Uhl - D. Rabsch, F. Eggenhofer, R. Backofen, et al. - Oxford University Press (OUP), 2021

Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
R. Rettenmaier - N. Thieme, J. Streubel, L. Di Bello, et al. - Microbiology Society, 2021

Viral suppressor of RNA silencing in vascular plants also interferes with the development of the bryophyte Physcomitrella patens
E. Marttinen - M. Lehtonen, N. van Gessel, R. Reski, et al. - Wiley, 2021

The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
I. Dimkić - V. Bhardwaj, V. Carpentieri-Pipolo, N. Kuzmanović, et al. - Public Library of Science (PLoS), 2021

Antibody escape and global spread of SARS-CoV-2 lineage A.27
T. Kaleta - L. Kern, S. Hong, M. Hölzer, et al. - Research Square - Springer Science and Business Media LLC, 2021 usegalaxy.eu

In-Depth Molecular Characterization of Neovascular Membranes Suggests a Role for Hyalocyte-to-Myofibroblast Transdifferentiation in Proliferative Diabetic Retinopathy
S. Boneva - J. Wolf, R. Hajdú, G. Prinz, et al. - Frontiers Media SA, 2021 usegalaxy.eu

All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells
M. Lenz - A. Eichler, P. Kruse, J. Muellerleile, et al. - eLife Sciences Publications, Ltd, 2021 usegalaxy.eu

Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted Arabidopsis halleri
G. Lee - H. Ahmadi, J. Quintana, L. Syllwasschy, et al. - Wiley, 2021

Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
J. Ma - J. Chen, B. Louro, R. Martins, et al. - Elsevier BV, 2021 usegalaxy.eu

ARTS-DB: a database for antibiotic resistant targets
M. Mungan - K. Blin, N. Ziemert, - Oxford University Press (OUP), 2021

Determination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages
J. Trouillon - L. Imbert, A. Villard, T. Vernet, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
A. Page-Karjian - L. Whitmore, B. Stacy, J. Perrault, et al. - MDPI AG, 2021 usegalaxy.eu

From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
M. Lauxmann - D. Vazquez, H. Schilbert, P. Neubauer, et al. - Wiley, 2021

Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
C. Pessoa Rodrigues - A. Chatterjee, M. Wiese, T. Stehle, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Characterization of Komagataeibacter Isolate Reveals New Prospects in Waste Stream Valorization for Bacterial Cellulose Production
P. Cannazza - A. Rissanen, D. Guizelini, P. Losoi, et al. - MDPI AG, 2021 usegalaxy.eu

A Comprehensive Molecular and Epidemiological Characterization of Influenza Viruses Circulating 2016–2020 in North Macedonia
M. Kuzmanovska - G. Boshevska, E. Janchevska, T. Buzharova, et al. - Frontiers Media SA, 2021 usegalaxy.eu

Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae
P. Singh - A. Chaudhuri, M. Banerjea, N. Marathe, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

Automatic identification and annotation of MYB gene family members in plants
B. Pucker - - bioRxiv - openRxiv, 2021

Complete Genome Sequences of Six Salmonella enterica Strains (S. enterica subsp. arizonae , S. enterica subsp. diarizonae , and S. enterica subsp. salamae ) Isolated from Poultry Houses
A. Lamas - P. Regal, A. Cepeda, C. Franco, et al. - American Society for Microbiology, 2021 usegalaxy.eu

Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
M. Früh - M. Fischer, A. Schilling, S. Gatidis, et al. - SPIE-Intl Soc Optical Eng, 2021

IMA Genome - F15
T. Duong - J. Aylward, C. Ametrano, B. Poudel, et al. - Pensoft Publishers, 2021 usegalaxy.eu

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
M. Ranchou-Peyruse - M. Guignard, F. Casteran, M. Abadie, et al. - Frontiers Media SA, 2021 usegalaxy.eu

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
J. Meier-Kolthoff - J. Carbasse, R. Peinado-Olarte, M. Göker, et al. - Oxford University Press (OUP), 2021

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Oxford University Press (OUP), 2021

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
C. Cantalapiedra - A. Hernández-Plaza, I. Letunic, P. Bork, et al. - Oxford University Press (OUP), 2021

Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
T. Stachurová - H. Piková, M. Bartas, J. Semerád, et al. - Elsevier BV, 2021 usegalaxy.eu

Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean
L. Colin - C. Yesson, C. Head, - Pensoft Publishers, 2021 usegalaxy.eu

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
W. Maier - S. Bray, M. van den Beek, D. Bouvier, et al. - Springer Science and Business Media LLC, 2021

OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
J. Saraiva - A. Bartholomäus, R. Kallies, M. Gomes, et al. - Life Science Alliance, LLC, 2021

Screening ofAzadirachta indicaphytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study
S. Chandel - R. Singh, A. Gautam, V. Ravichandiran, et al. - Informa UK Limited, 2021

Viral S protein histochemistry reveals few potential SARS-CoV-2 entry sites in human ocular tissues
G. Martin - J. Wolf, T. Lapp, H. Agostini, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Genomic organization of the autonomous regulatory domain of eyeless locus in Drosophila melanogaster
S. Verma - R. Pathak, R. Mishra, - Oxford University Press (OUP), 2021 usegalaxy.eu

Thrombospondin-4 Is a Soluble Dermal Inflammatory Signal That Selectively Promotes Fibroblast Migration and Keratinocyte Proliferation for Skin Regeneration and Wound Healing
M. Klaas - K. Mäemets-Allas, E. Heinmäe, H. Lagus, et al. - Frontiers Media SA, 2021 usegalaxy.eu

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
K. Peters - S. Herman, P. Khoonsari, J. Burman, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Genomic impact of stress-induced transposable element mobility in Arabidopsis
D. Roquis - M. Robertson, L. Yu, M. Thieme, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
O. Saleh - S. Dwiani, J. Rott, K. Kühn, et al. - Springer US, 2021 usegalaxy.eu

Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines
D. Brandt - M. Simunovic, T. Busche, M. Haak, et al. - MDPI AG, 2021

Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
A. Carattoli - G. Arcari, G. Bibbolino, F. Sacco, et al. - American Society for Microbiology, 2021 usegalaxy.eu

FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
C. Fell - A. Hagelkruys, A. Cicvaric, M. Horrer, et al. - bioRxiv - openRxiv, 2021 usegalaxy.eu

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
S. Hering - M. Jansson, M. Buhl, - Microbiology Society, 2021 usegalaxy.eu

The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
A. Migur - F. Heyl, J. Fuss, A. Srikumar, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
I. Apostolakos - A. Laconi, L. Mughini-Gras, Ö. Yapicier, et al. - Frontiers Media SA, 2021 usegalaxy.eu

First complete mitochondrial genome of Rhodinia species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
D. Chen - R. Zhang, X. Jin, J. Yang, et al. - Cambridge University Press (CUP), 2021 usegalaxy.eu

Bakta: Rapid & standardized annotation of bacterial genomes via alignment-free sequence identification
O. Schwengers - L. Jelonek, M. Dieckmann, S. Beyvers, et al. - bioRxiv - openRxiv, 2021

Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID
D. Katsanos - M. Ferrando-Marco, I. Razzaq, G. Aughey, et al. - The Company of Biologists, 2021 usegalaxy.eu

Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
T. Hepp - D. Blum, K. Armanious, B. Schölkopf, et al. - Elsevier BV, 2021

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
V. Glaros - R. Rauschmeier, A. Artemov, A. Reinhardt, et al. - Elsevier BV, 2021 usegalaxy.eu

Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
M. Kavas - K. Yıldırım, Z. Seçgin, M. Abdulla, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
J. Pérez-Schindler - B. Kohl, K. Schneider-Heieck, A. Leuchtmann, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Single‐cell omics: Overview, analysis, and application in biomedical science
C. Stein - R. Weiskirchen, F. Damm, P. Strzelecka, et al. - Wiley, 2021 usegalaxy.eu

Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
G. Cova - C. Taroni, M. Deau, Q. Cai, et al. - Rockefeller University Press, 2021 usegalaxy.eu

Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
D. Vazquez - H. Schilbert, V. Dodero, - MDPI AG, 2021

Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-Afflicted Green (Chelonia mydas), Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea Turtles
L. Whitmore - K. Yetsko, J. Farrell, A. Page-Karjian, et al. - MDPI AG, 2021 usegalaxy.eu

Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
J. Loske - J. Röhmel, S. Lukassen, S. Stricker, et al. - Springer Science and Business Media LLC, 2021

Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
S. Baron - O. Mediannikov, R. Abdallah, E. Kuete Yimagou, et al. - American Society for Microbiology, 2021 usegalaxy.eu

Characterization of the virome associated with Haemagogus mosquitoes in Trinidad, West Indies
R. Ali - J. Jayaraj, A. Mohammed, C. Chinnaraja, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors inArabidopsis
A. Barragán-Rosillo - C. Peralta-Alvarez, J. Ojeda-Rivera, R. Arzate-Mejía, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
E. Musmeci - F. Candeliere, A. Amaretti, M. Rossi, et al. - American Society for Microbiology, 2021 usegalaxy.eu

Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework
M. Föll - V. Volkmann, K. Enderle-Ammour, K. Wilhelm, et al. - bioRxiv - openRxiv, 2021 usegalaxy.eu

Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
S. Bandyopadhyay - O. Abiodun, B. Ogboo, A. Kola-Mustapha, et al. - Informa UK Limited, 2021 usegalaxy.eu

A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass
J. Hölper - F. Grey, J. Baillie, T. Regan, et al. - MDPI AG, 2021 usegalaxy.eu

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
K. Mauer - H. Schmidt, M. Dittrich, A. Fröbius, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species
J. Voelker - M. Shepherd, R. Mauleon, - GigaScience Press, 2021 usegalaxy.eu

The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
M. Bartas - V. Brázda, A. Volná, J. Červeň, et al. - MDPI AG, 2021 usegalaxy.eu

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.
L. Schaffert - M. Ruwe, J. Milse, K. Hanuschka, et al. - Microbiology Society, 2021

Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
A. Cvetkoska - E. Jovanovska, T. Hauffe, T. Donders, et al. - Elsevier BV, 2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
Y. Dorone - S. Boeynaems, E. Flores, B. Jin, et al. - Elsevier BV, 2021 usegalaxy.eu

Eplerenone Improves Pulmonary Vascular Remodeling and Hypertension by Inhibition of the Mineralocorticoid Receptor in Endothelial Cells
J. Kowalski - L. Deng, C. Suennen, D. Koca, et al. - Ovid Technologies (Wolters Kluwer Health), 2021 usegalaxy.eu

De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
L. Marisaldi - D. Basili, G. Gioacchini, A. Canapa, et al. - Elsevier BV, 2021 usegalaxy.eu

MOSGA 2: Comparative genomics and validation tools
R. Martin - H. Dreßler, G. Hattab, T. Hackl, et al. - bioRxiv - openRxiv, 2021

A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
D. Pelletier - D. Roos, M. Bouchoucha, T. Schohn, et al. - Frontiers Media SA, 2021 usegalaxy.eu

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
T. Bauer - K. Collmar, T. Kaltofen, A. Loeffler, et al. - MDPI AG, 2021 usegalaxy.eu

Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
T. Spradling - A. Place, A. Campbell, J. Demastes, et al. - Public Library of Science (PLoS), 2021 usegalaxy.eu

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
S. Beier - J. Werner, T. Bouvier, N. Mouquet, et al. - bioRxiv - openRxiv, 2021

Deep learning-based real-time detection of novel pathogens during sequencing
J. Bartoszewicz - U. Genske, B. Renard, - Oxford University Press (OUP), 2021

Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
S. Friedrich - H. Müller, C. Riesterer, H. Schüller, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
M. Hanussek - F. Bartusch, J. Krüger, - Public Library of Science (PLoS), 2021

Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
R. Pallares-Vega - G. Macedo, M. Brouwer, L. Hernandez Leal, et al. - Frontiers Media SA, 2021 usegalaxy.eu

Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
C. Bamford - L. Broadbent, E. Aranday-Cortes, M. McCabe, et al. - bioRxiv - openRxiv, 2021 usegalaxy.eu

The complete mitochondrial genome of the wild silkmoth Antheraea yamamai from Heilongjiang, China (Lepidoptera: Saturniidae)
S. Sun - J. Huang, Y. Liu, - Informa UK Limited, 2021 usegalaxy.eu

Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
J. Grzegorzewski - F. Bartsch, A. Köller, M. König, et al. - bioRxiv - openRxiv, 2021

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time
J. Theine - D. Holtgräwe, K. Herzog, F. Schwander, et al. - Springer Science and Business Media LLC, 2021

Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis
M. Winkler - A. Pan, - Research Square - Research Square Platform LLC, 2021 usegalaxy.eu

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
M. Neumann - X. Xu, C. Smaczniak, J. Schumacher, et al. - bioRxiv - openRxiv, 2021

ONT-Based Draft Genome Assembly and Annotation of Alternaria atra
B. Bonthala - C. Small, M. Lutz, A. Graf, et al. - Scientific Societies, 2021

Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone
P. Volkova - G. Duarte, E. Kazakova, E. Makarenko, et al. - Elsevier BV, 2021 usegalaxy.eu

Age-Net: An MRI-Based Iterative Framework for Brain Biological Age Estimation
K. Armanious - S. Abdulatif, W. Shi, S. Salian, et al. - Institute of Electrical and Electronics Engineers (IEEE), 2021

Genomic and Proteomic Study of Andreprevotia ripae Isolated from an Anthill Reveals an Extensive Repertoire of Chitinolytic Enzymes
S. Lorentzen - M. Arntzen, T. Hahn, T. Tuveng, et al. - American Chemical Society (ACS), 2021 usegalaxy.eu

De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel
M. Bakkali - R. Martín-Blázquez, M. Ruiz-Estévez, M. Garrido-Ramos, et al. - MDPI AG, 2021 usegalaxy.eu

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
S. Oselusi - A. Christoffels, S. Egieyeh, - MDPI AG, 2021 usegalaxy.eu

Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
X. Zhuang - G. Schlunck, J. Wolf, D. Rosmus, et al. - S. Karger AG, 2021 usegalaxy.eu

Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon
B. Abanda - M. Schmid, A. Paguem, H. Iffland, et al. - MDPI AG, 2021

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
M. Soares - D. Soares, V. Teixeira, A. Heskol, et al. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
L. Bichmann - S. Gupta, G. Rosenberger, L. Kuchenbecker, et al. - American Chemical Society (ACS), 2021

SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction
A. Rempel - R. Wittler, - Oxford University Press (OUP), 2021

Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
M. Bleher - L. Hahn, M. Neumann, J. Patiño-Galindo, et al. - medRxiv - openRxiv, 2021

Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy
K. Kimura - A. Ooms, K. Graf-Riesen, M. Kuppusamy, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Identification of lymphocyte cell-specific protein-tyrosine kinase (LCK) as a driver for invasion and migration of oral cancer by tumor heterogeneity exploitation
J. Weiße - J. Rosemann, L. Müller, M. Kappler, et al. - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
V. Kaiser - L. Talmane, Y. Kumar, F. Semple, et al. - bioRxiv - openRxiv, 2021 usegalaxy.eu

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
R. Gelhausen - T. Müller, S. Svensson, O. Alkhnbashi, et al. - bioRxiv - openRxiv, 2021

Assessing the role of polygenic background on the penetrance of monogenic forms in Parkinson’s disease
E. Hassanin - P. May, R. Aldisi, P. Krawitz, et al. - medRxiv - openRxiv, 2021

Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history
E. Hassanin - P. May, R. Aldisi, I. Spier, et al. - medRxiv - openRxiv, 2021

AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
C. Vanni - M. Schechter, T. Delmont, A. Eren, et al. - bioRxiv - openRxiv, 2021

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
M. Roncoroni - B. Droesbeke, I. Eguinoa, K. De Ruyck, et al. - Oxford University Press (OUP), 2021 usegalaxy.eu

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
C. Cantalapiedra - A. Hernández-Plaza, I. Letunic, P. Bork, et al. - bioRxiv - openRxiv, 2021

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Q. Gu - A. Kumar, S. Bray, A. Creason, et al. - Public Library of Science (PLoS), 2021 usegalaxy.eu

A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame
E. Yol - M. Basak, S. Kızıl, S. Lucas, et al. - Frontiers Media SA, 2021 usegalaxy.eu

Going to extremes – a metagenomic journey into the dark matter of life
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Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells
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CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification
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Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis
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COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints
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A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines
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SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities
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Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
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Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction
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Arganiella Giusti & Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?
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The FTZ-F1 gene encodes two functionally distinct nuclear receptor isoforms in the ectoparasitic copepod salmon louse (Lepeophtheirus salmonis)
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Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing
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EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
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The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts
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Fostering accessible online education using Galaxy as an e-learning platform
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Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration
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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
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Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties
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Peptidotriazolamers Inhibit Aβ(1–42) Oligomerization and Cross a Blood‐Brain‐Barrier Model
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Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants
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ZC3H4 restricts non-coding transcription in human cells
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Common virulence gene expression in adult first-time infected malaria patients and severe cases
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Draft genome of a biparental beetle species, Lethrus apterus
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Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates
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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
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Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
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Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae)
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A large-scale comparative study on peptide encodings for biomedical classification
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Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies
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A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation
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Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels
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Haplotype-resolved diverse human genomes and integrated analysis of structural variation
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Small Conductance Ca2 +-Activated K+ (SK) Channel mRNA Expression in Human Atrial and Ventricular Tissue: Comparison Between Donor, Atrial Fibrillation and Heart Failure Tissue
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Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment
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Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds
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Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy
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The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures
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Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the Xist locus
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User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
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Replication of a Novel Parkinson's Locus in a European Ancestry Population
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Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
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Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (Pimephales promelas)
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Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate
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Direct impact of commonly used dietary emulsifiers on human gut microbiota
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WASP: a versatile, web-accessible single cell RNA-Seq processing platform
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Single-Cell RNA Sequencing Procedures and Data Analysis
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Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
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Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis
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The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm,Antheraea pernyi (Lepidoptera: Saturniidae)
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Updates on metaQuantome Software for Quantitative Metaproteomics
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Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
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Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
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AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
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Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
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Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa
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Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
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VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
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Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring
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The secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans
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Transcription Inhibitors with XRE DNA-Binding and Cupin Signal-Sensing Domains Drive Metabolic Diversification in Pseudomonas
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Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture
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Complex-Type N-Glycans Influence the Root Hair Landscape of Arabidopsis Seedlings by Altering the Auxin Output
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Decitabine Induces Gene Derepression on Monosomic Chromosomes: In Vitro and In Vivo Effects in Adverse-Risk Cytogenetics AML
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DenovoProfiling: a webserver for de novo generated molecule library profiling
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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
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Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
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Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
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Detecting high-scoring local alignments in pangenome graphs
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Interpretable detection of novel human viruses from genome sequencing data
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Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
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Diabetes changes gene expression but not DNA methylation in cardiac cells
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3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis
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Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
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SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
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ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
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Secreted Phosphoprotein 1 Expression in Retinal Mononuclear Phagocytes Links Murine to Human Choroidal Neovascularization
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Deep learning-based real-time detection of novel pathogens during sequencing
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Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences
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Scarless engineering of the Drosophila genome near any site-specific integration site
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A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape
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Congenital heart disease risk loci identified by genome-wide association study in European patients
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Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
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Deep Learning‐Based Automated Abdominal Organ Segmentation in the UK Biobank and German National Cohort Magnetic Resonance Imaging Studies
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On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
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ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
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Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms
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SANS serif: alignment-free, whole-genome based phylogenetic reconstruction
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Current status of use of high throughput nucleotide sequencing in rheumatology
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Tool recommender system in Galaxy using deep learning
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Electroactive microorganisms in mouse feces
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The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry
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Self-Supervised Learning for Automated Anatomical Tracking in Medical Image Data with Minimal Human Labeling Effort
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RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
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MOSGA 2: Comparative genomics and validation tools
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RNA-Seq Data Analysis in Galaxy
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SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance
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Duration of Colonisation With Extended-spectrum Beta-lactamase-producing Escherichia Coli: Results of an Open Cohort Study With Dutch Nursing Home Residents (2013 – 2019)
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Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
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Tuning the Biological Activity of RGD Peptides with Halotryptophans
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Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance
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Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis )
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3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists
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Stable Protein Sialylation in Physcomitrella
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The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
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Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
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Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria
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Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue
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Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis
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A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans
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Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
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Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
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MOSGA: Modular Open-Source Genome Annotator
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A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
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CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
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Improving CLIP-seq data analysis by incorporating transcript information
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Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages
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CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequences
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
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RNA nucleation by MSL2 induces selective X chromosome compartmentalization
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Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
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Survey of metaproteomics software tools for functional microbiome analysis
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PK-DB: pharmacokinetics database for individualized and stratified computational modeling
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Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
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Fully Automated and Standardized Segmentation of Adipose Tissue Compartments via Deep Learning in 3D Whole-Body MRI of Epidemiologic Cohort Studies
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Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells
V. Čermák - D. Tyč, A. Přibylová, L. Fischer, et al. - Elsevier BV, 2020 usegalaxy.eu

Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues
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Next generation sequencing study on RNA viruses ofVespa velutinaandApis melliferasharing the same foraging area
F. Marzoli - M. Forzan, L. Bortolotti, M. Pacini, et al. - Wiley, 2020 usegalaxy.eu

High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh
S. Ahmed - T. Das, M. Islam, A. Herrero-Fresno, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets
Y. Gaafar - H. Ziebell, - PeerJ, 2020 usegalaxy.eu

Lack of Desmin in Mice Causes Structural and Functional Disorders of Neuromuscular Junctions
N. Eiber - F. Fröb, M. Schowalter, C. Thiel, et al. - Frontiers Media SA, 2020 usegalaxy.eu

The environment drives microbial trait variability in aquatic habitats
S. Beier - A. Andersson, P. Galand, C. Hochart, et al. - Wiley, 2020

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
T. Delmont - M. Gaia, D. Hinsinger, P. Fremont, et al. - bioRxiv - openRxiv, 2020

The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
A. Kumar - K. Kondhare, N. Malankar, A. Banerjee, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
J. Wolf - C. Auw-Haedrich, A. Schlecht, S. Boneva, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
M. Bazzucchi - I. Pierini, M. Giammarioli, G. De Mia, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
C. Zavala-Alvarado - O. Sismeiro, R. Legendre, H. Varet, et al. - Public Library of Science (PLoS), 2020 usegalaxy.eu

Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
P. Afouda - G. Dubourg, A. Levasseur, P. Fournier, et al. - MDPI AG, 2020 usegalaxy.eu

Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
T. Wilke - T. Hauffe, E. Jovanovska, A. Cvetkoska, et al. - American Association for the Advancement of Science (AAAS), 2020

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
M. Tekman - B. Batut, A. Ostrovsky, C. Antoniewski, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
S. Boneva - A. Schlecht, D. Böhringer, H. Mittelviefhaus, et al. - Elsevier BV, 2020 usegalaxy.eu

Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay
A. Dad - V. Dobrovolsky, R. Heflich, J. Revollo, et al. - Elsevier BV, 2020 usegalaxy.eu

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
W. de Koning - M. Miladi, S. Hiltemann, A. Heikema, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
L. Estrada Mallarino - C. Engel, İ. Ilık, D. Maticzka, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
L. Lezameta - D. Cuicapuza, A. Dávila-Barclay, S. Torres, et al. - American Society for Microbiology, 2020 usegalaxy.eu

Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing
R. Izquierdo-Lara - G. Elsinga, L. Heijnen, B. Oude Munnink, et al. - medRxiv - openRxiv, 2020 usegalaxy.eu

Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
R. Wirth - B. Pap, T. Böjti, P. Shetty, et al. - Frontiers Media SA, 2020 usegalaxy.eu

tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
S. Bose - A. Suescún, J. Song, C. Castillo-González, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
G. Greenfield - S. McPherson, J. Smith, A. Mead, et al. - MDPI AG, 2020 usegalaxy.eu

Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
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Polypharmacology of Some Medicinal Plant Metabolites Against SARS-CoV-2 and Host Targets: Molecular Dynamics Evaluation of NSP9 RNA Binding Protein
S. Bandyopadhyay - O. Abiodun, B. Ogboo, A. Kola-Mustapha, et al. - American Chemical Society (ACS), 2020 usegalaxy.eu

An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
L. Morandi - S. Sabattini, A. Renzi, A. Rigillo, et al. - MDPI AG, 2020 usegalaxy.eu

Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
S. Boneva - J. Wolf, D. Rosmus, A. Schlecht, et al. - Frontiers Media SA, 2020 usegalaxy.eu

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
D. Wibberg - B. Batut, P. Belmann, J. Blom, et al. - F1000 Research Ltd, 2020 usegalaxy.eu

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
S. Bray - T. Senapathi, C. Barnett, B. Grüning, et al. - Springer Science and Business Media LLC, 2020

Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
T. Wilke - J. Renz, T. Hauffe, D. Delicado, et al. - Institute of Malacology, 2020

Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
C. Mootapally - M. Mahajan, N. Nathani, - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
M. Núñez-Sánchez - J. Colom, L. Walsh, C. Buttimer, et al. - MDPI AG, 2020 usegalaxy.eu

Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
H. Chawla - H. Lee, I. Gabur, P. Vollrath, et al. - Wiley, 2020

Deep learning-based diatom taxonomy on virtual slides
M. Kloster - D. Langenkämper, M. Zurowietz, B. Beszteri, et al. - Springer Science and Business Media LLC, 2020

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
H. Schiebenhoefer - K. Schallert, B. Renard, K. Trappe, et al. - Springer Science and Business Media LLC, 2020

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
M. Bentsen - P. Goymann, H. Schultheis, K. Klee, et al. - Springer Science and Business Media LLC, 2020

DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
G. Di Dalmazi - L. Morandi, B. Rubin, C. Pilon, et al. - The Endocrine Society, 2020 usegalaxy.eu

Training Infrastructure as a Service
H. Rasche - B. Grüning, - bioRxiv - openRxiv, 2020 usegalaxy.eu

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
D. Baker - M. van den Beek, D. Blankenberg, D. Bouvier, et al. - Public Library of Science (PLoS), 2020 usegalaxy.eu

Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
P. Espíndola-Hernández - J. Mueller, M. Carrete, S. Boerno, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease
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Draft Genome Sequences of Three Clostridia Isolates Involved in Lactate-Based Chain Elongation
B. Liu - D. Popp, H. Sträuber, H. Harms, et al. - American Society for Microbiology, 2020

Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health
R. Wirth - G. Maróti, L. Lipták, M. Mester, et al. - Research Square - Springer Science and Business Media LLC, 2020 usegalaxy.eu

pyGenomeTracks: reproducible plots for multivariate genomic datasets 
L. Lopez-Delisle - L. Rabbani, J. Wolff, V. Bhardwaj, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates
B. Liu - D. Popp, H. Sträuber, H. Harms, et al. - Research Square - Springer Science and Business Media LLC, 2020

Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
M. Buhl - M. Marschal, - Microbiology Society, 2020 usegalaxy.eu

Autocrine IL6-Mediated Activation of the STAT3–DNMT Axis Silences the TNFα–RIP1 Necroptosis Pathway to Sustain Survival and Accumulation of Myeloid-Derived Suppressor Cells
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Ultrastructural, transcriptional, and functional differences between human reticulated and non‐reticulated platelets
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SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
S. Müller - S. Wallner, G. Schmitz, T. Loew, et al. - Elsevier BV, 2020 usegalaxy.eu

Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration
A. Schlecht - S. Boneva, M. Gruber, P. Zhang, et al. - Elsevier BV, 2020 usegalaxy.eu

A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
S. Dhamija - C. Yang, J. Seiler, K. Myacheva, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Benchmarking challenging small variants with linked and long reads
J. Wagner - N. Olson, L. Harris, J. McDaniel, et al. - bioRxiv - openRxiv, 2020

An Interactive Visualization for Feature Localization in Deep Neural Networks
M. Zurowietz - T. Nattkemper, - Frontiers Media SA, 2020

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
A. Hahn - D. Pensold, C. Bayer, J. Tittelmeier, et al. - Frontiers Media SA, 2020 usegalaxy.eu

Genome‐wide cooperation of EMT transcription factor ZEB 1 with YAP and AP ‐1 in breast cancer
N. Feldker - F. Ferrazzi, H. Schuhwerk, S. Widholz, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

The landscape of SARS-CoV-2 RNA modifications
M. Miladi - J. Fuchs, W. Maier, S. Weigang, et al. - bioRxiv - openRxiv, 2020

Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
C. Lange - J. Wolf, C. Auw‐Haedrich, A. Schlecht, et al. - Wiley, 2020 usegalaxy.eu

Lake expansion elevates equilibrium diversity via increasing colonization
T. Hauffe - D. Delicado, R. Etienne, L. Valente, et al. - Wiley, 2020

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
S. Mehta - C. Easterly, R. Sajulga, R. Millikin, et al. - MDPI AG, 2020

Enhanced COVID-19 data for improved prediction of survival
W. Zeng - A. Gautam, D. Huson, - bioRxiv - openRxiv, 2020

Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
S. Roth - P. Bose, M. Alhamdani, S. Mustafa, et al. - Ovid Technologies (Wolters Kluwer Health), 2020

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

The complete mitochondrial genome of antheraea pernyi strain qing_6 (lepidoptera: Saturniidae)
Y. Liu - X. Li, D. Chen, Y. Liu, et al. - Informa UK Limited, 2020 usegalaxy.eu

Unifying the known and unknown microbial coding sequence space
C. Vanni - M. Schechter, S. Acinas, A. Barberán, et al. - bioRxiv - openRxiv, 2020

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
V. Piro - T. Dadi, E. Seiler, K. Reinert, et al. - Oxford University Press (OUP), 2020

Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations
D. Guo - M. Föll, V. Volkmann, K. Enderle-Ammour, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
T. Villa - M. Barucco, M. Martin-Niclos, A. Jacquier, et al. - Elsevier BV, 2020 usegalaxy.eu

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve, et al. - MDPI AG, 2020 usegalaxy.eu

Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart
H. Lahm - M. Jia, M. Dreßen, F. Wirth, et al. - bioRxiv - openRxiv, 2020 usegalaxy.eu

Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research
R. Rajan - K. Divya, R. Kandadai, R. Yadav, et al. - Frontiers Media SA, 2020

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
R. Rettenmaier - M. Schneider, B. Munk, M. Lebuhn, et al. - MDPI AG, 2020

Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
M. Foschini - L. Morandi, A. Sanchez, A. Santoro, et al. - Frontiers Media SA, 2020 usegalaxy.eu

Specificities and functional coordination between the two Cas6 maturation endonucleases in Anabaena sp. PCC 7120 assign orphan CRISPR arrays to three groups
V. Reimann - M. Ziemann, H. Li, T. Zhu, et al. - Informa UK Limited, 2020 usegalaxy.eu

Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
R. Zhang - J. Gehlen, A. Kawalia, M. Melissari, et al. - Public Library of Science (PLoS), 2020

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
H. Nützmann - D. Doerr, A. Ramírez-Colmenero, J. Sotelo-Fonseca, et al. - Proceedings of the National Academy of Sciences, 2020

GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
R. Schäfer - S. Lott, J. Georg, B. Grüning, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
V. Jalili E. Afgan Q. Gu D. Clements D. Blankenberg J. Goecks J. Taylor A. Nekrutenko - - Oxford University Press (OUP), 2020

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
S. Bray - X. Lucas, A. Kumar, B. Grüning, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Galactic Circos: User-friendly Circos plots within the Galaxy platform
H. Rasche - S. Hiltemann, - Oxford University Press (OUP), 2020 usegalaxy.eu

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
A. Busch - M. Brüggemann, S. Ebersberger, K. Zarnack, et al. - Elsevier BV, 2020 usegalaxy.eu

Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus
N. Yoshida - C. Kaito, - Elsevier BV, 2020 usegalaxy.eu

Independent attenuation correction of whole body [18F]FDG-PET using a deep learning approach with Generative Adversarial Networks
K. Armanious - T. Hepp, T. Küstner, H. Dittmann, et al. - Springer Science and Business Media LLC, 2020

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
J. Oeyen - P. Baa-Puyoulet, J. Benoit, L. Beukeboom, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
T. Altenburg - S. Giese, S. Wang, T. Muth, et al. - bioRxiv - openRxiv, 2020

Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server
A. Kumar - A. Bangash, B. Gruening, - MDPI AG, 2020 usegalaxy.eu

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
M. Mungan M. Alanjary K. Blin T. Weber M. Medema N. Ziemert - - Oxford University Press (OUP), 2020

Two new genera and three new subterranean species of Hydrobiidae (Caenogastropoda: Truncatelloidea) from Tunisia
N. Khalloufi - M. Béjaoui, D. Delicado, - Museum National D'Histoire Naturelle, 2020

Phylogenetic relationships within Pseudamnicola Paulucci, 1878 (Caenogastropoda: Truncatelloidea) indicate two independent dispersal events from different continents to the Balearic Islands
K. Boulaassafer - M. Ghamizi, A. Machordom, D. Delicado, et al. - Informa UK Limited, 2020

Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
R. Winkler - I. Rosas-Román, - American Chemical Society (ACS), 2020 usegalaxy.eu

A framework for designing miRNA-based distributed cell classifier circuits
M. Nowicka - H. Siebert, - bioRxiv - openRxiv, 2020

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
N. Blomberg - K. Lauer, - Springer Science and Business Media LLC, 2020 usegalaxy.eu

LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity
A. Dorn - M. Glaß, C. Neu, B. Heydel, et al. - MDPI AG, 2020 usegalaxy.eu

A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases
P. Kumar - J. Johnson, C. Easterly, S. Mehta, et al. - American Chemical Society (ACS), 2020

A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
D. Becker - D. Popp, H. Harms, F. Centler, et al. - MDPI AG, 2020

Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
B. Öztürk J. Werner J. Meier-Kolthoff B. Bunk C. Spröer D. Springael - - Oxford University Press (OUP), 2020

The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
M. McGill - B. Sabikunnahar, Q. Fang, C. Teuscher, et al. - Elsevier BV, 2020 usegalaxy.eu

MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome
I. Parenti - F. Diab, S. Gil, E. Mulugeta, et al. - Elsevier BV, 2020 usegalaxy.eu

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
S. Chen - G. Sun, Y. Yan, K. Konstantinidis, et al. - Proceedings of the National Academy of Sciences, 2020

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm, et al. - bioRxiv - openRxiv, 2020 usegalaxy.eu

Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
T. Hepp - M. Fischer, M. Winkelmann, S. Baldenhofer, et al. - Ovid Technologies (Wolters Kluwer Health), 2020

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
H. Lee - H. Chawla, C. Obermeier, F. Dreyer, et al. - Frontiers Media SA, 2020

Novel Divisome-Associated Protein Spatially Coupling the Z-Ring with the Chromosomal Replication Terminus in Caulobacter crescentus
S. Ozaki - U. Jenal, T. Katayama, - American Society for Microbiology, 2020 usegalaxy.eu

Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
W. Logroño - D. Popp, S. Kleinsteuber, H. Sträuber, et al. - MDPI AG, 2020

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
G. Lodewijk - D. Fernandes, I. Vretzakis, J. Savage, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

Preparing for the KIL: Receptor Analysis of Pseudomonas syringae pv. porri Phages and Their Impact on Bacterial Virulence
D. Holtappels - A. Kerremans, Y. Busschots, J. Van Vaerenbergh, et al. - MDPI AG, 2020 usegalaxy.eu

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
J. Wolff L. Rabbani R. Gilsbach G. Richard T. Manke R. Backofen B. Grüning - - Oxford University Press (OUP), 2020 usegalaxy.eu

An epigenetic map of malaria parasite development from host to vector
K. Witmer - S. Fraschka, D. Vlachou, R. Bártfai, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
M. Tangaro - G. Donvito, M. Antonacci, M. Chiara, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

The importance of incorporating transcript information in CLIP-seq data analysis
M. Uhl - D. Tran, R. Backofen, - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
T. McGowan - J. Johnson, P. Kumar, R. Sajulga, et al. - Oxford University Press (OUP), 2020 usegalaxy.eu

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
F. Uellendahl-Werth - M. Wolfien, A. Franke, O. Wolkenhauer, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
S. Kumaran - A. Ngo, F. Schultes, D. Tischler, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
I. Hernández - C. Sant, R. Martínez, C. Fernández, et al. - Frontiers Media SA, 2020 usegalaxy.eu

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells
O. Genolet - A. Monaco, I. Dunkel, M. Boettcher, et al. - bioRxiv - openRxiv, 2020 usegalaxy.eu

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
O. Schwengers - A. Hoek, M. Fritzenwanker, L. Falgenhauer, et al. - Public Library of Science (PLoS), 2020

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
I. Maus - M. Klocke, J. Derenkó, Y. Stolze, et al. - Springer Science and Business Media LLC, 2020

Effects of simulated dose variation on contrast-enhanced CT-based radiomic analysis for Non-Small Cell Lung Cancer
T. Hepp - A. Othman, A. Liebgott, J. Kim, et al. - Elsevier BV, 2020

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
J. Werner - E. Nour, B. Bunk, C. Spröer, et al. - Frontiers Media SA, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
J. Garrido - M. Aguilar, P. Prieto, - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Pluripotency factors determine gene expression repertoire at zygotic genome activation
M. Gao - M. Veil, M. Rosenblatt, A. Riesle, et al. - bioRxiv - openRxiv, 2020 usegalaxy.eu

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
B. Stelbrink - R. Richter, F. Köhler, F. Riedel, et al. - Oxford University Press (OUP), 2020

Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann, et al. - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
G. Farmiloe - G. Lodewijk, S. Robben, E. van Bree, et al. - The Royal Society, 2020 usegalaxy.eu

Interpretable detection of novel human viruses from genome sequencing data
J. Bartoszewicz - A. Seidel, B. Renard, - bioRxiv - openRxiv, 2020

Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins
C. Lee - A. Putnam, T. Lu, S. He, et al. - eLife Sciences Publications, Ltd, 2020 usegalaxy.eu

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
D. Hofacker - J. Broche, L. Laistner, S. Adam, et al. - MDPI AG, 2020 usegalaxy.eu

Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages
F. Candeliere - S. Raimondi, G. Spampinato, M. Tay, et al. - American Society for Microbiology, 2020 usegalaxy.eu

BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
M. Hanussek - F. Bartusch, J. Krüger, - Elsevier BV, 2020

MedGAN: Medical image translation using GANs
K. Armanious - C. Jiang, M. Fischer, T. Küstner, et al. - Elsevier BV, 2020

Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
M. Zurowietz - T. Nattkemper, - Institute of Electrical and Electronics Engineers (IEEE), 2020

Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye, et al. - Springer International Publishing, 2020

BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
T. Senapathi - C. Barnett, K. Naidoo, - Bio-Protocol, LLC, 2020 usegalaxy.eu

GLP: A requirement in cell therapies - perspectives for the cardiovascular field
U. Müller-Ruch - A. Skorska, H. Lemcke, G. Steinhoff, et al. - Elsevier BV, 2020 usegalaxy.eu

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
G. Sevillya D. Doerr Y. Lerner J. Stoye M. Steel S. Snir - - Oxford University Press (OUP), 2019

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Y. Perez‐Riverol - P. Moreno, - Wiley, 2019 usegalaxy.eu

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
M. Lewinski - Y. Bramkamp, T. Köster, D. Staiger, et al. - bioRxiv - openRxiv, 2019

A Glyphosate Pulse to Brackish Long-Term Microcosms Has a Greater Impact on the Microbial Diversity and Abundance of Planktonic Than of Biofilm Assemblages
R. Janßen - W. Skeff, J. Werner, M. Wirth, et al. - Frontiers Media SA, 2019

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
D. Gissi - A. Tarsitano, A. Gabusi, R. Rossi, et al. - MDPI AG, 2019 usegalaxy.eu

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger, et al. - Oxford University Press (OUP), 2019

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
G. Etherington - N. Soranzo, S. Mohammed, W. Haerty, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
M. Miladi - E. Sokhoyan, T. Houwaart, S. Heyne, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts
R. Janßen - J. Zabel, U. von Lukas, M. Labrenz, et al. - Elsevier BV, 2019

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata, - bioRxiv - openRxiv, 2019 usegalaxy.eu

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
J. Werner - A. Géron, J. Kerssemakers, S. Matallana-Surget, et al. - Springer Science and Business Media LLC, 2019

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
J. Torres-Paz - J. Leclercq, S. Rétaux, - eLife Sciences Publications, Ltd, 2019 usegalaxy.eu

Expression Atlas update: from tissues to single cells
I. Papatheodorou - P. Moreno, J. Manning, A. Fuentes, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
A. Géron - J. Werner, R. Wattiez, P. Lebaron, et al. - Frontiers Media SA, 2019

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
M. Emperle - S. Adam, S. Kunert, M. Dukatz, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

Highly Efficient Library Preparation for Ion Torrent Sequencing Using Y-Adapters
L. Forth - D. Höper, - Informa UK Limited, 2019 usegalaxy.eu

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage
R. Wirth - T. Böjti, G. Lakatos, G. Maróti, et al. - Frontiers Media SA, 2019 usegalaxy.eu

An intrinsically disordered proteins community for ELIXIR
N. Davey - M. Babu, M. Blackledge, A. Bridge, et al. - F1000 Research Ltd, 2019 usegalaxy.eu

Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
S. Lambrecht - Y. Kanesaki, J. Fuss, B. Huettel, et al. - Springer Science and Business Media LLC, 2019 usegalaxy.eu

Development of novel microsatellite markers for Alkanna tinctoria by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer, et al. - Wiley, 2019 usegalaxy.eu

Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies
F. Larsen - B. Bed’Hom, B. Guldbrandtsen, T. Dalgaard, et al. - Elsevier BV, 2019 usegalaxy.eu

Bacterial Metabolites Produced Under Iron Limitation Kill Pinewood Nematode and Attract Caenorhabditis elegans
D. Proença - T. Heine, C. Senges, J. Bandow, et al. - Frontiers Media SA, 2019 usegalaxy.eu

Candida auris in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen, et al. - Centers for Disease Control and Prevention (CDC), 2019 usegalaxy.eu

ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
M. Haas - J. Gómez Vázquez, D. Sun, H. Tran, et al. - Elsevier BV, 2019 usegalaxy.eu

Historical faunal exchange between the Pontocaspian Basin and North America
J. Vandendorpe - C. van Baak, B. Stelbrink, D. Delicado, et al. - Wiley, 2019

Draft Genome Sequence of a Chitinimonas Species from Hudson Valley Waterways That Expresses Violacein Pigment
B. Jude - - American Society for Microbiology, 2019 usegalaxy.eu

Pheno-seq – linking visual features and gene expression in 3D cell culture systems
S. Tirier - J. Park, F. Preußer, L. Amrhein, et al. - Springer Science and Business Media LLC, 2019

Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
R. Rauschmeier - C. Gustafsson, A. Reinhardt, N. A‐Gonzalez, et al. - Springer Science and Business Media LLC, 2019 usegalaxy.eu

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
T. Wollmann - M. Gunkel, I. Chung, H. Erfle, et al. - Elsevier BV, 2019

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
L. Sánchez - B. Burger, C. Horro, A. Fabregat, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

UseGalaxy.eu: Community, Training, Infrastructure, and Users
H. Rasche - . , - F1000 Research Ltd, 2019 usegalaxy.eu

Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion, et al. - American Chemical Society (ACS), 2019

Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts
S. Cantarella - D. Carnevali, M. Morselli, A. Conti, et al. - MDPI AG, 2019 usegalaxy.eu

U2 AF 65 assemblies drive sequence‐specific splice site recognition
M. Tari - V. Manceau, J. de Matha Salone, A. Kobayashi, et al. - Springer Science and Business Media LLC, 2019 usegalaxy.eu

Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis
I. Lengfelder - I. Sava, J. Hansen, K. Kleigrewe, et al. - Frontiers Media SA, 2019 usegalaxy.eu

A pan-cancer analysis of synonymous mutations
Y. Sharma - M. Miladi, S. Dukare, K. Boulay, et al. - Springer Science and Business Media LLC, 2019 usegalaxy.eu

de.NBI Cloud federation through ELIXIR AAI
P. Belmann - B. Fischer, J. Krüger, M. Procházka, et al. - F1000 Research Ltd, 2019

Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells
C. Ritter - T. Wollmann, P. Bernhard, M. Gunkel, et al. - Springer Science and Business Media LLC, 2019

Versatile interactions and bioinformatics analysis of noncoding RNAs
Q. Chen - X. Meng, Q. Liao, M. Chen, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
J. Nelkner - C. Henke, T. Lin, W. Pätzold, et al. - MDPI AG, 2019

RNApolis: Computational Platform for RNA Structure Analysis
M. Szachniuk - - Walter de Gruyter GmbH, 2019 usegalaxy.eu

BIIGLE2Go—A scalable image annotation system for easy deployment on cruises
M. Zurowietz - D. Langenkamper, T. Nattkemper, - IEEE, 2019

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
B. Pucker - D. Holtgräwe, K. Stadermann, K. Frey, et al. - Public Library of Science (PLoS), 2019

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
J. Meier-Kolthoff - M. Göker, - Springer Science and Business Media LLC, 2019

The RNA workbench 2.0: next generation RNA data analysis
J. Fallmann - P. Videm, A. Bagnacani, B. Batut, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

Reproducible Scientific Workflows for High Performance and Cloud Computing
F. Bartusch - M. Hanussek, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

BOOTABLE: Bioinformatics Benchmark Tool Suite
M. Hanussek - F. Bartusch, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

Mapping-based Genome Size Estimation
S. Natarajan - J. Gehrke, B. Pucker, - bioRxiv - openRxiv, 2019

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
M. Brunet X. Roucou - - MyJove Corporation, 2019 usegalaxy.eu

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
J. Espenshade - S. Thijs, S. Gawronski, H. Bové, et al. - Frontiers Media SA, 2019 usegalaxy.eu

Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
L. Youssar - V. Wernet, N. Hensel, X. Yu, et al. - Public Library of Science (PLoS), 2019 usegalaxy.eu

1,4-Disubstituted 1H-1,2,3-Triazole Containing Peptidotriazolamers: A New Class of Peptidomimetics With Interesting Foldamer Properties
D. Schröder - O. Kracker, T. Fröhr, J. Góra, et al. - Frontiers Media SA, 2019

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
J. Teikari - R. Popin, S. Hou, M. Wahlsten, et al. - Springer Science and Business Media LLC, 2019 usegalaxy.eu

Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus
D. Delicado - B. Arconada, A. Aguado, M. Ramos, et al. - Oxford University Press (OUP), 2019

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi - S. Bray, C. Barnett, B. Grüning, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu

CAMISIM: simulating metagenomes and microbial communities
A. Fritz - P. Hofmann, S. Majda, E. Dahms, et al. - Springer Science and Business Media LLC, 2019

Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
K. Wylie - T. Wylie, P. Minx, D. Rosen, et al. - Frontiers Media SA, 2019 usegalaxy.eu

Improve your Galaxy text life: The Query Tabular Tool
J. Johnson - P. Kumar, C. Easterly, M. Esler, et al. - F1000 Research Ltd, 2019 usegalaxy.eu

Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms
D. Kolosov - M. O'Donnell, - The Company of Biologists, 2019 usegalaxy.eu

Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis
A. Lother - L. Deng, M. Huck, D. Fürst, et al. - Bioscientifica, 2019 usegalaxy.eu

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
N. Owen - M. Moosajee, - SAGE Publications, 2019 usegalaxy.eu

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
A. Bagnacani - M. Wolfien, O. Wolkenhauer, - Springer New York, 2019 usegalaxy.eu

Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
A. Kalmbach - C. Schröder, L. Klein-Hitpass, K. Nordström, et al. - S. Karger AG, 2019 usegalaxy.eu

Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
I. Prislan - S. Sajko, N. Ulrih, L. Fürst, et al. - Royal Society of Chemistry (RSC), 2019 usegalaxy.eu

Workflow Development for the Functional Characterization of ncRNAs
M. Wolfien - D. Brauer, A. Bagnacani, O. Wolkenhauer, et al. - Springer New York, 2019 usegalaxy.eu

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
P. Kumar - P. Panigrahi, J. Johnson, W. Weber, et al. - American Chemical Society (ACS), 2018 usegalaxy.eu

Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
S. Matallana-Surget - J. Werner, R. Wattiez, K. Lebaron, et al. - Frontiers Media SA, 2018

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
S. Weise - G. Arumugam, A. Villarreal, P. Videm, et al. - Springer Science and Business Media LLC, 2018 usegalaxy.eu

Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation
N. Blagitko-Dorfs - P. Schlosser, G. Greve, D. Pfeifer, et al. - Springer Science and Business Media LLC, 2018 usegalaxy.eu

MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
M. Zurowietz - D. Langenkämper, B. Hosking, H. Ruhl, et al. - Public Library of Science (PLoS), 2018

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J. Huerta-Cepas - D. Szklarczyk, D. Heller, A. Hernández-Plaza, et al. - Oxford University Press (OUP), 2018

Aequatus: an open-source homology browser
A. Thanki - N. Soranzo, J. Herrero, W. Haerty, et al. - Oxford University Press (OUP), 2018 usegalaxy.eu

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
P. Bovio - H. Franz, S. Heidrich, T. Rauleac, et al. - Springer Science and Business Media LLC, 2018 usegalaxy.eu

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
V. Piro - T. Dadi, E. Seiler, K. Reinert, et al. - bioRxiv - openRxiv, 2018

Common ELIXIR Service for Researcher Authentication and Authorisation
M. Linden - M. Prochazka, I. Lappalainen, D. Bucik, et al. - F1000 Research Ltd, 2018

Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium
G. Retamal-Morales - T. Heine, J. Tischler, B. Erler, et al. - Elsevier BV, 2018 usegalaxy.eu

Ultrastructural alterations in the retinal pigment epithelium and photoreceptors of a Stargardt patient and three Stargardt mouse models: indication for the central role of RPE melanin in oxidative stress
T. Taubitz - A. Tschulakow, M. Tikhonovich, B. Illing, et al. - PeerJ, 2018

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
I. Maus - M. Rumming, I. Bergmann, K. Heeg, et al. - Springer Science and Business Media LLC, 2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J. Wolff - V. Bhardwaj, S. Nothjunge, G. Richard, et al. - Oxford University Press (OUP), 2018 usegalaxy.eu

Community-Driven Data Analysis Training for Biology
B. Batut - S. Hiltemann, A. Bagnacani, D. Baker, et al. - Elsevier BV, 2018 usegalaxy.eu

ASaiM: a Galaxy-based framework to analyze microbiota data
B. Batut - K. Gravouil, C. Defois, S. Hiltemann, et al. - Oxford University Press (OUP), 2018 usegalaxy.eu

Biology Needs Evolutionary Software Tools: Let’s Build Them Right
A. Nekrutenko - G. Team, J. Goecks, J. Taylor, et al. - Oxford University Press (OUP), 2018 usegalaxy.eu

Structure and Interaction Prediction in Prokaryotic RNA Biology
P. Wright* - M. Mann*, R. Backofen*, - American Society for Microbiology, 2018 usegalaxy.eu

CMV: visualization for RNA and protein family models and their comparisons
F. Eggenhofer - I. Hofacker, R. Backofen, C. Höner zu Siederdissen, et al. - Oxford University Press (OUP), 2018 usegalaxy.eu

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
P. Bovio D. Roidl S. Heidrich T. Vogel H. Franz - - MyJove Corporation, 2018 usegalaxy.eu

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
Y. Stolze - A. Bremges, I. Maus, A. Pühler, et al. - Wiley, 2017

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
I. Maus - A. Bremges, Y. Stolze, S. Hahnke, et al. - Springer Science and Business Media LLC, 2017

The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
T. Wołkowicz - - Oxford University Press (OUP), 2017 usegalaxy.eu

Workflows for microscopy image analysis and cellular phenotyping
T. Wollmann - H. Erfle, R. Eils, K. Rohr, et al. - Elsevier BV, 2017

Bioinformatics for NGS-based metagenomics and the application to biogas research
S. Jünemann - N. Kleinbölting, S. Jaenicke, C. Henke, et al. - Elsevier BV, 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
B. Grüning - J. Fallmann, D. Yusuf, S. Will, et al. - Oxford University Press (OUP), 2017 usegalaxy.eu

Deep residual Hough voting for mitotic cell detection in histopathology images
T. Wollmann - K. Rohr, - IEEE, 2017

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper, et al. - Frontiers Media SA, 2017

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Y. Stolze - A. Bremges, M. Rumming, C. Henke, et al. - Springer Science and Business Media LLC, 2016

Estudio de mecanismos de adaptación y persistencia desplegados por patógenos multirresistentes durante la infección pulmonar crónica en personas con fibrosis quística
L. León - . , - Universidad Nacional de La Plata - Universidad Nacional de La Plata, None usegalaxy.eu

Genomas dos fungos Trichoderma lentiforme e Trichoderma camerunense e a interação na cultura do tomateiro e com fitopatógenos
C. Medeiros - . , - Instituto Biológico - Instituto Biologico, None usegalaxy.eu

Analysis and classification of human microbiomes: detection of bioindicators and optimization through machine learning
J. Kasmanas - - Universidade de São Paulo - Universidade de São Paulo. Agência de Bibliotecas e Coleções Digitais, None