Publications

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Currently 887 publications with reference to de.NBI Cloud are listed.

Recently added publication

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


Dataset from RNAseq analysis of differential gene expression among developmental stages of two non-marine ostracodes
M. Vences - S. Anslan, J. Sabino-Pinto, M. Bonilla-Flores, et al. - Data in Brief, 2024

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

Genome sequence of the medicinal and ornamental plant<i>Digitalis purpurea</i>reveals the molecular basis of flower color variation
K. Wolff - R. Friedhoff, J. Horz, B. Pucker, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

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

Anthropogenic contamination sources drive differences in antimicrobial-resistant <i>Escherichia coli</i> in three urban lakes
J. Wight - A. Byrne, K. Tahlan, A. Lang, et al. - Applied and Environmental Microbiology, 2024 usegalaxy.eu

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

From Complexity to Precision—Charting Decision-Making Through Normative Modeling
P. Kumar - P. Dayan, T. Wolfers, - JAMA Psychiatry, 2024

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. - Current Biology, 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. - Computational Biology and Chemistry, 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. - Nature Biotechnology, 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. - Microorganisms, 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. - GAMM-Mitteilungen, 2024

First detection of a cefiderocol-resistant and extensively drug-resistant Acinetobacter baumannii clinical isolate in Bulgaria
T. Strateva - S. Peykov, - Acta Microbiologica et Immunologica Hungarica, 2024 usegalaxy.eu

Transcriptomic characterization of the human segmental endotoxin challenge model
C. Gress - T. Litzenburger, R. Schmid, K. Xiao, et al. - Scientific Reports, 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. - Nature Communications, 2024 usegalaxy.eu

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

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. - IEEE Transactions on Engineering Management, 2024

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. - Genomics &amp; Informatics, 2023 usegalaxy.eu

Ribosome profiling reveals the fine-tuned response of <i>Escherichia coli</i> to mild and severe acid stress
K. Schumacher - R. Gelhausen, W. Kion-Crosby, L. Barquist, et al. - mSystems, 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. - Nature Communications, 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. - Nature Protocols, 2023

Construction and analysis of pseudogene-related ceRNA network in breast cancer
H. Mohebifar - A. Sabbaghian, T. Farazmandfar, M. Golalipour, et al. - Scientific Reports, 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. - Nature Communications, 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. - Journal of Experimental Botany, 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

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments
S. Chen - F. Musat, H. Richnow, M. Krüger, et al. - Journal of Environmental Sciences, 2023

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. - Journal of Global Antimicrobial Resistance, 2023 usegalaxy.eu

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

<scp>MuDoGeR</scp>: <scp>Multi‐Domain</scp> Genome recovery from metagenomes made easy
U. Rocha - J. Coelho Kasmanas, R. Kallies, J. Saraiva, et al. - Molecular Ecology Resources, 2023

Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach
B. Mallol - J. Grzegorzewski, H. Tautenhahn, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 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. - Nature Communications, 2023 usegalaxy.eu

Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model
Y. Hodzhev - - Biotechnology &amp; Biotechnological Equipment, 2023 usegalaxy.eu

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

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, - Journal of Biomolecular Structure and Dynamics, 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. - Nature Microbiology, 2023 usegalaxy.eu

A rabies-related lyssavirus from a <i>Nycticeinops schlieffeni</i> bat with neurological signs, South Africa
N. Viljoen - A. Ismail, J. Weyer, W. Markotter, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

Exploring the potential of fluoro‐flavonoid derivatives as <scp>anti‐lung</scp> cancer agents: <scp>DFT</scp>, molecular docking, and molecular dynamics techniques
N. Esha - S. Quayum, M. Saif, M. Almatarneh, et al. - International Journal of Quantum Chemistry, 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. - International Journal of Cancer, 2023 usegalaxy.eu

Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins
S. Palecanda - E. Madrid, M. Porter, - Journal of Molecular Evolution, 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. - Nature Communications, 2023

Non-antibiotic drugs break colonization resistance against pathogenic<i>Gammaproteobacteria</i>
A. Grießhammer - J. de la Cuesta-Zuluaga, T. Zahir, P. Müller, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

RNA interaction format: a general data format for RNA interactions
R. Schäfer - D. Rabsch, G. Scholz, P. Stadler, et al. - Bioinformatics, 2023

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

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

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

Individual-level deviations from normative brain morphology in violence, psychosis, and psychopathy
U. Haukvik - T. Wolfers, N. Tesli, C. Bell, et al. - medRxiv - Cold Spring Harbor Laboratory, 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. - Neuro-Oncology, 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 in Plant Science, 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 in Plant Science, 2023

Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins
G. Farmiloe - E. van Bree, S. Robben, L. Janssen, et al. - Genome Biology and Evolution, 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. - International Journal of Legal Medicine, 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. - Parasites &amp; Vectors, 2023 usegalaxy.eu

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. - Nature Communications, 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. - Molecular Genetics and Genomics, 2023 usegalaxy.eu

A Galaxy of informatics resources for MS-based proteomics
S. Mehta - M. Bernt, M. Chambers, M. Fahrner, et al. - Expert Review of Proteomics, 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. - Applied Soil Ecology, 2023 usegalaxy.eu

Pangenome graph layout by Path-Guided Stochastic Gradient Descent
S. Heumos - A. Guarracino, J. Schmelzle, J. Li, et al. - bioRxiv - Cold Spring Harbor Laboratory, 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. - Acta Microbiologica et Immunologica Hungarica, 2023 usegalaxy.eu

Complete genome sequence of a human bacteremia isolate of <i>Kalamiella piersonii</i>
M. Howard - J. Maki, S. Connelly, D. Hardy, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia
N. Mathlouthi - H. Oumarou Hama, I. Belguith, S. Charfi, et al. - Current Issues in Molecular Biology, 2023 usegalaxy.eu

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. - Plant Biotechnology Reports, 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 - Cold Spring Harbor Laboratory, 2023

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. - International Journal of Molecular Sciences, 2023 usegalaxy.eu

Distribution, inducibility, and characteristics of <i>Latilactobacillus curvatus</i> temperate phages
C. Ambros - M. Ehrmann, - Microbiome Research Reports, 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 in Plant Science, 2023

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. - Comparative Immunology, Microbiology and Infectious Diseases, 2023 usegalaxy.eu

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

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

Bridging the gap in African biodiversity genomics and bioinformatics
A. Sharaf - C. Ndiribe, T. Omotoriogun, L. Abueg, et al. - Nature Biotechnology, 2023 usegalaxy.eu

Transcription factors operate on a limited vocabulary of binding motifs in<i>Arabidopsis thaliana</i>
S. Zenker - D. Wulf, A. Meierhenrich, S. Becker, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Precision Genome Engineering in <i>Streptococcus suis</i> Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
A. Gussak - M. Ferrando, M. Schrama, P. van Baarlen, et al. - ACS Synthetic Biology, 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. - Scientific Reports, 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. - Microbiology Spectrum, 2023 usegalaxy.eu

Regional, circuit and network heterogeneity of brain abnormalities in psychiatric disorders
A. Segal - L. Parkes, K. Aquino, S. Kia, et al. - Nature Neuroscience, 2023

A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome
J. Wang - B. Chew, Y. Lai, H. Dong, et al. - Nature Protocols, 2023 usegalaxy.eu

Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study
M. Fischer - T. Küstner, S. Pappa, T. Niendorf, et al. - BMC Medical Imaging, 2023

Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning
A. Hawkins-Hooker - G. Visonà, T. Narendra, M. Rojas-Carulla, et al. - Nature Communications, 2023

A translational regulator MHZ9 modulates ethylene signaling in rice
Y. Huang - J. Han, B. Ma, W. Cao, et al. - Nature Communications, 2023 usegalaxy.eu

A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell
M. Deepa Maheshvare - S. Raha, M. König, D. Pal, et al. - Frontiers in Endocrinology, 2023

Pathovar-Specific PCR Method for Detection and Identification of <i>Xanthomonas translucens</i> pv. <i>undulosa</i>
H. Alvandi - S. Taghavi, M. Khojasteh, T. Rahimi, et al. - Plant Disease, 2023 usegalaxy.eu

A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (<i>Rissa tridactyla</i>), a Declining Circumpolar Seabird
M. Sozzoni - J. Ferrer Obiol, G. Formenti, A. Tigano, et al. - Genome Biology and Evolution, 2023 usegalaxy.eu

Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet
R. Hu - X. Li, Y. Hu, R. Zhang, et al. - Cell, 2023

The design of functional proteins using tensorized energy calculations
K. Maksymenko - A. Maurer, N. Aghaallaei, C. Barry, et al. - Cell Reports Methods, 2023

Insight into the nodal cells transcriptome of the streptophyte green alga <i>Chara braunii</i> S276
D. Heß - A. Holzhausen, W. Hess, - Physiologia Plantarum, 2023 usegalaxy.eu

Proteogenomic data and resources for pan-cancer analysis
Y. Li - Y. Dou, F. Da Veiga Leprevost, Y. Geffen, et al. - Cancer Cell, 2023 usegalaxy.eu

Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage
C. Beck - D. Ramanujam, P. Vaccarello, F. Widenmeyer, et al. - Nature Communications, 2023 usegalaxy.eu

Combination of two rare mutations in the SARS-CoV-2 M gene in patients with severe and prolonged COVID-19
A. Trifonova - A. Syarov, S. Takov, K. Angelov, et al. - Infectious Diseases, 2023 usegalaxy.eu

Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae)
I. Batista da Silva - D. Aciole Barbosa, K. Kavalco, L. Nunes, et al. - Scientific Reports, 2023 usegalaxy.eu

Unified fate mapping in multiview single-cell data
P. Weiler - M. Lange, M. Klein, D. Pe’er, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa
K. Farias - M. Ferreira, G. Amaral, M. Zugaib, et al. - International Journal of Molecular Sciences, 2023 usegalaxy.eu

Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
A. Grigorjew - A. Gynter, F. Dias, B. Buchfink, et al. - Genome Biology, 2023

Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans
F. Xu - R. Li, E. von Gromoff, F. Drepper, et al. - Nature Communications, 2023 usegalaxy.eu

Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil
C. Camargo - A. Yamada, A. Souza, M. Lima, et al. - Pathogens, 2023 usegalaxy.eu

Integrative meta-omics in Galaxy and beyond
V. Schiml - F. Delogu, P. Kumar, B. Kunath, et al. - Environmental Microbiome, 2023 usegalaxy.eu

Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells
S. Fischer - V. Trinh, C. Simon, L. Weber, et al. - Cell Chemical Biology, 2023 usegalaxy.eu

EODIE — Earth Observation Data Information Extractor
S. Wittke - A. Fouilloux, P. Lehti, J. Varho, et al. - SoftwareX, 2023 usegalaxy.eu

The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses
M. Lenz - A. Eichler, P. Kruse, C. Galanis, et al. - The Journal of Neuroscience, 2023 usegalaxy.eu

Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48
I. Sánchez-León - T. García-Martínez, S. Diene, E. Pérez-Nadales, et al. - Antibiotics, 2023 usegalaxy.eu

A biologist’s guide to planning and performing quantitative bioimaging experiments
R. Senft - B. Diaz-Rohrer, P. Colarusso, L. Swift, et al. - PLOS Biology, 2023 usegalaxy.eu

Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
A. Guerler - D. Baker, M. van den Beek, B. Gruening, et al. - BMC Bioinformatics, 2023 usegalaxy.eu

Identification of annotation artifacts concerning the chalcone synthase (CHS)
M. Bartas - A. Volna, J. Cerven, B. Pucker, et al. - BMC Research Notes, 2023

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
M. Potgieter - A. Nel, S. Fortuin, S. Garnett, et al. - PLOS Computational Biology, 2023 usegalaxy.eu

The autoPET challenge: Towards fully automated lesion segmentation in oncologic PET/CT imaging
S. Gatidis - M. Früh, M. Fabritius, S. Gu, et al. - Research Square - Research Square Platform LLC, 2023

Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone
V. Voronezhskaya - P. Volkova, S. Bitarishvili, E. Shesterikova, et al. - Plants, 2023 usegalaxy.eu

A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland
A. Fernandez-Guerra - G. Borrel, T. Delmont, B. Elberling, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut
I. Bazukyan - D. Georgieva-Miteva, T. Velikova, S. Dimov, et al. - Insects, 2023 usegalaxy.eu

Su(Hw) interacts with Combgap to establish long-range chromatin contacts
N. Vorobyeva - A. Krasnov, M. Erokhin, D. Chetverina, et al. - Research Square - Research Square Platform LLC, 2023 usegalaxy.eu

Genetic factors explaining anthocyanin pigmentation differences
M. Recinos - B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2023

MR-DNA: Flexible 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification
W. Zeng - D. Huson, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Ribosome profiling reveals the fine-tuned response of<i>Escherichia coli</i>to mild and severe acid stress
K. Schumacher - R. Gelhausen, W. Kion-Crosby, L. Barquist, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması
Ö. ILIKKAN - - Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2023 usegalaxy.eu

A Roadmap for the Human Gut Cell Atlas
M. Zilbauer - K. James, M. Kaur, S. Pott, et al. - Nature Reviews Gastroenterology &amp; Hepatology, 2023 usegalaxy.eu

CpG DNA methylation changes during epididymal sperm maturation in bulls
E. Capra - F. Turri, B. Lazzari, S. Biffani, et al. - Epigenetics &amp; Chromatin, 2023 usegalaxy.eu

SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022
K. Subramoney - N. Mtileni, A. Davis, J. Giandhari, et al. - PLOS ONE, 2023 usegalaxy.eu

Species Delineation and Comparative Genomics within the<i>Campylobacter ureolyticus</i>Complex
J. Maki - M. Howard, S. Connelly, M. Pettengill, et al. - Journal of Clinical Microbiology, 2023 usegalaxy.eu

β-Cell–Specific <i>E2f1</i> Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
F. Oger - C. Bourouh, M. Friano, E. Courty, et al. - Diabetes, 2023 usegalaxy.eu

<i>De Novo</i> Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
M. Livingstone - P. Jorgensen, M. McCall, J. Thomson, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
L. Whitmore - M. McCauley, J. Farrell, M. Stammnitz, et al. - Nature Ecology &amp; Evolution, 2023 usegalaxy.eu

Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte -<i>Alternaria burnsii</i>NCIM 1409
S. Natarajan - B. Pucker, S. Srivastava, - bioRxiv - Cold Spring Harbor Laboratory, 2023

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

MpoxRadar: a worldwide MPXV genomic surveillance dashboard
F. Nasri - K. Kongkitimanon, A. Wittig, J. Cortés, et al. - Nucleic Acids Research, 2023

Mapping cells through time and space with moscot
D. Klein - G. Palla, M. Lange, M. Klein, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
M. Schwabenland - O. Mossad, A. Sievert, A. Peres, et al. - Nature Communications, 2023 usegalaxy.eu

Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge
S. Williams - C. Back, E. Best, J. Mantell, et al. - Microbial Genomics, 2023 usegalaxy.eu

Genetic architecture of brain age and its causal relations with brain and mental disorders
E. Leonardsen - D. Vidal-Piñeiro, J. Roe, O. Frei, et al. - Molecular Psychiatry, 2023

A draft human pangenome reference
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - Nature, 2023

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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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. - Pathogens, 2023 usegalaxy.eu

Automatic annotation of the bHLH gene family in plants
C. Thoben - B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
U. Nunes da Rocha - J. Kasmanas, R. Toscan, D. Sanches, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
A. Othman - C. Liang, Y. Komma, M. Munz, et al. - Radiology, 2023

ODNA: identification of organellar DNA by machine learning
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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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
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Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
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Increasing complexity of opsin expression across stomatopod development
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How does particulate matter affect plant transcriptome and microbiome?
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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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Mapping lineage-traced cells across time points with moslin
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A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
J. Küttner - J. Grzegorzewski, H. Tautenhahn, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

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

Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion
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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
R. Spanò - S. Fortunato, V. Linsalata, I. D’Antuono, et al. - Plants, 2023 usegalaxy.eu

Building pangenome graphs
E. Garrison - A. Guarracino, S. Heumos, F. Villani, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

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, - Plant Systematics and Evolution, 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 in Energy Research, 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 in Energy Research, 2023

Proteome alterations in human autopsy tissues in relation to time after death
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The complete reference genome for grapevine (<i>Vitis vinifera</i>L.) 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)
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DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
H. Roux - S. Figueiredo, L. Sareoua, M. Salmona, et al. - Cell Reports Methods, 2023 usegalaxy.eu

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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External <scp>DNA</scp> 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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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. - Nature, 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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Sex-biased gene expression in nutrient-sensing pathways
S. Bennett-Keki - E. Fowler, L. Folkes, S. Moxon, et al. - Proceedings of the Royal Society B: Biological Sciences, 2023 usegalaxy.eu

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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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
A. Nathansen - K. Klein, B. Renard, M. Nowicka, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43
M. Herrera - M. Amundarain, J. Santos, - Archives of Biochemistry and Biophysics, 2023

Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease
M. do Carmo Santos - N. dos Santos Lopes, M. Ferreira, G. Amaral, et al. - Physiological and Molecular Plant Pathology, 2023 usegalaxy.eu

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
L. Liu - K. Han, H. Sun, L. Han, et al. - Briefings in Bioinformatics, 2023 usegalaxy.eu

MeganServer: facilitating interactive access to metagenomic data on a server
A. Gautam - W. Zeng, D. Huson, - Bioinformatics, 2023

Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru
M. Fernández-Díaz - A. Montalván-Avalos, G. Isasi-Rivas, D. Villanueva-Pérez, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
A. Hedhly - M. Guerra, J. Grimplet, J. Rodrigo, et al. - International Journal of Molecular Sciences, 2023 usegalaxy.eu

Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
A. de Jesus Bertani - T. Vieira, A. Reis, C. dos Santos, et al. - Scientific Reports, 2023 usegalaxy.eu

Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution
G. Arcari - R. Polani, F. Bruno, V. Capitani, et al. - Microbial Genomics, 2023 usegalaxy.eu

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. - Microorganisms, 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. - Nature Communications, 2023

MpoxRadar: a worldwide Mpox genomic surveillance dashboard
F. Nasri - K. Kongkitimanon, A. Wittig, J. Cortés, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera
V. Moris - L. Podsiadlowski, S. Martin, J. Oeyen, et al. - Communications Biology, 2023 usegalaxy.eu

Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach
F. Bartsch - J. Grzegorzewski, H. Pujol, H. Tautenhahn, et al. - medRxiv - Cold Spring Harbor Laboratory, 2023

Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression
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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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A Physcomitrella <scp>PIN</scp> protein acts in spermatogenesis and sporophyte retention
V. Lüth - C. Rempfer, N. van Gessel, O. Herzog, et al. - New Phytologist, 2023

Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
B. Buchfink - H. Ashkenazy, K. Reuter, J. Kennedy, et al. - bioRxiv - Cold Spring Harbor Laboratory, 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. - Parasites &amp; Vectors, 2023

The Full Genome Sequences of Pseudomonas sp. Strain MM221 and <i>Pseudoarthrobacter</i> sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
M. Eisenhut - M. Hawrylo, K. Trevlopoulou, H. Fingerhut, et al. - Microbiology Resource Announcements, 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. - JCI Insight, 2023 usegalaxy.eu

Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat
S. Annor - K. Salazar, S. Pillai, C. Kerth, et al. - Applied Microbiology, 2023 usegalaxy.eu

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 - Cold Spring Harbor Laboratory, 2023

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. - Communications Biology, 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, - Horticulture, Environment, and Biotechnology, 2023 usegalaxy.eu

Endosomal vesicle fusion machinery is involved with the contractile vacuole in <i>Dictyostelium discoideum</i>
P. Manna - L. Barlow, I. Ramirez-Macias, E. Herman, et al. - Journal of Cell Science, 2023 usegalaxy.eu

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. - Antibiotics, 2023 usegalaxy.eu

A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
G. Hattab - A. Anžel, S. Spänig, N. Neumann, et al. - NAR Genomics and Bioinformatics, 2023

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
E. Deutsch - J. Vizcaíno, A. Jones, P. Binz, et al. - Journal of Proteome Research, 2023

MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments
D. Kohler - M. Kaza, C. Pasi, T. Huang, et al. - Journal of Proteome Research, 2023 usegalaxy.eu

Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma
J. Wolf - T. Reinhard, R. Hajdu, G. Schlunck, et al. - Biomolecules, 2023 usegalaxy.eu

MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
W. Zeng - A. Gautam, D. Huson, - bioRxiv - Cold Spring Harbor Laboratory, 2023

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
A. Soorni - M. Karimi, B. Al Sharif, K. Habibi, et al. - BMC Plant Biology, 2023 usegalaxy.eu

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. - IEEE Signal Processing Magazine, 2023

CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway
K. Myacheva - A. Walsh, M. Riester, G. Pelos, et al. - Cancer Letters, 2023 usegalaxy.eu

RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.
O. Olagoke - A. Segatto, B. Afolabi, D. Ardisson-Araujo, et al. - Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 2023 usegalaxy.eu

The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves
B. Seckin Dinler - H. Cetinkaya, Z. Secgin, - Physiology and Molecular Biology of Plants, 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. - Plant Communications, 2023 usegalaxy.eu

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

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. - Computational and Structural Biotechnology Journal, 2023

A bibliometric analysis and visualization of spatially resolved transcriptomics
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DIAMOND +  MEGAN Microbiome Analysis
A. Gautam - W. Zeng, D. Huson, - Springer US, 2023

Avoiding Shortcut-Learning by Mutual Information Minimization in Deep Learning-Based Image Processing
L. Fay - E. Cobos, B. Yang, S. Gatidis, et al. - IEEE Access, 2023

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

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. - Cellular and Molecular Gastroenterology and Hepatology, 2023

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

Hybrid Genome Assembly of Short and Long Reads in Galaxy
T. Ohta - Y. Shiwa, - Springer US, 2023 usegalaxy.eu

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. - Journal of Veterinary Medical 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

Analysis of RNA Sequences and Modifications Using NASE
S. Wein - - Springer US, 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. - Informatics in Medicine Unlocked, 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. - Cellular and Molecular Gastroenterology and Hepatology, 2023 usegalaxy.eu

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. - Molecular Genetics and Genomics, 2022 usegalaxy.eu

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. - Molecular Genetics and Genomics, 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. - GigaScience, 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. - Scientific Reports, 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. - Nature Methods, 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. - Nucleic Acids Research, 2022 usegalaxy.eu

Better Together
S. Gatidis - T. Kart, M. Fischer, S. Winzeck, et al. - Investigative Radiology, 2022

Better Together
S. Gatidis - T. Kart, M. Fischer, S. Winzeck, et al. - Investigative Radiology, 2022

Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
S. Tajuddin - A. Khan, L. Chong, C. Wong, et al. - Applied Microbiology and Biotechnology, 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. - The ISME Journal, 2022 usegalaxy.eu

Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
A. Andersson - A. Behanova, C. Avenel, J. Windhager, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

MGnify: the microbiome sequence data analysis resource in 2023
L. Richardson - B. Allen, G. Baldi, M. Beracochea, et al. - Nucleic Acids Research, 2022

STAT3 signaling induced by IL-6 family cytokines modulates angiogenesis
J. Rapp - M. Jung, R. Klar, J. Wolf, et al. - Journal of Cell Science, 2022 usegalaxy.eu

Rapid detection and online analysis of microbial changes through flow cytometry
J. Kupschus - S. Janssen, A. Hoek, J. Kuska, et al. - Cytometry Part A, 2022

Renewal of planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction by benthic colonizers
R. Morard - C. Hassenrück, M. Greco, A. Fernandez-Guerra, et al. - Nature Communications, 2022

MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
M. Nata’ala - A. Avila Santos, J. Coelho Kasmanas, A. Bartholomäus, et al. - Environmental Microbiome, 2022

Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
M. Orantes-Bonilla - M. Makhoul, H. Lee, H. Chawla, et al. - Frontiers in Plant Science, 2022

Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink
S. Kim - C. Summage-West, M. Reyna, S. Kim, et al. - Microbiology Resource Announcements, 2022 usegalaxy.eu

Revisiting pangenome openness with k-mers
L. Parmigiani - R. Wittler, J. Stoye, - bioRxiv - Cold Spring Harbor Laboratory, 2022

Replication collisions induced by de-repressed S-phase transcription are connected with malignant transformation of adult stem cells
T. Zhang - C. Künne, D. Ding, S. Günther, et al. - Nature Communications, 2022 usegalaxy.eu

Small proteome of the nitrogen-fixing plant symbiont<i>Sinorhizobium meliloti</i>
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Antibiotics, 2022

Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
A. Afrizal - S. Jennings, T. Hitch, T. Riedel, et al. - Cell Host &amp; Microbe, 2022

Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium
J. Breidenbach - B. French, T. Gordon, A. Kleinhenz, et al. - Environment International, 2022 usegalaxy.eu

Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism
A. Soriano-Sexto - D. Gallego, F. Leal, N. Castejón-Fernández, et al. - International Journal of Molecular Sciences, 2022 usegalaxy.eu

Multi-histone ChIP-Seq Analysis with DecoDen
T. Narendra - G. Visonà, C. de Jesus Cardona, G. Schweikert, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
S. Beier - J. Werner, T. Bouvier, N. Mouquet, et al. - Frontiers in Microbiology, 2022

Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower
M. Gallus - I. Beer, N. Ivleva, M. Ehrmann, et al. - International Journal of Systematic and Evolutionary Microbiology, 2022 usegalaxy.eu

Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
J. Singh - H. Elhabashy, P. Muthukottiappan, M. Stepath, et al. - Nature Communications, 2022

Semi-automated assembly of high-quality diploid human reference genomes
E. Jarvis - G. Formenti, A. Rhie, A. Guarracino, et al. - Nature, 2022 usegalaxy.eu

Thin‐Plate Superstructures of the Immunogenic 33‐mer Gliadin Peptide
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A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use
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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 <i>Arabidopsis thaliana</i> telomeres
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Multivalent binding kinetics resolved by fluorescence proximity sensing
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A whole-body FDG-PET/CT Dataset with manually annotated Tumor Lesions
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Self-supervised learning for automated anatomical tracking in medical image data with minimal human labeling effort
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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
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Transgressive and parental dominant gene expression and cytosine methylation during seed development in<i>Brassica napus</i>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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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
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Biogenesis of <i>C. elegans</i> spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease
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Phased grapevine genome sequence of an<i>Rpv12</i>carrier for biotechnological exploration of resistance to<i>Plasmopara viticola</i>
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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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Genetic and genomic diversity in the sorghum gene bank collection of Uganda
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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
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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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MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
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Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
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Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
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KIPEs3: Automatic annotation of biosynthesis pathways
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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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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
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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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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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Structural analysis of microbiomes from salt caverns used for underground gas storage
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Sequence-based pangenomic core detection
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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 <i>APOE</i> 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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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
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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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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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Age-related brain deviations and aggression
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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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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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NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
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Critical Assessment of Metagenome Interpretation: the second round of challenges
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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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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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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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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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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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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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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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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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Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
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Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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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
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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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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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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
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SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
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Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
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Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
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Expanding the Galaxy’s reference data
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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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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Canonical Workflows to Make Data FAIR
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
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Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
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PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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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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Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
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LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
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Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
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Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
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Expression Atlas update: gene and protein expression in multiple species
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Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
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New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
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Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
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Peakhood: individual site context extraction for CLIP-seq peak regions
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The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
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ARTS-DB: a database for antibiotic resistant targets
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Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
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Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
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Automatic identification and annotation of MYB gene family members in plants
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Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
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Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
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TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
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Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
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Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
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Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
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OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
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Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
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Genomic impact of stress-induced transposable element mobility in Arabidopsis
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Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
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Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
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FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
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Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
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The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
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Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
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First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
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Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
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Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
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Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
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Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
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Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
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RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
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Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
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Single‐cell omics: Overview, analysis, and application in biomedical science
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Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
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Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in <i>Arabidopsis</i>
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Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
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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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Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
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The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
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Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
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A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
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De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
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A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
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Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
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Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
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Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
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Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
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Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
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Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis
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Age-Net: An MRI-Based Iterative Framework for Brain Biological Age Estimation
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ONT-Based Draft Genome Assembly and Annotation of <i>Alternaria atra</i>
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Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone
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Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
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DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
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Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
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Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy
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Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
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Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history
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RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
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Assessing the role of polygenic background on the penetrance of monogenic forms in Parkinson’s disease
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AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
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A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
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Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
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A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame
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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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COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints
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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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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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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
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Peptidotriazolamers Inhibit Aβ(1–42) Oligomerization and Cross a Blood‐Brain‐Barrier Model
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Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties
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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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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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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<i>Xist</i>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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Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (<i>Pimephales promelas</i>)
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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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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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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
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Large scale genomic rearrangements in selected <i>Arabidopsis thaliana</i> T-DNA lines are caused by T-DNA insertion mutagenesis
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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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Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
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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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Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa
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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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Decitabine Induces Gene Derepression on Monosomic Chromosomes: <i>In Vitro</i> and <i>In Vivo</i> Effects in Adverse-Risk Cytogenetics AML
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DenovoProfiling: a webserver for de novo generated molecule library profiling
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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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Detecting high-scoring local alignments in pangenome graphs
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
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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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Scarless engineering of the<i>Drosophila</i>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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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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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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Electroactive microorganisms in mouse feces
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Tool recommender system in Galaxy using deep learning
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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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MOSGA 2: Comparative genomics and validation tools
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RNA-Seq Data Analysis in Galaxy
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RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
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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 <i>Solanum chilense</i> reveal geographically structured major gene-mediated pathogen resistance
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Genomic analysis provides novel insights into diversification and taxonomy of<i>Allorhizobium vitis</i>(i.e.<i>Agrobacterium vitis</i>)
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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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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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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<i>C. elegans</i>
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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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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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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<i>Coxiella burnetii</i>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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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
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Next generation sequencing study on RNA viruses of<i>Vespa velutina</i>and<i>Apis mellifera</i>sharing the same foraging area
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High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh
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Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
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The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
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Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
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Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
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The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
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Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
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Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
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3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
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Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay
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Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
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Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
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Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
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tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
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Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
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Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
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Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
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Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
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Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
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Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
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Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
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Deep learning-based diatom taxonomy on virtual slides
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
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DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
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No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
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Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
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Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
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Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health
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pyGenomeTracks: reproducible plots for multivariate genomic datasets 
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Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates
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Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
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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
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A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
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Benchmarking challenging small variants with linked and long reads
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An Interactive Visualization for Feature Localization in Deep Neural Networks
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DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
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Genome‐wide cooperation of <scp>EMT</scp> transcription factor <scp>ZEB</scp> 1 with <scp>YAP</scp> and <scp>AP</scp> ‐1 in breast cancer
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The landscape of SARS-CoV-2 RNA modifications
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Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
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Lake expansion elevates equilibrium diversity via increasing colonization
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Enhanced COVID-19 data for improved prediction of survival
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Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
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ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
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Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
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Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
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Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
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<scp>GLASSgo</scp> in <scp>Galaxy</scp>: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
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The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
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Galactic Circos: User-friendly Circos plots within the Galaxy platform
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iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
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Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
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AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
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