Publications

As a de.NBI Cloud user you are able to add your publication to this list. Have a look at our wiki to find out how you can add your publications to this list. When doing so, please pay particular attention to the information on the desired type of citation.

Currently 1395 publications with reference to de.NBI Cloud are listed.

Recently added publication

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

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

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

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

De novo assembly and annotation of the pantranscriptome of Astyanax lacustris on the liver and pituitary-gonadal axis
D. Aciole Barbosa - G. Branco, A. Dal'Olio Gomes, C. Tolussi, et al. - Marine Genomics, 2025 usegalaxy.eu

Dataset of benthic foraminiferal community structure from sediment eDNA of Sundarbans mangrove ecosystem
A. Mandal - A. Ghosh, G. Kumar, P. Bhadury, et al. - Data in Brief, 2025 usegalaxy.eu

Expansion of SARS-CoV-2 mutations in patient with B-cell lymphoma and rare combination of ACE2, TLR4, DDX58 and IFIH1 variations: A retrospective analysis of the virus-host interplay
A. Trifonova - A. Yosifova, A. Syarov, A. Velichkov, et al. - Clinical Immunology Communications, 2025 usegalaxy.eu

Complete genome sequence of <i>Planococcus koreensis</i> isolated from soil in Fort Collins, Colorado
P. Gruber - A. Freedman, K. Malmstrom, B. Borlee, et al. - Microbiology Resource Announcements, 2025 usegalaxy.eu

Identification of <i>Toxoplasma gondii</i> antigenic proteins using an <i>in vivo</i> approach and <i>in silico</i> investigation of their polymorphism
J. Denis - C. Gommenginger, L. Beal, B. Cimon, et al. - Microbiology Spectrum, 2025 usegalaxy.eu

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

A homozygous human <i>WNT11</i> variant is associated with laterality, heart and renal defects
H. Berns - D. Weber, M. Haas, Z. Bakey, et al. - Disease Models &amp; Mechanisms, 2025 usegalaxy.eu

A transcriptional atlas of gut-innervating neurons reveals activation of interferon signaling and ferroptosis during intestinal inflammation
P. Forster - M. Jakob, D. Yusuf, M. Bubeck, et al. - Neuron, 2025

Social Cognition and Functional Connectivity in Early and Chronic Schizophrenia
S. Rutherford - C. Lasagna, S. Blain, A. Marquand, et al. - Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 2025

Imaging mass cytometry-based characterisation of fibroblast subsets and their cellular niches in systemic sclerosis
A. Rius Rigau - M. Liang, V. Devakumar, R. Neelagar, et al. - Annals of the Rheumatic Diseases, 2025

Characterization of Ribosome inactivating protein genes and their transcripts in Trialeurodes vaporariorum
W. Lapadula - M. Cañadas, M. Ayub, - Gene, 2025 usegalaxy.eu

Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules
A. Sliti - R. Kim, D. Lee, J. Shin, et al. - Microbial Pathogenesis, 2025 usegalaxy.eu

Coxsackievirus A24: A Causative Agent of Acute Haemorrhagic Conjunctivitis Outbreak in Dar es Salaam, Tanzania, between January and February 2024
L. Mapunda - P. van Heusden, R. Baluhya, O. Machange, et al. - medRxiv - Cold Spring Harbor Laboratory, 2025 usegalaxy.eu

Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities
A. Santos - M. Nunes, A. Filipa-Silva, V. Pimentel, et al. - International Journal of Environmental Research and Public Health, 2025 usegalaxy.eu

<i>Staphylococcus aureus</i> AgrA Modulators From South African Antimicrobial Plants
C. Aruwa - S. Sabiu, - Chemistry &amp; Biodiversity, 2025 usegalaxy.eu

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

The cytokinesis associated proteins CITK and ASPM-1 regulate neuronal microtubule dynamics and polarity in<i>C. elegans</i>
S. Sharma - K. Ponniah, A. Ghosh-Roy, - bioRxiv - Cold Spring Harbor Laboratory, 2025 usegalaxy.eu

Bakta Web – rapid and standardized genome annotation on scalable infrastructures
S. Beyvers - L. Jelonek, A. Goesmann, O. Schwengers, et al. - Nucleic Acids Research, 2025

Hangover regulates gene expression by limiting NSL-mediated H4K16 acetylation
J. Lenz - L. Schmelzer, I. Forné, A. Nist, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2025 usegalaxy.eu

Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations
I. Kampouris - T. Kuhl-Nagel, J. Behr, L. Sommermann, et al. - Research Square - Springer Science and Business Media LLC, 2025

Genome characterization, pathogenicity, and evaluation of therapeutics of Klebsiella aerogenes in Bombyx larvae infection model
T. Kabir - M. Hossain, T. Jepu, M. Sarker, et al. - BMC Microbiology, 2025 usegalaxy.eu

Closed genome sequence of <i>Fretibacterium fastidiosum</i> , a potential contributor to periodontal disease
A. Mori - M. Kudoh, M. Kuboniwa, C. Rückert-Reed, et al. - Microbiology Resource Announcements, 2025

Nucleotide-level characterization and improvement of <scp>l</scp>-arabinose- and <scp>l</scp>-rhamnose-inducible systems in <i>E. coli</i> using a high-throughput approach
N. Kim - D. Peng, N. Sandoval, - Nucleic Acids Research, 2025 usegalaxy.eu

Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer
T. Fullstone - H. Rohm, T. Kaltofen, S. Hierlmayer, et al. - NAR Cancer, 2025 usegalaxy.eu

Developmental pathways underlying sexual differentiation in the U/V sex chromosome system of giant kelp
D. Liesner - G. Cossard, M. Zheng, O. Godfroy, et al. - Developmental Cell, 2025

Olfactory specialization in the Senegalese sole (Solea senegalensis): CO2 acidified water triggers nostril-specific immune processes
R. Costa - P. Hubbard, M. Manchado, D. Power, et al. - Comparative Biochemistry and Physiology Part A: Molecular &amp; Integrative Physiology, 2025 usegalaxy.eu

Case–Control Study of Factors Associated with Hemolytic Uremic Syndrome among Shiga Toxin–Producing <i>Escherichia coli</i> Patients, Ireland, 2017–2020
D. Espadinha - M. Brady, C. Brehony, D. Hamilton, et al. - Emerging Infectious Diseases, 2025 usegalaxy.eu

Mitochondrial Genomes of Three <i>Melampus</i> Species (Ellobiidae; Gastropoda)
T. Inäbnit - R. Tiedemann, A. Dennis, - Ecology and Evolution, 2025 usegalaxy.eu

Inspired by molecular dynamic simulation, exploring chemical constituents of alcoholic extract of <i>Garuga pinnata</i> computationally as inhibitors of GluN2B-containing NMDA receptors
J. Shinge - A. Muthal, V. Walhekar, C. Bagul, et al. - Journal of Biomolecular Structure and Dynamics, 2025 usegalaxy.eu

Novel tools for genomic modification and heterologous gene expression in the phylum Planctomycetota
T. Haufschild - J. Hammer, N. Rabold, V. Plut, et al. - Applied Microbiology and Biotechnology, 2025 usegalaxy.eu

Accelerated maturation of branched organoids confined in collagen droplets
I. Ruider - A. Pastucha, M. Raich, W. Xu, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2025 usegalaxy.eu

SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences
F. Kolesch - M. Sohn, A. Rempel, P. Hippel, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2025

Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages
A. Simonis - S. Theobald, A. Koch, R. Mummadavarapu, et al. - Molecular Systems Biology, 2025 usegalaxy.eu

Genome Skimming of Thysanoptera (Arthropoda, Insecta) and Its Taxonomic and Systematic Applications
E. Wahlberg - - Diversity, 2025 usegalaxy.eu

Facilitating Reproducibility in Catalysis Research with Managed Workflows and RO‐Crates: A Galaxy Case Study
A. Nieva de la Hidalga - L. Liborio, P. Austin, S. Devadasan, et al. - ChemCatChem, 2025 usegalaxy.eu

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

Discovery of a human parvovirus B19 analog (Erythroparvovirus) in cats
G. Lanave - F. Pellegrini, G. Diakoudi, C. Catella, et al. - Scientific Reports, 2025 usegalaxy.eu

First report of Moraxella oculi in Brazil in an infectious bovine keratoconjunctivitis outbreak
C. de Carvalho - R. Domingues, C. de Carvalho Coutinho, N. de Brito Silva Honório, et al. - Veterinary Research Communications, 2025 usegalaxy.eu

The complete mitochondrial genome of <i>Crocidura rapax</i> Allen, 1923 and its phylogenetic analyses
Z. Liu - L. Miao, Q. Guo, M. Han, et al. - Mitochondrial DNA Part B, 2025 usegalaxy.eu

The suberin transporter StABCG1 is required for barrier formation in potato leaves
E. Benatto Perino - U. Smolka, K. Gorzolka, R. Grützner, et al. - Scientific Reports, 2025 usegalaxy.eu

Isolation and characterization of fMGyn-Pae01, a phiKZ-like jumbo phage infecting Pseudomonas aeruginosa
K. Ranta - M. Skurnik, S. Kiljunen, - Virology Journal, 2025 usegalaxy.eu

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

RLB-MALBAC: a rapid, non-transposase method for synthesizing unbiased sequencing libraries from low amount of genomic DNA for Nanopore sequencing
V. Gadkar - D. Goldfarb, S. Dhaliwal, J. Gubbay, et al. - BMC Methods, 2025 usegalaxy.eu

The role of <scp>DNA</scp> content in shaping chromatin architecture and gene expression
A. Barragán‐Rosillo - R. Chávez Montes, L. Herrera‐Estrella, - The Plant Journal, 2025 usegalaxy.eu

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

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

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

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

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

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

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

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

A splice donor in <i>E6</i> influences keratinocyte immortalization by beta-HPV49
T. Rehm - T. Iftner, F. Stubenrauch, - Journal of Virology, 2025 usegalaxy.eu

Maternal PRDM10 activates essential genes for oocyte-to-embryo transition
M. Seah - B. Han, Y. Huang, L. Rasmussen, et al. - Nature Communications, 2025 usegalaxy.eu

SETD1A-dependent EME1 transcription drives PARPi sensitivity in HR deficient tumour cells
E. Sweatman - R. Bayley, R. Selemane, M. Higgs, et al. - British Journal of Cancer, 2025 usegalaxy.eu

Theoretical studies on safety and efficacy of 16 small-molecule MC4R antagonists as therapeutics for obesity
S. Joshi - R. Srivastava, - Journal of Proteins and Proteomics, 2025 usegalaxy.eu

Revealing the hidden diversity of Chlorella heliozoae-infecting giant viruses
L. Henriques - B. Botelho, R. Carlson, J. Carvalho, et al. - npj Viruses, 2025 usegalaxy.eu

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

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

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
L. Dony - A. Krontira, L. Kaspar, R. Ahmad, et al. - Science Advances, 2025

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

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

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

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

sORFdb – a database for sORFs, small proteins, and small protein families in bacteria
J. Hahnfeld - O. Schwengers, L. Jelonek, S. Diedrich, et al. - BMC Genomics, 2025

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

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

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

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

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

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

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

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

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

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

Mapping cells through time and space with moscot
D. Klein - G. Palla, M. Lange, M. Klein, et al. - Nature, 2025

<i>In silico</i> analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells
P. de la Cruz-Ojeda - E. Parras-Martínez, R. Rey-Pérez, J. Muntané, et al. - World Journal of Gastroenterology, 2025 usegalaxy.eu

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

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

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

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

Pharmacophore modeling and QSAR analysis of anti-HBV flavonols
B. Baei - P. Askari, F. Askari, S. Kiani, et al. - PLOS ONE, 2025 usegalaxy.eu

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

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

Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer
J. Perez - J. Duda, J. Ryu, M. Shetty, et al. - Scientific Reports, 2025 usegalaxy.eu

<i>Hairpin in a haystack</i>: <i>In silico</i> identification and characterization of plant-conserved microRNA in Rafflesiaceae
A. Wicaksono - K. Meitha, K. Wan, M. Mat Isa, et al. - Open Life Sciences, 2025 usegalaxy.eu

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

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

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

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

A type 4 resistant potato starch alters the cecal microbiome, gene expression and resistance to colitis in mice fed a Western diet based on NHANES data
E. Pletsch - H. Dawson, L. Cheung, J. Ragonese, et al. - Food &amp; Function, 2025 usegalaxy.eu

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

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

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

Enhanced biocompatibility of 3D printed resin parts <i>via</i> wet autoclave postprocessing: implications for stem cell organ-on-a-chip culture
A. Jönsson - A. Iatrou, L. Wildfang, D. Neumann, et al. - Materials Advances, 2025 usegalaxy.eu

Spatially informed phenotyping by cyclic-in-situ-hybridization identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis
Y. Li - T. Filla, A. Györfi, M. Liang, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Bacterial Communities, Pathogens, Resistomes, and Mobilomes Associated with a Wastewater Treatment Plant in Mexico: A Metagenomics Approach
O. Oyedara - C. Ruíz-Amaro, N. Heredia, S. García, et al. - International Journal of Environmental Research, 2024 usegalaxy.eu

Canonical androgen response element motifs are tumor suppressive regulatory elements in the prostate
X. Chen - M. Augello, D. Liu, K. Lin, et al. - Nature Communications, 2024 usegalaxy.eu

Enhanced sensitivity of <scp>TAPscan</scp> v4 enables comprehensive analysis of streptophyte transcription factor evolution
R. Petroll - D. Varshney, S. Hiltemann, H. Finke, et al. - The Plant Journal, 2024 usegalaxy.eu

RNA binding by Periphilin plays an essential role in initiating silencing by the HUSH complex
S. Bloor - N. Wit, P. Lehner, - Nucleic Acids Research, 2024 usegalaxy.eu

ATP-Gated P2X7-Ion Channel on Kidney-Resident Natural Killer T Cells and Memory T Cells in Intrarenal Inflammation
M. Junge - N. Liaukouskaya, N. Schwarz, C. Pinto-Espinoza, et al. - Journal of the American Society of Nephrology, 2024 usegalaxy.eu

MHCquant2 refines immunopeptidomics tumor antigen discovery
J. Scheid - S. Lemke, N. Hoenisch-Gravel, A. Dengler, et al. - Research Square - Springer Science and Business Media LLC, 2024

PCI-DB: A novel primary tissue immunopeptidome database to guide next-generation peptide-based immunotherapy development
S. Lemke - M. Dubbelaar, P. Zimmermann, J. Bauer, et al. - Research Square - Springer Science and Business Media LLC, 2024

Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases
C. Rempfer - S. Hoernstein, N. van Gessel, A. Graf, et al. - Computational and Structural Biotechnology Journal, 2024

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, 2024

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

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

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

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

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

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

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

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

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

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

Panacus: fast and exact pangenome growth and core size estimation
L. Parmigiani - E. Garrison, J. Stoye, T. Marschall, et al. - Bioinformatics, 2024

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

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

Plant Thermosensors
J. Casal - G. Murcia, L. Bianchimano, - Annual Review of Genetics, 2024 usegalaxy.eu

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

An integrated transcriptomic cell atlas of human neural organoids
Z. He - L. Dony, J. Fleck, A. Szałata, et al. - Nature, 2024

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

Genomics and evolutionary analysis of <i>Chlorella variabilis-</i> infecting viruses demarcate criteria for defining species of giant viruses
J. Carvalho - R. Carlson, J. Ghosh, V. Queiroz, et al. - Journal of Virology, 2024 usegalaxy.eu

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

Deciphering the molecular logic of WOX5 function in the root stem cell organizer
N. Zhang - P. Bitterli, P. Oluoch, M. Hermann, et al. - The EMBO Journal, 2024 usegalaxy.eu

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

Complete genome sequences of <i>Chitinophaga</i> sp. strain MM2321 and <i>Microbacterium</i> sp. strain MM2322, isolated from a sand sample in Harsewinkel, Germany
M. Eisenhut - T. Schulze, F. Matten, A. Sengewald, et al. - Microbiology Resource Announcements, 2024

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

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

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

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

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization
P. Liu - J. Vigneau, R. Craig, J. Barrera-Redondo, et al. - Nature Communications, 2024

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

The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation
K. Yu - G. Wang, S. Guo, F. Bassermann, et al. - EMBO Reports, 2024 usegalaxy.eu

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

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

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

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

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

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

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

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

Mitogenome of a new Ramazzottius species (Tardigrada: Eutardigrada: Ramazzottiidae) discovered in rock pools along with its temperature and desiccation-related proteins repertoire
M. Vecchi - D. Stec, - Organisms Diversity &amp; Evolution, 2024 usegalaxy.eu

Changes in growth, lanthanide binding, and gene expression in <i>Pseudomonas alloputida</i> KT2440 in response to light and heavy lanthanides
L. Gorniak - S. Bucka, B. Nasr, J. Cao, et al. - mSphere, 2024

The multifaceted role of mitochondria in cardiac function: insights and approaches
S. Ravindran - C. Rau, - Cell Communication and Signaling, 2024 usegalaxy.eu

Glut3 promotes cellular O-GlcNAcylation as a distinctive tumor-supportive feature in Treg cells
A. Sharma - G. Sharma, Z. Gao, K. Li, et al. - Cellular &amp; Molecular Immunology, 2024

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

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

Epigenetic modulation via the C-terminal tail of H2A.Z
L. Imre - P. Nánási, I. Benhamza, K. Enyedi, et al. - Nature Communications, 2024 usegalaxy.eu

A transcriptomic hourglass in brown algae
J. Lotharukpong - M. Zheng, R. Luthringer, D. Liesner, et al. - Nature, 2024

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

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

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

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery
U. Rocha - J. Kasmanas, R. Toscan, D. Sanches, et al. - PLOS Computational Biology, 2024

In-Silico Perspectives on the Potential Therapeutic Aids of Hesperetin Derivatives for Lung Cancer
A. Asiri - - Advancements in Life Sciences, 2024 usegalaxy.eu

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

Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome
L. Pyöriä - D. Pratas, M. Toppinen, P. Simmonds, et al. - Nucleic Acids Research, 2024 usegalaxy.eu

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

Mapping lineage-traced cells across time points with moslin
M. Lange - Z. Piran, M. Klein, B. Spanjaard, et al. - Genome Biology, 2024

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

JunB is required for CD8+ T cell responses to acute infections
S. Sarkar - N. Taira, T. Hsieh, H. Chien, et al. - International Immunology, 2024 usegalaxy.eu

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

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

Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations
V. Pham - C. Rödel, M. Valentino, M. Malinverno, et al. - EMBO Molecular Medicine, 2024 usegalaxy.eu

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

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

Artificial intelligence-enhanced detection of subclinical coronary artery disease in athletes: diagnostic performance and limitations
J. Kübler - J. Brendel, T. Küstner, J. Walterspiel, et al. - The International Journal of Cardiovascular Imaging, 2024

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

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

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

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

A snapshot of the Physcomitrella N-terminome reveals N-terminal methylation of organellar proteins
S. Hoernstein - A. Schlosser, K. Fiedler, N. van Gessel, et al. - Plant Cell Reports, 2024

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

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

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

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

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

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

miRNA-mediated gene silencing in Drosophila larval development involves GW182-dependent and independent mechanisms
E. Matsuura-Suzuki - K. Kiyokawa, S. Iwasaki, Y. Tomari, et al. - The EMBO Journal, 2024 usegalaxy.eu

EXCRETE workflow enables deep proteomics of the microbial extracellular environment
D. Russo - D. Oliinyk, G. Pohnert, F. Meier, et al. - Communications Biology, 2024 usegalaxy.eu

Unravelling the main genomic features of Mycoplasma equirhinis
M. Martineau - C. Ambroset, S. Lefebvre, É. Kokabi, et al. - BMC Genomics, 2024 usegalaxy.eu

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

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

Evidence for phosphate-dependent control of symbiont cell division in the model anemone <i>Exaiptasia diaphana</i>
N. Faulstich - A. Deloach, Y. Ksor, G. Mesa, et al. - mBio, 2024 usegalaxy.eu

DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing
M. Kristen - M. Lander, L. Kilz, L. Gleue, et al. - Nucleic Acids Research, 2024 usegalaxy.eu

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

Nanopore sequencing of IPNV vp2 gene in Peruvian Andean trout ( <i>Oncorhynchus mykiss</i> ) cultures
S. Tapia - J. Orellana, Y. Duran, J. Rodriguez, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

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

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

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

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

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

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

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

Gene expression networks in endothelial cells from failing human hearts
L. Wirth - E. Erny, M. Krane, H. Lahm, et al. - American Journal of Physiology-Heart and Circulatory Physiology, 2024 usegalaxy.eu

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

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

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

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

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

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

Viral hijacking of hnRNPH1 unveils a G-quadruplex-driven mechanism of stress control
P. Schult - B. Kümmerer, M. Hafner, K. Paeschke, et al. - Cell Host &amp; Microbe, 2024 usegalaxy.eu

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

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

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR
N. Choudhary - B. Pucker, - PLOS ONE, 2024

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

Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species
A. Uncu - A. Patat, A. Uncu, - Functional &amp; Integrative Genomics, 2024 usegalaxy.eu

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

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

Coordinated metabolic adaptation of <i>Arabidopsis thaliana</i> to high light
G. Balcke - K. Vahabi, J. Giese, I. Finkemeier, et al. - The Plant Journal, 2024 usegalaxy.eu

Inference of Host–Pathogen Interaction Matrices from Genome-Wide Polymorphism Data
H. Märkle - S. John, L. Metzger, . , et al. - Molecular Biology and Evolution, 2024

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

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

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

Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
M. Hoshino - G. Cossard, F. Haas, E. Kane, et al. - Nature Ecology &amp; Evolution, 2024

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

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

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

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

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

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

Genomic Evaluation of Multidrug-Resistant Extended-Spectrum β-Lactamase (ESBL)-Producing <i>Escherichia coli</i> from Irrigation Water and Fresh Produce in South Africa: A Cross-Sectional Analysis
L. Richter - S. Duvenage, E. du Plessis, T. Msimango, et al. - Environmental Science &amp; Technology, 2024 usegalaxy.eu

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing
A. Sime - B. Kifle, A. Woldesemayat, M. Gemeda, et al. - BMC Microbiology, 2024 usegalaxy.eu

Attention-Aware Non-Rigid Image Registration for Accelerated MR Imaging
A. Ghoul - J. Pan, A. Lingg, J. Kübler, et al. - IEEE Transactions on Medical Imaging, 2024

Biofoams with untapped enzymatic potential produced from beer bagasse by indigenous fungal strains
C. Aguirre Pranzoni - J. Bonilla, Á. Carrillo, M. López-Vidal, et al. - Bioresource Technology, 2024 usegalaxy.eu

Acute Hypoxia Does Not Alter Tumor Sensitivity to FLASH Radiation Therapy
R. Leavitt - A. Almeida, V. Grilj, P. Montay-Gruel, et al. - International Journal of Radiation Oncology*Biology*Physics, 2024 usegalaxy.eu

Differences in activity and stability drive transposable element variation in tropical and temperate maize
S. Ou - A. Scheben, T. Collins, Y. Qiu, et al. - Genome Research, 2024 usegalaxy.eu

Bioelectrochemical protein production valorising NH3-rich pig manure-derived wastewater and CO2 from anaerobic digestion
G. Soggia - A. Goglio, P. Cristiani, I. Luciani, et al. - Renewable Energy, 2024 usegalaxy.eu

Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks
T. Hauffe - J. Cantalapiedra, D. Silvestro, - Science Advances, 2024

Prostaglandin D2 receptor 2 downstream signaling and modulation of type 2 innate lymphoid cells from patients with asthma
C. Gress - M. Fuchs, S. Carstensen-Aurèche, M. Müller, et al. - PLOS ONE, 2024 usegalaxy.eu

Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
S. Godbole - H. Voß, A. Gocke, S. Schlumbohm, et al. - Nature Communications, 2024 usegalaxy.eu

An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease
M. Kruk - S. Mehta, K. Murray, L. Higgins, et al. - mSystems, 2024 usegalaxy.eu

Trusted Research Environments: Analysis of Characteristics and Data Availability
M. Weise - A. Rauber, - International Journal of Digital Curation, 2024 usegalaxy.eu

Sulcation in children with autism spectrum disorders
S. Burckard - I. Dupong, Y. Leprince, C. Fischer, et al. - Research Square - Springer Science and Business Media LLC, 2024

Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations
N. Tyborski - T. Koehler, F. Steiner, S. Tung, et al. - Frontiers in Microbiology, 2024

Transcription Factor 23 is an Essential Determinant of Murine Term Parturition
F. Minisy - H. Shawki, T. Fujita, A. Moustafa, et al. - Molecular and Cellular Biology, 2024 usegalaxy.eu

Spotlight on Secondary Metabolites Produced by an Early-Flowering Apulian Artichoke Ecotype Sanitized from Virus Infection by Meristem-Tip-Culture and Thermotherapy
R. Spanò - P. Gena, V. Linsalata, V. Sini, et al. - Antioxidants, 2024 usegalaxy.eu

Cytochrome <scp>P450 2J2</scp> is required for the natural compound austocystin D to elicit cancer cell toxicity
Y. Kojima - S. Fujieda, L. Zhou, M. Takikawa, et al. - Cancer Science, 2024 usegalaxy.eu

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis
Y. He - H. Zhao, Y. Wang, C. Qu, et al. - BMC Genomics, 2024 usegalaxy.eu

ProSwats: A Proxy-based Scientific Workflow Retrieval Approach by Bridging the Gap between Textual and Structural Semantics
Y. Gu - J. Cao, S. Qian, N. Zhu, et al. - IEEE, 2024 usegalaxy.eu

Decoding the language of chromatin modifications with MARCS
A. Tvardovskiy - S. Lukauskas, - Nature Reviews Genetics, 2024

Biodiversity and potential functionality of biofilm-sediment biotope in La Muerte lagoon, Monegros Desert, Spain
M. Berlanga - P. Picart, A. Blasco, R. Benaiges-Fernandez, et al. - Frontiers in Ecology and Evolution, 2024 usegalaxy.eu

Identification and Characterization of ATOH7-Regulated Target Genes and Pathways in Human Neuroretinal Development
D. Atac - K. Maggi, S. Feil, J. Maggi, et al. - Cells, 2024 usegalaxy.eu

ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists
R. Sethi - K. Ang, M. Li, Y. Long, et al. - Nature Communications, 2024 usegalaxy.eu

Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle
E. Skalon - N. Panyushev, O. Podgornaya, A. Smolyaninova, et al. - Non-Coding RNA, 2024 usegalaxy.eu

The effect of successive summer drought periods on bacterial diversity along a plant species richness gradient
Y. de Souza - R. Siani, C. Albracht, Y. Huang, et al. - FEMS Microbiology Ecology, 2024 usegalaxy.eu

Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil
B. Kifle - A. Sime, M. Gemeda, A. Woldesemayat, et al. - Scientific Reports, 2024 usegalaxy.eu

Complete mitochondrial genomes of Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua (Diptera: Tephritidae) and their phylogenetic relationships with other congeners
H. Yong - S. Song, K. Chua, Y. Liew, et al. - Arthropod Systematics &amp; Phylogeny, 2024 usegalaxy.eu

Pangenome graph layout by Path-Guided Stochastic Gradient Descent
S. Heumos - A. Guarracino, J. Schmelzle, J. Li, et al. - Bioinformatics, 2024

Genomic prediction in <i>Brassica napus</i>: evaluating the benefit of imputed whole-genome sequencing data
S. Weber - L. Roscher-Ehrig, T. Kox, A. Abbadi, et al. - Genome, 2024

Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417
T. Ercole - V. Kava, D. Petters-Vandresen, R. Ribeiro, et al. - Current Microbiology, 2024 usegalaxy.eu

Deciphering the Key Players of the Bacterial Microbiota Associated with Aerial Crown Gall Tumors on Rhododendron: Insights into the Gallobiome
N. Kuzmanović - J. Nesme, J. Wolf, M. Neumann-Schaal, et al. - Phytobiomes Journal, 2024

Motion-Compensated MR CINE Reconstruction With Reconstruction-Driven Motion Estimation
J. Pan - W. Huang, D. Rueckert, T. Küstner, et al. - IEEE Transactions on Medical Imaging, 2024

Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms
L. Schäfer - J. Jehle, R. Kleespies, J. Wennmann, et al. - Journal of Invertebrate Pathology, 2024

Characterization of a highly thermostable recombinant xylanase from Anoxybacillus ayderensis
Z. Akpinar - H. Karaoglu, - Protein Expression and Purification, 2024 usegalaxy.eu

Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient
R. AlJindan - N. Mahmoud, D. AlEraky, N. Almandil, et al. - Journal of Infection and Public Health, 2024 usegalaxy.eu

A reproducible workflow for assembling the mitochondrial genome of <i>Acheta domesticus</i> (Orthoptera: Gryllidae)
S. Homchan - W. Kutanan, Y. Gupta, - Ecology and Evolution, 2024 usegalaxy.eu

Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation
P. Sarkar - P. Gopi, P. Pandya, S. Paria, et al. - Heliyon, 2024 usegalaxy.eu

Meiotic maturation failure in primary ovarian insufficiency: insights from a bovine model
S. Pietroforte - P. Dey, E. Ibáñez, A. Luciano, et al. - Journal of Assisted Reproduction and Genetics, 2024 usegalaxy.eu

Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java
C. Bielow - N. Hoffmann, D. Jimenez-Morales, T. Van Den Bossche, et al. - Journal of the American Society for Mass Spectrometry, 2024

Overview of transcriptome changes and phenomic profile of sanitized artichoke vis‐à‐vis non‐sanitized plants
R. Spanò - A. Petrozza, S. Summerer, S. Fortunato, et al. - Plant Biology, 2024 usegalaxy.eu

First Indonesian report of WGS-based MTBC L3 discovery
Y. Rukminiati - F. Mesak, D. Lolong, P. Sudarmono, et al. - BMC Research Notes, 2024 usegalaxy.eu

Iron Chelation in Soil: Scalable Biotechnology for Accelerating Carbon Dioxide Removal by Enhanced Rock Weathering
D. Epihov - S. Banwart, S. McGrath, D. Martin, et al. - Environmental Science &amp; Technology, 2024 usegalaxy.eu

Generation of functionally active resident macrophages from adipose tissue by 3D cultures
A. Arlat - M. Renoud, J. Nakhle, M. Thomas, et al. - Frontiers in Immunology, 2024 usegalaxy.eu

Wall-Associated Kinase (WAK) and WAK-like Kinase Gene Family in Sugar Beet: Genome-Wide Characterization and In Silico Expression Analysis in Response to Beet Cyst Nematode (Heterodera schachtii Schmidt) Infection
J. Hamdi - N. Kmeli, I. Bettaieb, D. Bouktila, et al. - Journal of Plant Growth Regulation, 2024 usegalaxy.eu

Exploring the biotechnological potential of novel soil-derived Klebsiella sp. and Chryseobacterium sp. strains using phytate as sole carbon source
J. Maldonado-Pava - V. Tapia-Perdomo, L. Estupinan-Cardenas, E. Puentes-Cala, et al. - Frontiers in Bioengineering and Biotechnology, 2024 usegalaxy.eu

Path-based reasoning for biomedical knowledge graphs with BioPathNet
Y. Hu - S. Oleshko, S. Firmani, Z. Zhu, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily<i>Victoria cruziana</i>
M. Nowak - B. Harder, S. Meckoni, R. Friedhoff, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Nodulating Aeschynomene indica without Nod Factor Synthesis Genes: In Silico Analysis of Evolutionary Relationship
M. Zhao - J. Dong, Z. Zhang, E. Wang, et al. - Agronomy, 2024 usegalaxy.eu

DeepNeo: Deep Learning for neointimal tissue characterization using optical coherence tomography
V. Koch - O. Holmberg, E. Blum, E. Sancar, et al. - medRxiv - Cold Spring Harbor Laboratory, 2024

CellRank 2: unified fate mapping in multiview single-cell data
P. Weiler - M. Lange, M. Klein, D. Pe’er, et al. - Nature Methods, 2024

The genomic and phylogenetic analysis of <i>Marseillevirus cajuinensis</i> raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization
B. de Azevedo - V. Queiroz, I. de Aquino, T. Machado, et al. - Journal of Virology, 2024 usegalaxy.eu

Complete genome sequence of the <i>Microbacterium enclense</i> bacteriophage phiMiGM15
E. Camacho-Beltrán - J. Morales-Aguilar, M. López-Meyer, G. Rincón-Enríquez, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

Examining Transcriptomic Alterations in Rat Models of Intracerebral Hemorrhage and Severe Intracerebral Hemorrhage
S. Thangameeran - S. Tsai, H. Liew, C. Pang, et al. - Biomolecules, 2024 usegalaxy.eu

Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation: a novel adjuvant option?
S. Heine - F. Alessandrini, J. Grosch, C. Graß, et al. - Frontiers in Immunology, 2024 usegalaxy.eu

Partial hepatectomy accelerates colorectal metastasis by priming an inflammatory premetastatic niche in the liver
J. Luenstedt - F. Hoping, R. Feuerstein, B. Mauerer, et al. - Frontiers in Immunology, 2024 usegalaxy.eu

Genetic influence on vascular smooth muscle cell apoptosis
D. McVey - C. Andreadi, P. Gong, P. Stanczyk, et al. - Cell Death &amp; Disease, 2024 usegalaxy.eu

De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders
L. Jovović - J. Bedek, F. Malard, H. Bilandžija, et al. - Scientific Data, 2024 usegalaxy.eu

Nuclear position and local acetyl-CoA production regulate chromatin state
P. Willnow - A. Teleman, - Nature, 2024 usegalaxy.eu

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study
J. Pirnay - S. Djebara, G. Steurs, J. Griselain, et al. - Nature Microbiology, 2024 usegalaxy.eu

From genes to toxins: Profiling Prymnesium parvum during a riverine harmful algal bloom
D. Mora - M. Schlüsener, H. Fischer, J. Kleinteich, et al. - Harmful Algae, 2024

Altered socio-affective communication and amygdala development in mice with protocadherin10-deficient interneurons
T. Aerts - A. Boonen, L. Geenen, A. Stulens, et al. - Open Biology, 2024 usegalaxy.eu

Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies
A. Pustam - J. Jayaraman, A. Ramsubhag, - Journal of Global Antimicrobial Resistance, 2024 usegalaxy.eu

SmCYP71D373 of Salvia miltiorrhiza catalyzes the methyl oxidation reaction of tanshinone IIA-19 position
X. Qiu - Y. Zhang, Y. Luo, Y. Zhang, et al. - Industrial Crops and Products, 2024 usegalaxy.eu

Carbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain
R. Sabala - A. Fukuda, C. Nakajima, Y. Suzuki, et al. - Journal of Infection and Public Health, 2024 usegalaxy.eu

Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Isolate in Hawaii
A. Shipman - M. Tian, - Phytopathology®, 2024 usegalaxy.eu

Detection of KPC-216, a Novel KPC-3 Variant, in a Clinical Isolate of Klebsiella pneumoniae ST101 Co-Resistant to Ceftazidime-Avibactam and Cefiderocol
M. Giufrè - G. Errico, M. Del Grosso, M. Pagnotta, et al. - Antibiotics, 2024 usegalaxy.eu

JAK-2 V617F Mutation in Endothelial Cells of Patients with Atherosclerotic Carotid Disease
R. Diz-Küçükkaya - T. İyigün, Ö. Albayrak, C. Eker, et al. - Turkish Journal of Hematology, 2024 usegalaxy.eu

Robust Graph Pruning for Efficient Segmentation and Cluster Splitting of Cell Nuclei Using Deformable Shape Models
L. Kostrykin - K. Rohr, - IEEE, 2024 usegalaxy.eu

Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae
I. Kandinov - B. Shaskolskiy, D. Kravtsov, M. Filippova, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Elucidating the impact of Y chromosome microdeletions and altered gene expression on male fertility in assisted reproduction
N. Pazoki - M. Salehi, S. Angaji, M. Abdollahpour-Alitappeh, et al. - Human Molecular Genetics, 2024 usegalaxy.eu

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
R. Waterhouse - A. Adam-Blondon, B. Balech, E. Barta, et al. - F1000Research, 2024 usegalaxy.eu

Unveiling soil bacterial ecosystems in andean citrus orchards of Santander, Colombia
G. Castillo-Villamizar - V. Tapia-Perdomo, J. Maldonado-Pava, P. Santamaría-Gálvis, et al. - Frontiers in Ecology and Evolution, 2024 usegalaxy.eu

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs
R. Pachanon - N. Khine, N. Phumthanakorn, T. Wongsurawat, et al. - Frontiers in Veterinary Science, 2024 usegalaxy.eu

Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast
L. Deng - Y. Zhou, Z. Cai, J. Zhu, et al. - Science Advances, 2024 usegalaxy.eu

Divergence within the Taxon ‘Candidatus Phytoplasma asteris’ Confirmed by Comparative Genome Analysis of Carrot Strains
R. Toth - A. Ilic, B. Huettel, B. Duduk, et al. - Microorganisms, 2024 usegalaxy.eu

Apoplastomes of contrasting cacao genotypes to witches’ broom disease reveals differential accumulation of PR proteins
I. De Oliveira - S. Alves, M. Ferreira, A. Santos, et al. - Frontiers in Plant Science, 2024 usegalaxy.eu

Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
L. Dossmann - M. Emperle, M. Dukatz, A. de Mendoza, et al. - Communications Biology, 2024 usegalaxy.eu

Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response
C. Ehle - A. Iyer-Bierhoff, Y. Wu, S. Xing, et al. - Communications Biology, 2024 usegalaxy.eu

Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca)
M. López - B. Denoyes, E. Bucher, - BMC Plant Biology, 2024 usegalaxy.eu

A practical guide to bioimaging research data management in core facilities
C. Schmidt - T. Boissonnet, J. Dohle, K. Bernhardt, et al. - Journal of Microscopy, 2024 usegalaxy.eu

First Isolation of the Heteropathotype Shiga Toxin-Producing and Extra-Intestinal Pathogenic (STEC-ExPEC) E. coli O80:H2 in French Healthy Cattle: Genomic Characterization and Phylogenetic Position
N. Soleau - S. Ganet, S. Werlen, L. Collignon, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Modeling brain sex in the limbic system as phenotype for female-prevalent mental disorders
G. Matte Bon - D. Kraft, E. Comasco, B. Derntl, et al. - Biology of Sex Differences, 2024

Cluster efficient pangenome graph construction with nf-core/pangenome
S. Heumos - M. Heuer, F. Hanssen, L. Heumos, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression
C. Bode - S. Preissl, L. Hein, A. Lother, et al. - Intensive Care Medicine Experimental, 2024 usegalaxy.eu

Reduction of APOE accounts for neurobehavioral deficits in fetal alcohol spectrum disorders
H. Hwang - S. Yamashita, Y. Matsumoto, M. Ito, et al. - Molecular Psychiatry, 2024 usegalaxy.eu

Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp
O. Edet - B. Ubi, T. Ishii, - Scientific Reports, 2024 usegalaxy.eu

Assessment and Partial Characterization of Candidate Genes in Dihydrochalcone and Arbutin Biosynthesis in an Apple–Pear Hybrid by <i>De Novo</i> Transcriptome Assembly
S. Miranda - M. Koop, A. Angeli, J. Lagrèze, et al. - Journal of Agricultural and Food Chemistry, 2024 usegalaxy.eu

Removing scanner effects with a multivariate latent approach: A RELIEF for the ABCD imaging data?
D. Kraft - G. Bon, É. Breton, P. Seidel, et al. - Imaging Neuroscience, 2024

Tolperisone hydrochloride improves motor functions in Parkinson’s disease via MMP-9 inhibition and by downregulating p38 MAPK and ERK1/2 signaling cascade
B. Zaman - I. Mostafa, T. Hassan, S. Ahmed, et al. - Biomedicine &amp; Pharmacotherapy, 2024 usegalaxy.eu

Metagenomic Study of Bacteria Diversity and Functional Profile in Bulk and Rhizosphere Soils of Fusarium-Wilt Infected Plantain (Musa paradisiaca)
N. C.C. - E. B.A., O. E.C., - Journal of Advances in Microbiology, 2024 usegalaxy.eu

Evaluation of novel pyridoxal isonicotinoyl hydrazone (<scp>PIH</scp>) derivatives as potential <scp>anti‐tuberculosis</scp> agents: An in silico investigation
M. Hossain - S. Al Abbad, Z. Alsunaidi, S. Rahman, et al. - International Journal of Quantum Chemistry, 2024 usegalaxy.eu

Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer
S. Joshi - R. Srivastava, - Vietnam Journal of Chemistry, 2024 usegalaxy.eu

The Damietta Server: a comprehensive protein design toolkit
I. Grin - K. Maksymenko, T. Wörtwein, M. ElGamacy, et al. - Nucleic Acids Research, 2024

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
J. Galvis - J. Guyon, B. Dartigues, H. Hecht, et al. - Bioinformatics, 2024 usegalaxy.eu

Revisiting pangenome openness with k-mers
L. Parmigiani - R. Wittler, J. Stoye, - Peer Community Journal, 2024

Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue
J. Fischer - A. Fedotova, C. Bühler, L. Darriba, et al. - Viruses, 2024 usegalaxy.eu

Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells
S. Watson - H. Porter, I. Sudbery, R. Thompson, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

The Celiac‐Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model
M. Herrera - M. Amundarain, P. Dörfler, V. Dodero, et al. - Angewandte Chemie International Edition, 2024

A Transcriptomic Hourglass In Brown Algae
J. Lotharukpong - M. Zheng, R. Luthringer, H. Drost, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Nicheformer: a foundation model for single-cell and spatial omics
A. Schaar - A. Tejada-Lapuerta, G. Palla, R. Gutgesell, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

A Minimal Metadata Schema and Its Tool to Improve the Searchableness of Research Data in Bioinformatics
O. Brandt - H. Gauza, J. Kaltenbach, M. Müller, et al. - Journal of Library Metadata, 2024

Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice
B. Oakes - M. Famelis, H. Sahraoui, - ACM Transactions on Software Engineering and Methodology, 2024 usegalaxy.eu

In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae
J. Aribisala - N. S’thebe, S. Sabiu, - Scientific Reports, 2024 usegalaxy.eu

Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
K. Tóth - I. Damjanova, L. Laczkó, L. Buzgó, et al. - Antibiotics, 2024 usegalaxy.eu

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
V. Bonthala - B. Stich, - Plant Cell Reports, 2024

Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients
S. Castellana - V. De Laurentiis, A. Bianco, L. Del Sambro, et al. - Microorganisms, 2024 usegalaxy.eu

Deep Regression for Biological Age Estimation in Multiple Organs: Investigations on 40,000 Subjects of the UK Biobank
V. Ecker - M. Früh, B. Yang, S. Gatidis, et al. - IEEE, 2024

Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets
F. Lim - J. González-Cabrera, J. Keilwagen, R. Kleespies, et al. - Scientific Reports, 2024

Complete genome sequence of <i>Pseudomonas aeruginosa</i> phage Knedl
E. Maffei - C. Manner, U. Jenal, A. Harms, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

Complete genome sequence of <i>Escherichia coli</i> MP1
K. Pick - P. Stothard, T. Raivio, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Comparative Transcriptomics of Fat Bodies between Symbiotic and Quasi-Aposymbiotic Adult Females of Blattella germanica with Emphasis on the Metabolic Integration with Its Endosymbiont Blattabacterium and Its Immune System
F. Silva - R. Domínguez-Santos, A. Latorre, C. García-Ferris, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Enhancing the image analysis community in Galaxy
L. Kostrykin - T. Woller, M. Kalaš, B. Özdemir, et al. - Center for Open Science, 2024 usegalaxy.eu

Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships
E. Depari - N. Wijayanto, L. Karlinasari, M. Rafi, et al. - F1000Research, 2024 usegalaxy.eu

The Intellectual Disability Risk Gene<i>Kdm5b</i>Regulates Long-Term Memory Consolidation in the Hippocampus
L. Pérez-Sisqués - S. Bhatt, R. Matuleviciute, T. Gileadi, et al. - The Journal of Neuroscience, 2024 usegalaxy.eu

RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats
M. Choudalakis - P. Bashtrykov, A. Jeltsch, - Mobile DNA, 2024 usegalaxy.eu

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

ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3
F. Dehghanian - P. Bovio, F. Gather, S. Probst, et al. - Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2024 usegalaxy.eu

Molecular characteristics of Cryptosporidium spp. in human cases in five Finnish hospital districts during 2021: first findings of Cryptosporidium mortiferum (Cryptosporidium chipmunk genotype I) in Finland
T. Häkkänen - R. Rimhanen-Finne, J. Antikainen, E. Ruotsalainen, et al. - International Journal for Parasitology, 2024 usegalaxy.eu

The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis
T. Zhu - C. Wei, Y. Yu, Z. Zhang, et al. - Developmental Cell, 2024 usegalaxy.eu

Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation
D. Pinto - G. Themudo, A. Pereira, A. Botelho, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
J. Schmitz - N. Aggarwal, L. Laufer, J. Walter, et al. - Bioinformatics, 2024

Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria
A. Palacios-Rodriguez - A. Espinoza-Culupú, Y. Durán, T. Sánchez-Rojas, et al. - Antibiotics, 2024 usegalaxy.eu

Menarche, pubertal timing and the brain: female-specific patterns of brain maturation beyond age-related development
N. Gottschewsky - D. Kraft, T. Kaufmann, - Biology of Sex Differences, 2024

The mitochondrial genome sequence of Syagrus coronata (Mart.) Becc. (Arecaceae) is characterized by gene insertion within intergenic spaces
S. de Melo - A. Marques, C. Almeida, - Tree Genetics &amp; Genomes, 2024 usegalaxy.eu

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

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

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

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

SpatialData: an open and universal data framework for spatial omics
L. Marconato - G. Palla, K. Yamauchi, I. Virshup, et al. - Nature Methods, 2024

An <scp>RRM</scp> domain protein <scp>SOE</scp> suppresses transgene silencing in rice
R. Zhao - W. Wu, Y. Huang, X. Li, et al. - New Phytologist, 2024 usegalaxy.eu

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress
S. Hosseinzadeh - K. Hasanpur, - Scientific Reports, 2024 usegalaxy.eu

Private and well drinking water are reservoirs for antimicrobial resistant bacteria
M. Alawi - C. Smyth, D. Drissner, A. Zimmerer, et al. - npj Antimicrobials and Resistance, 2024 usegalaxy.eu

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

Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
Ö. Kahraman-Ilıkkan - - Molecular Genetics and Genomics, 2024 usegalaxy.eu

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

Draft genome sequences of two <i>Micromonospora</i> strains isolated from the root nodules of <i>Alnus glutinosa</i>
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression
L. Deng - L. Pollmeier, R. Bednarz, C. Cao, et al. - Science Advances, 2024 usegalaxy.eu

Human Metagenome Analysis with COVID-19 Infectious Disease
K. Jain - R. Yadav, - Current Trends in Biotechnology and Pharmacy, 2024 usegalaxy.eu

Characterization of the major autolysin (AtlC) of Staphylococcus carnosus
M. Merz - C. Schiffer, A. Klingl, M. Ehrmann, et al. - BMC Microbiology, 2024 usegalaxy.eu

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

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

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

Decoding chromatin states by proteomic profiling of nucleosome readers
S. Lukauskas - A. Tvardovskiy, N. Nguyen, M. Stadler, et al. - Nature, 2024

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

A synthetic biology approach to assemble and reboot clinically relevant <i>Pseudomonas aeruginosa</i> tailed phages
T. Ipoutcha - R. Racharaks, S. Huttelmaier, C. Wilson, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

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

Identification of genetic determinants of bedaquiline resistance in <i>Mycobacterium tuberculosis</i> in Ural region, Russia
T. Umpeleva - E. Chetverikova, D. Belyaev, N. Eremeeva, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

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

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

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

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

Identification of the odorant binding proteins of Western Flower Thrips ( <i>Frankliniella occidentalis</i> ), characterization and binding analysis of <i>FoccOBP3</i> with molecular modelling, molecular dynamics simulations and a confirmatory field trial
Z. Zafar - M. Wood, S. Fatima, M. Bhatti, et al. - Journal of Biomolecular Structure and Dynamics, 2024 usegalaxy.eu

Identification and functional characterisation of a locus for target site integration in Fusarium graminearum
M. Darino - M. Urban, N. Kaur, A. Machado Wood, et al. - Fungal Biology and Biotechnology, 2024 usegalaxy.eu

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

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

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

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

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

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

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

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

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

Draft genome sequence of <i>Streptomyces poriferorum</i> RTGN2, a bacterial endophyte isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Draft genome sequences of five <i>Mycobacterium</i> strains, isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Effect of <scp>Anti‐S100A4</scp> Monoclonal Antibody Treatment on Experimental Skin Fibrosis and Systemic Sclerosis–Specific Transcriptional Signatures in Human Skin
T. Trinh‐Minh - A. Györfi, M. Tomcik, C. Tran‐Manh, et al. - Arthritis &amp; Rheumatology, 2024 usegalaxy.eu

Neoadjuvant chemo‐ or chemo‐radiation‐therapy of pancreatic ductal adenocarcinoma differentially shift <scp>ECM</scp> composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass
M. Stillger - K. Kurowski, P. Bronsert, E. Brombacher, et al. - International Journal of Cancer, 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

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

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

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

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

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

The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient
Y. de Souza - M. Schloter, W. Weisser, Y. Huang, et al. - Environmental Microbiome, 2024 usegalaxy.eu

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

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

Predicting the Identities of su(met-2) and met-3 in Neurospora crassa by Genome Resequencing
K. McCluskey - D. Brown, E. Bredeweg, S. Baker, et al. - Fungal Genetics Reports, 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

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

Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing
A. Nugroho - I. Siregar, D. Matra, U. Siregar, et al. - Data in Brief, 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

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

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

Integrated Analysis of Transcriptome and Epigenome Reveals <i>ENSR00000272060</i> as a Potential Biomarker in Gastric Cancer
B. Bahrami - M. Wolfien, P. Nikpour, - Epigenomics, 2024 usegalaxy.eu

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

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

Rat1 promotes premature transcription termination at R-loops
J. Mérida-Cerro - P. Maraver-Cárdenas, A. Rondón, A. Aguilera, et al. - Nucleic Acids Research, 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

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

Nonpreferential but Detrimental Accumulation of Macrophages With Clonal Hematopoiesis-Driver Mutations in Cardiovascular Tissues—Brief Report
T. Dederichs - A. Yerdenova, H. Horstmann, T. Vico, et al. - Arteriosclerosis, Thrombosis, &amp; Vascular Biology, 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

Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga
V. Moris - L. Bruneau, J. Berthe, A. Heuskin, et al. - BMC Biology, 2024 usegalaxy.eu

Challenges and perspectives for naming lipids in the context of lipidomics
M. Witting - A. Malik, A. Leach, A. Bridge, et al. - Metabolomics, 2024

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

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

Genetic variability of New Caledonian <i>Boeckella</i> De Guerne &amp; Richard, 1889 (Copepoda: Calanoida), with the description of a new species
C. Royaux - N. Charpin, N. Rabet, - Journal of Crustacean Biology, 2024 usegalaxy.eu

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

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis
V. Pilliol - M. Beye, L. Terlier, J. Balmelle, et al. - Microorganisms, 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

Mitochondrial genome of Hancornia speciosa gomes: intergenic regions containing retrotransposons and predicted genes
F. de Souza - A. Marques, C. Almeida, - Molecular Biology Reports, 2024 usegalaxy.eu

Draft genome sequence of <i>Amycolatopsis camponoti</i> RTGN1, a bacterial endophyte isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Origin and evolutionary trajectories of brown algal sex chromosomes
J. Barrera-Redondo - A. Lipinska, P. Liu, E. Dinatale, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

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

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

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

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

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

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

Oncostatin M Reduces Pathological Neovascularization in the Retina Through Müller Cell Activation
J. Rapp - A. Hospach, P. Liang, M. Schwämmle, et al. - Investigative Opthalmology &amp; Visual Science, 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

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

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

American lobster (<i>Homarus americanus</i>) hepatopancreas transcriptome reveals the significance of chitin-related genes during impoundment shell disease
N. Argenta - M. Rampaul, K. Clark, - FACETS, 2024 usegalaxy.eu

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

Two male-killing <i>Wolbachia</i> from <i>Drosophila birauraia</i> that are closely related but distinct in genome structure
H. Arai - M. Watada, D. Kageyama, - Royal Society Open Science, 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

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

<tt>CheRRI</tt>—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
T. Müller - S. Mautner, P. Videm, F. Eggenhofer, et al. - GigaScience, 2024

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

Development of Similarity Measures From Graph-Structured Bibliographic Metadata: An Application to Identify Scientific Convergence
T. Melnychuk - L. Galke, E. Seidlmayer, S. Bröring, et al. - IEEE Transactions on Engineering Management, 2024

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

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

Deepdefense: annotation of immune systems in prokaryotes using deep learning
S. Hauns - O. Alkhnbashi, R. Backofen, - GigaScience, 2024

Biofoams with Untapped Enzymatic Potential Produced from Beer Bagasse by Indigenous Fungal Strains
C. Aguirre Pranzoni - J. Bonilla, Á. Carrillo, M. López-Vidal, et al. - Elsevier BV, 2024 usegalaxy.eu

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

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

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

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

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

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

<tt>CheRRI</tt>—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
T. Müller - S. Mautner, P. Videm, F. Eggenhofer, et al. - GigaScience, 2024 usegalaxy.eu

Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases
B. Raubenolt - D. Blankenberg, - GigaScience, 2024 usegalaxy.eu

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

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

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

Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistron
M. Cedeño-Sanchez - T. Cheng, C. Lambert, M. Kolarík, et al. - Mycological Progress, 2023

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

Transcriptional Comparison of Human and Murine Retinal Neovascularization
L. Pauleikhoff - S. Boneva, M. Boeck, A. Schlecht, et al. - Investigative Opthalmology &amp; Visual Science, 2023 usegalaxy.eu

Detailing Early Shoot Growth Arrest in Kro-0 x BG-5 Hybrids of <i>Arabidopsis thaliana</i>
K. Sageman-Furnas - G. Duarte, R. Laitinen, - Plant And Cell Physiology, 2023 usegalaxy.eu

A systematic review of the Iberian springsnail subgenus <i>Alzoniella</i> (<i>Navarriella</i>) (Caenogastropoda: Hydrobiidae), with the description of a new potentially relict subfamily
F. García-Guerrero - J. Miller, D. Delicado, M. Novo, et al. - Zoological Journal of the Linnean Society, 2023

Genome-wide identification and characterization of the plant defensins (Pdfs) gene family in selected Leguminous crops and their expression profiles in response to biotic and abiotic stresses
Z. Hassan - A. Abbas, I. Shafique, - Phytopathogenomics and Disease Control, 2023 usegalaxy.eu

In Vivo Silencing of Regulatory Elements Using a Single AAV-CRISPRi Vector
P. Laurette - C. Cao, D. Ramanujam, M. Schwaderer, et al. - Circulation Research, 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

Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae
A. Vieira Da Cruz - J. Jiménez-Castellanos, C. Börnsen, L. Van Maele, et al. - EMBO Molecular Medicine, 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

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

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

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

A reappraisal of transcriptional regulation by NR5A1 and beta-catenin in adrenocortical carcinoma
E. Lalli - - Frontiers in Endocrinology, 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

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

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

Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families
S. Mathura - F. Sutton, V. Bowrin, - BMC Plant Biology, 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

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

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

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

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

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

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

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

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

Low prevalence of germline TP53 and PALB2 mutations in unselected cohort of breast cancer patients from Brunei Darussalam
S. Matusin - Z. Lu, M. Haji Abdul Hamid, - F1000Research, 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

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

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

A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy
D. Jhinjharia - A. Kaushik, S. Sahi, - Journal of Biomolecular Structure and Dynamics, 2023 usegalaxy.eu

Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020–2021
A. Gladkikh - T. Cao, E. Klyuchnikova, M. Dao, et al. - BMC Infectious Diseases, 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

Exploring the influences of geographical variation on sequence signatures in the human gut microbiome
G. Kumar - P. Bhadury, - Journal of Genetics, 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

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

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

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

Characterization and expression analysis of SnRK2, PYL, and ABF/ AREB/ ABI5 gene families in sweet potato
S. Mathura - F. Sutton, V. Bowrin, - PLOS ONE, 2023 usegalaxy.eu

MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice
C. Göbel - S. Godbole, M. Schoof, D. Holdhof, et al. - Acta Neuropathologica Communications, 2023 usegalaxy.eu

Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease
B. Mairhörmann - A. Castelblanco, F. Häfner, V. Koliogiannis, et al. - Radiology: Artificial Intelligence, 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

Genotypic Evolution of <i>Klebsiella pneumoniae</i> Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy
G. Arcari - F. Cecilia, A. Oliva, R. Polani, et al. - Emerging Infectious Diseases, 2023 usegalaxy.eu

SWORTS: A Scientific Workflow Retrieval Approach by Learning Textual and Structural Semantics
Y. Gu - J. Cao, S. Qian, W. Guan, et al. - IEEE Transactions on Services Computing, 2023 usegalaxy.eu

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

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

Toxic effects and molecular mechanisms of estuarian crustaceans (Scylla paramamosain) exposed to five commonly used benzophenones
Y. Zhou - W. Dong, M. Shu, - Marine Pollution Bulletin, 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

Genetic background of neomycin resistance in clinical <i>Escherichia coli</i> isolated from Danish pig farms
P. Subramani - G. Menichincheri, M. Pirolo, G. Arcari, et al. - Applied and Environmental Microbiology, 2023 usegalaxy.eu

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

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

Domain adapted brain network fusion captures variance related to pubertal brain development and mental health
D. Kraft - D. Alnæs, T. Kaufmann, - Nature Communications, 2023

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

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

Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins
G. Farmiloe - E. van Bree, S. Robben, L. Janssen, et al. - 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

Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast
G. Guesdon - G. Gourgues, F. Rideau, T. Ipoutcha, et al. - ACS Synthetic Biology, 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

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

SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
M. Yousif - S. Rachida, S. Taukobong, N. Ndlovu, et al. - 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

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

LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies
D. Kopczynski - N. Hoffmann, N. Troppmair, C. Coman, et al. - Analytical Chemistry, 2023

Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in <i>Tetrahymena</i>
C. Lee - W. Maier, Y. Jiang, K. Nakano, et al. - Journal of Cell Science, 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

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

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

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

<i>Cuscuta campestris</i>fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts
T. Bawin - A. Didriksen, C. Faehn, S. Olsen, et al. - Plant Physiology, 2023 usegalaxy.eu

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

Activator-blocker model of transcriptional regulation by pioneer-like factors
A. Riesle - M. Gao, M. Rosenblatt, J. Hermes, et al. - Nature Communications, 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

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

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

German Human Genome-Phenome Archive in an International Context: Toward a Federated Infrastructure for Managing and Analyzing Genomics and Health Data
L. Gadelha - J. Eufinger, - Proceedings of the Conference on Research Data Infrastructure, 2023

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities
N. Hoffmann - I. Maus, S. Beier, P. Belmann, et al. - Proceedings of the Conference on Research Data Infrastructure, 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

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

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

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

Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
S. Meckoni - B. Nass, B. Pucker, - BMC Research Notes, 2023

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

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

Mitochondrial polymorphism m.3017C&gt;T of SHLP6 relates to heterothermy
S. Emser - C. Spielvogel, E. Millesi, R. Steinborn, et al. - Frontiers in Physiology, 2023 usegalaxy.eu

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

Multiplicity of <i>bla</i> <sub>KPC</sub> Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307
G. Arcari - R. Polani, S. Santilli, V. Capitani, et al. - Antimicrobial Agents and Chemotherapy, 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

<i>kcnj13</i>regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between<i>Danio</i>species
M. Podobnik - A. Singh, Z. Fu, C. Dooley, et al. - Development, 2023

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

Efficient assembly of plant genomes: A case study with evolutionary implications in<i>Ranunculus</i>(Ranunculaceae)
K. Karbstein - N. Choudhary, T. Xie, S. Tomasello, et al. - bioRxiv - Cold Spring Harbor Laboratory, 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

The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns
J. Mukhopadhyay - A. Wai, G. Hausner, - Frontiers in Microbiology, 2023 usegalaxy.eu

Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches
Z. Zinati - L. Nazari, - Scientific Reports, 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

An Empirical Approach to Derive Water <scp>T<sub>1</sub></scp> from Multiparametric <scp>MR</scp> Images Using an Automated Pipeline and Comparison With Liver Stiffness
F. Michelotti - Y. Kupriyanova, T. Mori, T. Küstner, et al. - Journal of Magnetic Resonance Imaging, 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

Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic <i>Jeongeupia</i> species
N. Arnold - D. Garbe, T. Brück, - MicrobiologyOpen, 2023 usegalaxy.eu

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

Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications
W. Lapadula - M. Juri Ayub, - Gene, 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

Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide
M. Bonatelli - T. Rohwerder, D. Popp, Y. Liu, et al. - Frontiers in Microbiology, 2023

Fine-grained topographic organization within somatosensory cortex during resting-state and emotional face-matching task and its association with ASD traits
C. Isakoglou - K. Haak, T. Wolfers, D. Floris, et al. - Translational Psychiatry, 2023

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

Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of <i>Rhizobium</i> spp. and Their Differentiation from Other Ti and Ri Plasmids
N. Kuzmanović - J. Wolf, S. Will, K. Smalla, et al. - Genome Biology and Evolution, 2023

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

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients
S. Bihani - A. Gupta, S. Mehta, A. Rajczewski, et al. - Journal of Proteome Research, 2023 usegalaxy.eu

Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes
P. Brück - D. Wasser, J. Soppa, - Genes, 2023 usegalaxy.eu

CRISPR library screening to develop HEK293-derived cell lines with improved lentiviral vector titers
B. Iaffaldano - M. Marino, J. Reiser, - Frontiers in Genome Editing, 2023 usegalaxy.eu

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

Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil
F. Vitali - A. Frascella, G. Semenzato, S. Del Duca, et al. - Antibiotics, 2023 usegalaxy.eu

Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies
A. Pustam - J. Jayaraman, A. Ramsubhag, - PLOS ONE, 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

A YAP/TAZ–ARHGAP29–RhoA Signaling Axis Regulates Podocyte Protrusions and Integrin Adhesions
M. Rogg - J. Maier, M. Helmstädter, A. Sammarco, et al. - Cells, 2023 usegalaxy.eu

WHIRLY proteins maintain seed longevity by effects on seed oxygen signalling during imbibition
R. Taylor - W. Waterworth, C. West, C. Foyer, et al. - Biochemical Journal, 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

The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several <i>Gracilaria</i> Species
A. Lipinska - S. Krueger-Hadfield, O. Godfroy, S. Dittami, et al. - Genome Biology and Evolution, 2023 usegalaxy.eu

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

Phylogenetic placement of<i>Ceratophyllum submersum</i>based on a complete plastome sequence derived from nanopore long read sequencing data
S. Meckoni - B. Nass, B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of <i>Escherichia coli</i> towards interventive antibacterial therapy
J. Aribisala - K. Idowu, T. Makhanya, S. Sabiu, et al. - Molecular Simulation, 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

Genome-wide identification and comparative in-silico characterization of β-galactosidase (GH-35) in ascomycetes and its role in germ tube development of Aspergillus fumigatus via RNA-seq analysis
D. Baig - Z. Zafar, H. Khan, A. Younus, et al. - PLOS ONE, 2023 usegalaxy.eu

Genome-wide Identification of the Auxin Transporter Gene Families in Sweet Potato (Ipomoea batatas) and their Expression During Tuberization
S. Mathura - F. Sutton, V. Bowrin, - Tropical Plant Biology, 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

Towards the discovery of novel molecular clocks in Prokaryotes
A. Géron - J. Werner, R. Wattiez, S. Matallana-Surget, et al. - Critical Reviews in Microbiology, 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 - Springer Science and Business Media 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

Two-million-year-old microbial communities from the Kap København Formation in North Greenland
A. Fernandez-Guerra - L. Wörmer, G. Borrel, T. Delmont, 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

A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin
K. Bowran - S. Garrett, A. van Vliet, T. Palmer, et al. - Microbial Genomics, 2023 usegalaxy.eu

Enhanced 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification and a Domain-specific Loss Function
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

Proline and Silver Nitrate Promotes Multiple Shoot Induction from Mature Embryo and Shoot Tip Explants of Sorghum
B. Pawar - N. Markad, R. Wagh, M. Neumann, et al. - Sugar Tech, 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

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

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
S. Pan - X. Zhao, L. Coelho, - Bioinformatics, 2023 usegalaxy.eu

Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
M. Chanama - P. Prombutara, S. Chanama, - Scientific Reports, 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

Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
V. Capitani - G. Arcari, A. Oliva, F. Sacco, et al. - Antibiotics, 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

Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
S. Anbazhagan - K. Himani, R. Karthikeyan, L. Prakasan, et al. - International Microbiology, 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

APOE expression and secretion are modulated by mitochondrial dysfunction
M. Wynne - O. Ogunbona, A. Lane, A. Gokhale, et al. - eLife, 2023 usegalaxy.eu

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

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

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

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
N. Ahmad - M. Ritz, A. Calchera, J. Otte, et al. - Journal of Fungi, 2023 usegalaxy.eu

Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
B. Frommer - S. Müllner, D. Holtgräwe, P. Viehöver, et al. - Frontiers in Plant Science, 2023

Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia
I. Kandinov - E. Dementieva, M. Filippova, A. Vinokurova, et al. - Microorganisms, 2023 usegalaxy.eu

Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition
L. Le Corre - D. Padovani, - Scientific Reports, 2023 usegalaxy.eu

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

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

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

Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress
S. Hosseinzadeh - K. Hasanpur, - Frontiers in Genetics, 2023 usegalaxy.eu

ODNA: identification of organellar DNA by machine learning
R. Martin - M. Nguyen, N. Lowack, D. Heider, et al. - Bioinformatics, 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

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

Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
A. Bafna - G. Banks, M. Hastings, P. Nolan, et al. - Genome Research, 2023 usegalaxy.eu

Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
M. Belair - J. Restrepo-Leal, C. Praz, F. Fontaine, et al. - Fungal Biology, 2023 usegalaxy.eu

Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
A. Boutigny - B. Remenant, B. Legendre, V. Beven, et al. - Journal of Microbiological Methods, 2023 usegalaxy.eu

Building on Communities to Further Software Sustainability
A. Fouilloux - J. Iaquinta, A. Gupta, H. Struthers, et al. - Computing in Science &amp; Engineering, 2023 usegalaxy.eu

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
R. Izquierdo-Lara - L. Heijnen, B. Oude Munnink, C. Schapendonk, et al. - Science of The Total Environment, 2023 usegalaxy.eu

Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium
K. Karthik - S. Anbazhagan, M. Ananda Chitra, R. Ramya, et al. - Gene, 2023 usegalaxy.eu

Increasing complexity of opsin expression across stomatopod development
S. Palecanda - M. Steck, M. Porter, - Ecology and Evolution, 2023 usegalaxy.eu

How does particulate matter affect plant transcriptome and microbiome?
C. Vergata - F. Contaldi, I. Baccelli, M. Basso, et al. - Environmental and Experimental Botany, 2023 usegalaxy.eu

DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate
Y. Yan - J. Zhang, L. Tian, X. Yan, et al. - Water Research, 2023 usegalaxy.eu

Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
U. Patel - K. Desai, R. Dabhi, J. Maru, et al. - Journal of Molecular Modeling, 2023 usegalaxy.eu

Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
J. Miller - D. Delicado, F. García-Guerrero, N. Khalloufi, et al. - European Journal of Taxonomy, 2023

Galaxy for open-source computational drug discovery solutions
A. Singh Gaur - S. Nagamani, L. Priyadarsinee, H. Mahanta, et al. - Expert Opinion on Drug Discovery, 2023 usegalaxy.eu

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

Epidemiological Description and Detection of Antimicrobial Resistance in Various Aquatic Sites in Marseille, France
S. El-Sawalhi - O. Revol, A. Chamieh, A. Lacoste, et al. - Microbiology Spectrum, 2023 usegalaxy.eu

Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion
M. Lenz - A. Eichler, P. Kruse, P. Stöhr, et al. - Frontiers in Molecular Neuroscience, 2023 usegalaxy.eu

Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient
L. Jaki - S. Weigang, L. Kern, S. Kramme, et al. - Nature Communications, 2023 usegalaxy.eu

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
É. Kocsmár - M. Schmid, M. Cosenza-Contreras, I. Kocsmár, et al. - Cellular and Molecular Life Sciences, 2023 usegalaxy.eu

The complete reference genome for grapevine (<i>Vitis vinifera</i>L.) genetics and breeding
X. Shi - S. Cao, X. Wang, S. Huang, et al. - Horticulture Research, 2023

mlf-core: a framework for deterministic machine learning
L. Heumos - P. Ehmele, L. Kuhn Cuellar, K. Menden, et al. - Bioinformatics, 2023

Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)
M. Warabieda - N. Kuzmanović, P. Trzciński, J. Puławska, et al. - Systematic and Applied Microbiology, 2023

Mapping Normative Trajectories of Cognitive Function and Its Relation to Psychopathology Symptoms and Genetic Risk in Youth
R. Kjelkenes - T. Wolfers, D. Alnæs, D. van der Meer, et al. - Biological Psychiatry Global Open Science, 2023

Identification of a Czc-like operon of the periodontal pathobiont Porphyromonas gingivalis involved in metal ion efflux
A. Gains - D. Lambert, G. Stafford, - Anaerobe, 2023 usegalaxy.eu

A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages
C. Härdtner - A. Kumar, C. Ehlert, T. Vico, et al. - Atherosclerosis, 2023 usegalaxy.eu

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

Genomics of the “tumorigenes” clade of the family <i>Rhizobiaceae</i> and description of <i>Rhizobium rhododendri</i> sp. nov.
N. Kuzmanović - G. diCenzo, B. Bunk, C. Spröer, et al. - MicrobiologyOpen, 2023

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
J. Nelkner - L. Huang, T. Lin, A. Schulz, et al. - Environmental Microbiome, 2023

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
J. Nelkner - L. Huang, T. Lin, A. Schulz, et al. - Environmental Microbiome, 2023

Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin
a. izzo - i. akol, A. Villarreal, M. Garcia-Miralles, et al. - Research Square - Springer Science and Business Media LLC, 2023 usegalaxy.eu

Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
N. Khine - T. Wongsurawat, P. Jenjaroenpun, D. Hampson, et al. - Scientific Reports, 2023 usegalaxy.eu

Experience of Klebsiella pneumoniae genome sequencing using the short read method on the Illumina platform
A. Shaforost - A. Ziatskov, E. Voropaev, O. Osipkina, et al. - Health and Ecology Issues, 2023 usegalaxy.eu

Phenotypic and Molecular Characteristics of Carbapenem-Resistant Acinetobacter baumannii Isolates from Bulgarian Intensive Care Unit Patients
T. Strateva - I. Sirakov, T. Stoeva, A. Stratev, et al. - Microorganisms, 2023 usegalaxy.eu

External <scp>DNA</scp> contamination and efficiency of bleach decontamination for arthropod diet analysis
M. Huszarik - N. Röder, L. Eberhardt, S. Kennedy, et al. - Environmental DNA, 2023 usegalaxy.eu

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
A. Velt - B. Frommer, S. Blanc, D. Holtgräwe, et al. - G3: Genes, Genomes, Genetics, 2023

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
J. Barrera-Redondo - J. Lotharukpong, H. Drost, S. Coelho, et al. - Genome Biology, 2023

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
N. Leonidou - A. Renz, R. Mostolizadeh, A. Dräger, et al. - PLOS Computational Biology, 2023

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes
J. Saraiva - A. Bartholomäus, R. Toscan, P. Baldrian, et al. - Molecular Ecology Resources, 2023

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

Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses
N. Mohamed - N. Ngah, A. Abas, N. Talip, et al. - Agriculture, 2023 usegalaxy.eu

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
M. Amundarain - A. Vietri, V. Dodero, M. Costabel, et al. - The Journal of Physical Chemistry B, 2023

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
P. Siatra - G. Vatsellas, A. Chatzianastasiou, E. Balafas, et al. - npj Regenerative Medicine, 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. - Research Square - Research Square Platform LLC, 2023

Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness
U. Khan - I. Rana, N. Shaheen, Q. Raza, et al. - Scientific Reports, 2023 usegalaxy.eu

Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L.
G. Semenzato - S. Del Duca, A. Vassallo, A. Bechini, et al. - International Journal of Molecular Sciences, 2023 usegalaxy.eu

Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022)
T. Strateva - A. Trifonova, I. Sirakov, D. Borisova, et al. - Acta Microbiologica et Immunologica Hungarica, 2023 usegalaxy.eu

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

Embryogenesis of a calanoid copepod analyzed by transcriptomics
M. Acebal - L. Dalgaard, T. Jørgensen, B. Hansen, et al. - Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2023 usegalaxy.eu

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
M. Figiel - F. Szubert, E. Luchinat, P. Bonarek, et al. - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2023 usegalaxy.eu

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

Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint
M. Kloster - A. Burfeid-Castellanos, D. Langenkämper, T. Nattkemper, et al. - PLOS ONE, 2023

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

Co‐action of <scp>COP1</scp>, <scp>SPA</scp> and cryptochrome in light signal transduction and photomorphogenesis of the moss <i>Physcomitrium patens</i>
M. Kreiss - F. Haas, M. Hansen, S. Rensing, et al. - The Plant Journal, 2023

Pilot Study on the Action of Thymus vulgaris Essential Oil in Treating the Most Common Bacterial Contaminants and Salmonella enterica subsp. enterica Serovar Derby in Poultry Litter
M. Galgano - F. Pellegrini, G. Fracchiolla, D. Mrenoshki, et al. - Antibiotics, 2023 usegalaxy.eu

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

Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples
G. Jeon - H. Kim, J. Kim, J. Baek, et al. - Animals, 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
J. Broche - A. Köhler, F. Kühnel, B. Osteresch, et al. - Communications Biology, 2023 usegalaxy.eu

Biodegradable microplastic increases CO2 emission and alters microbial biomass and bacterial community composition in different soil types
A. Rauscher - N. Meyer, A. Jakobs, R. Bartnick, et al. - Applied Soil Ecology, 2023

Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents
S. Shi - H. Roest, T. van den Bosch, M. Bijvelds, et al. - eBioMedicine, 2023 usegalaxy.eu

Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling
J. Werner - P. Bernhard, M. Cosenza-Contreras, N. Pinter, et al. - Neoplasia, 2023 usegalaxy.eu

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

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

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

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

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

Complete Genome Sequences of Pseudomonas sp. Strains MM223 and MM227 and <i>Rheinheimera</i> sp. Strain MM224, Isolated from a Pond Edge in Bielefeld, Germany
B. Frommer - T. Folchert, A. Witschel, M. Reddeker, 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

Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study
S. Phillip - M. Mushi, A. Decano, J. Seni, et al. - Pathogens, 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

Apiaceae FNS I originated from F3H through tandem gene duplication
B. Pucker - M. Iorizzo, - PLOS ONE, 2023

New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors
S. Cherrad - B. Gillet, J. Dellinger, L. Bellaton, et al. - PLOS ONE, 2023 usegalaxy.eu

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis
S. Hoernstein - B. Özdemir, N. van Gessel, A. Miniera, et al. - 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

Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia
T. Wallach - M. Raden, L. Hinkelmann, M. Brehm, et al. - Frontiers in Immunology, 2023

Azithromycin Susceptibility Testing and Molecular Investigation of Neisseria gonorrhoeae Isolates Collected in Russia, 2020–2021
I. Kandinov - B. Shaskolskiy, D. Kravtsov, A. Vinokurova, et al. - Antibiotics, 2023 usegalaxy.eu

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge
N. Abdulkadir - J. Saraiva, F. Schattenberg, R. Toscan, et al. - Microorganisms, 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

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

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

Transcription factors mediating regulation of photosynthesis
W. Halpape - D. Wulf, B. Verwaaijen, A. Stasche, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

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

DIAMOND +  MEGAN Microbiome Analysis
A. Gautam - W. Zeng, D. Huson, - Springer US, 2023

Characterization of mercury species and microbial communities in sediments and suspended particulate matter from historically contaminated river systems
J. Wiederhold - L. Gfeller, N. Marquardt, A. Alten, et al. - European Association of Geochemistry, 2023

A bibliometric analysis and visualization of spatially resolved transcriptomics
D. Huang . - Y. Gou, X. Wang, Q. Li, et al. - Blood&amp;Genomics, 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

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

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

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

Revealing the small proteome of<i>Haloferax volcanii</i>by combining ribosome profiling and small-protein optimized mass spectrometry
L. Hadjeras - J. Bartel, L. Maier, S. Maaß, et al. - microLife, 2023

Unraveling the small proteome of the plant symbiont <i>Sinorhizobium meliloti</i> by ribosome profiling and proteogenomics
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - microLife, 2023

Unraveling the small proteome of the plant symbiont <i>Sinorhizobium meliloti</i> by ribosome profiling and proteogenomics
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - microLife, 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

The first cavefish in the Dinaric Karst? Cave colonization made possible by phenotypic plasticity in &lt;i&gt;Telestes karsticus&lt;/i&gt;
M. Čupić . . - Z. Marčić, M. Lukić, R. Gračan, et al. - Zoological Research, 2023 usegalaxy.eu

SWARM: A Scientific Workflow Fragments Recommendation Approach via Contrastive Learning and Semantic Matching
Y. Gu - J. Cao, J. Tang, S. Qian, et al. - Springer Nature Switzerland, 2023 usegalaxy.eu

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

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

Identification of Taxa and Functional Pathway Information of Mycobacterium tuberculosis Microbiome and High Throughput Simulation Studies with Mycobacteriophage
D. Verma - I. Murthy, P. Bagchi, - Atlantis Press International BV, 2023 usegalaxy.eu

Morpho-functional Characterisation of Cœlomocytes in the Aquacultivated Sea Cucumber Holothuria Scabra: From Cell Diversity to Transcriptomic Immune Response
N. Wambreuse - G. Caulier, I. Eeckhaut, L. Borrello, et al. - SSRN Electronic Journal, 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

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

A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data
A. Atxaerandio-Landa - A. Arrieta-Gisasola, L. Laorden, J. Bikandi, et al. - Microorganisms, 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

Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov
K. Gašić - N. Zlatković, N. Kuzmanović, - Frontiers in Plant Science, 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

Complete Genome Sequence of Terrisporobacter glycolicus Strain WW3900, Isolated from Influent Wastewater at a Research Center with Multiple-Species Research Animal Facilities
S. Kim - C. Summage-West, M. Reyna, K. Feye, et al. - Microbiology Resource Announcements, 2022 usegalaxy.eu

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

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

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

Functional and Safety Characterization of Weissella paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics
I. Apostolakos - S. Paramithiotis, M. Mataragas, - Dairy, 2022 usegalaxy.eu

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen<i>Campylobacter jejuni</i>
K. Froschauer - S. Svensson, R. Gelhausen, E. Fiore, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Further Extension of Lifespan by Unc-43/CaMKII and Egl-8/PLCβ Mutations in Germline-Deficient Caenorhabditis elegans
H. Mack - L. Buck, S. Skalet, J. Kremer, et al. - Cells, 2022

Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
T. Kart - M. Fischer, S. Winzeck, B. Glocker, et al. - Scientific Reports, 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

Two New <i>Rhizobiales</i> Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies
S. Ashrafi - N. Kuzmanović, S. Patz, U. Lohwasser, et al. - Microbiology Spectrum, 2022

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

Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan
J. Grzegorzewski - J. Brandhorst, M. König, - Frontiers in Pharmacology, 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

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
E. Özkurt - J. Fritscher, N. Soranzo, D. Ng, et al. - Microbiome, 2022 usegalaxy.eu

Thin‐Plate Superstructures of the Immunogenic 33‐mer Gliadin Peptide
M. Herrera - M. Amundarain, F. Nicoletti, M. Drechsler, et al. - ChemBioChem, 2022

A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use
A. Ardisasmita - I. Schene, I. Joore, G. Kok, et al. - Communications Biology, 2022 usegalaxy.eu

Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
O. Nonn - O. Debnath, D. Valdes, K. Sallinger, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia
E. Valadez-Moctezuma - S. Samah, J. Mascorro-Gallardo, N. Marbán-Mendoza, et al. - Genetic Resources and Crop Evolution, 2022 usegalaxy.eu

Epigenetic nature of <i>Arabidopsis thaliana</i> telomeres
M. Vaquero-Sedas - M. Vega-Palas, - Plant Physiology, 2022 usegalaxy.eu

Multivalent binding kinetics resolved by fluorescence proximity sensing
C. Schulte - A. Soldà, S. Spänig, N. Adams, et al. - Communications Biology, 2022

Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations
S. Mehta - V. Carvalho, A. Rajczewski, O. Pible, et al. - Viruses, 2022 usegalaxy.eu

Transcriptome-wide modulation by<i>Sargassum vulgare</i>and<i>Acanthophora spicifera</i>extracts results in a prime-triggered plant signalling cascade in tomato and sweet pepper
O. Ali - A. Ramsubhag, J. Jayaraman, - AoB PLANTS, 2022 usegalaxy.eu

A whole-body FDG-PET/CT Dataset with manually annotated Tumor Lesions
S. Gatidis - T. Hepp, M. Früh, C. La Fougère, et al. - Scientific Data, 2022

Self-supervised learning for automated anatomical tracking in medical image data with minimal human labeling effort
M. Frueh - T. Kuestner, M. Nachbar, D. Thorwarth, et al. - Computer Methods and Programs in Biomedicine, 2022

Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent
K. Korfmann - T. Sellinger, F. Freund, M. Fumagalli, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica
M. Tabarelli - M. Malnoy, K. Janik, - Genes, 2022 usegalaxy.eu

Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time
T. Neubauer - M. Harzhauser, J. Hartman, D. Silvestro, et al. - Scientific Reports, 2022

Transgressive and parental dominant gene expression and cytosine methylation during seed development in<i>Brassica napus</i>hybrids
M. Orantes-Bonilla - H. Wang, H. Lee, A. Golicz, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

On the way to plant data commons – a genotyping use case
M. Feser - P. König, A. Fiebig, D. Arend, et al. - Journal of Integrative Bioinformatics, 2022

Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
J. Bartoszewicz - F. Nasri, M. Nowicka, B. Renard, et al. - Bioinformatics, 2022

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
A. Mitrofanov - M. Ziemann, O. Alkhnbashi, W. Hess, et al. - Bioinformatics, 2022 usegalaxy.eu

In silico drug repurposing against SARS-CoV-2 using an integrative transcriptomic profiling approach: Hydrocortisone and Benzhydrocodone as potential drug candidates against COVID-19
S. Mirmohammadi - A. Kianmehr, A. Sabbaghian, A. Mohebbi, et al. - Infection, Genetics and Evolution, 2022 usegalaxy.eu

Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
A. Nasereddin - H. Golan Berman, D. Wolf, E. Oiknine-Djian, et al. - Microbiology Spectrum, 2022 usegalaxy.eu

Development of a Hybrid-Imaging-Based Prognostic Index for Metastasized-Melanoma Patients in Whole-Body 18F-FDG PET/CT and PET/MRI Data
T. Küstner - J. Vogel, T. Hepp, A. Forschner, et al. - Diagnostics, 2022

DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
W. Zeng - A. Gautam, D. Huson, - Bioinformatics, 2022

Redistribution of the SWI/SNF Complex Dictates Coordinated Transcriptional Control over Epithelial–Mesenchymal Transition of Normal Breast Cells through TGF-β Signaling
S. Jdeed - M. Lengyel, I. Uray, - Cells, 2022 usegalaxy.eu

The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation
R. Meier - G. Greve, D. Zimmer, H. Bresser, et al. - Blood Cancer Journal, 2022 usegalaxy.eu

Biogenesis of <i>C. elegans</i> spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease
H. Tsai - H. Cheng, Y. Tsai, - Science Advances, 2022 usegalaxy.eu

Phased grapevine genome sequence of an<i>Rpv12</i>carrier for biotechnological exploration of resistance to<i>Plasmopara viticola</i>
B. Frommer - S. Müllner, D. Holtgräwe, P. Viehöver, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Delineating genome-wide alternative splicing landscapes and their functional significance in orchids
A. Hazra - P. Mahadani, - South African Journal of Botany, 2022

Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydrobiidae)
J. Miller - D. Delicado, F. García-Guerrero, M. Ramos, et al. - Molecular Phylogenetics and Evolution, 2022

An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
F. Sacco - G. Raponi, A. Oliva, G. Bibbolino, et al. - International Journal of Antimicrobial Agents, 2022 usegalaxy.eu

Genetic and genomic diversity in the sorghum gene bank collection of Uganda
S. Chakrabarty - R. Mufumbo, S. Windpassinger, D. Jordan, et al. - BMC Plant Biology, 2022

Microbiome of the freshwater sponge <i>Ephydatia muelleri</i> shares compositional and functional similarities with those of marine sponges
S. Sugden - J. Holert, E. Cardenas, W. Mohn, et al. - The ISME Journal, 2022

Potential of enriched and stabilized anaerobic lignocellulolytic fungi coexisting with bacteria and methanogens for enhanced methane production from rice straw
N. Thongbunrod - P. Chaiprasert, - Biomass Conversion and Biorefinery, 2022 usegalaxy.eu

Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
A. Nasereddin - S. Ereqat, A. Al-Jawabreh, M. Taradeh, et al. - Parasites &amp; Vectors, 2022 usegalaxy.eu

Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
H. Bokharaie - W. Kolch, A. Krstic, - Biomolecules, 2022 usegalaxy.eu

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat
M. Makhoul - H. Chawla, B. Wittkop, A. Stahl, et al. - Frontiers in Plant Science, 2022

A Draft Human Pangenome Reference
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

A fully phased interspecific grapevine rootstock genome sequence representing<i>V. riparia</i>and<i>V. cinerea</i>and allele-aware annotation of the phylloxera resistance locus<i>Rdv1</i>
B. Frommer - L. Hausmann, D. Holtgräwe, P. Viehöver, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
K. Tzanakis - T. Nattkemper, K. Niehaus, S. Albaum, et al. - BMC Bioinformatics, 2022

Custos Secrets: a Service for Managing User-Provided Resource Credential Secrets for Science Gateways
I. Ranawaka - N. Goonasekara, E. Afgan, J. Basney, et al. - ACM, 2022 usegalaxy.eu

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
A. Wittig - F. Miranda, M. Hölzer, T. Altenburg, et al. - Bioinformatics, 2022

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
G. Formenti - L. Abueg, A. Brajuka, N. Brajuka, et al. - Bioinformatics, 2022 usegalaxy.eu

Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
J. Pérez-Schindler - E. Vargas-Fernández, B. Karrer-Cardel, D. Ritz, et al. - Scientific Reports, 2022 usegalaxy.eu

KIPEs3: Automatic annotation of biosynthesis pathways
A. Rempel - N. Choudhary, B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2022

Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response
M. Kavas - K. Mostafa, Z. Seçgin, B. Yerlikaya, et al. - Genetic Resources and Crop Evolution, 2022 usegalaxy.eu

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
S. Feng - C. Rastogi, R. Loker, W. Glassford, et al. - Nature Communications, 2022 usegalaxy.eu

Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
M. Liu - A. Hernandez-Morales, J. Clark, T. Le, et al. - Nature Communications, 2022 usegalaxy.eu

A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
N. Hoffmann - G. Mayer, C. Has, D. Kopczynski, et al. - Metabolites, 2022

Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)
N. Kuzmanović - E. Biondi, J. Overmann, J. Puławska, et al. - BMC Genomics, 2022

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
U. Nunes da Rocha - J. Kasmanas, R. Kallies, J. Saraiva, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
V. Ngo - B. Fleischmann, M. Jung, L. Hein, et al. - Journal of the American Heart Association, 2022 usegalaxy.eu

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
W. Ouyang - F. Beuttenmueller, E. Gómez-de-Mariscal, C. Pape, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis
H. Yu - Y. Wang, X. Zhang, Z. Wang, et al. - NAR Genomics and Bioinformatics, 2022 usegalaxy.eu

AB12PHYLO: An Integrated Pipeline for Maximum Likelihood Phylogenetic Inference from ABI Trace Data
L. Kaindl - C. Small, R. Stam, - PhytoFrontiers™, 2022

Genomic Analyses of Rose Crown Gall-Associated Bacteria Revealed Two New <i>Agrobacterium</i> Species: <i>Agrobacterium burrii</i> sp. nov. and <i>Agrobacterium shirazense</i> sp. nov.
H. Mafakheri - S. Taghavi, K. Khezerpour, N. Kuzmanović, et al. - Phytopathology®, 2022

Sequence-based pangenomic core detection
T. Schulz - R. Wittler, J. Stoye, - iScience, 2022

Structural analysis of microbiomes from salt caverns used for underground gas storage
L. Schwab - D. Popp, G. Nowack, P. Bombach, et al. - International Journal of Hydrogen Energy, 2022

P989: DYNAMIC CHANGES IN THE HISTONE H3 LYSINE 27 TRIMETHYLATION EPIGENETIC LANDSCAPE FOLLOWING RUXOLITINIB ADMINISTRATION
G. Greenfield - M. McMullin, K. Mills, - HemaSphere, 2022 usegalaxy.eu

Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
A. Lopez-Santamarina - A. Cardelle-Cobas, A. del Carmen Mondragon, L. Sinisterra-Loaiza, et al. - Food Research International, 2022 usegalaxy.eu

Association of DNA methylation and genetic variations of the <i>APOE</i> gene with the risk of diabetic dyslipidemia
S. Ereqat - S. Cauchi, K. Eweidat, M. Elqadi, et al. - Biomedical Reports, 2022 usegalaxy.eu

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
M. Neumann - X. Xu, C. Smaczniak, J. Schumacher, et al. - Nature Communications, 2022

Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
A. Patat - F. Sen, B. Erdogdu, A. Uncu, et al. - Functional &amp; Integrative Genomics, 2022 usegalaxy.eu

Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
A. Napoli - D. Micheletti, M. Pindo, S. Larger, et al. - Scientific Reports, 2022 usegalaxy.eu

Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
M. Mungan - T. Harbig, N. Perez, S. Edenhart, et al. - Nucleic Acids Research, 2022

Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
O. Ali - A. Ramsubhag, S. Daniram Benn Jr. Ramnarine, J. Jayaraman, et al. - Scientific Reports, 2022 usegalaxy.eu

Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation
J. Yuan - Q. Zhu, X. Zhang, Z. Wen, et al. - Cell Death &amp; Differentiation, 2022 usegalaxy.eu

ODGI: understanding pangenome graphs
A. Guarracino - S. Heumos, S. Nahnsen, P. Prins, et al. - Bioinformatics, 2022

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
K. Fröhlich - E. Brombacher, M. Fahrner, D. Vogele, et al. - Nature Communications, 2022 usegalaxy.eu

Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes
V. Bonthala - B. Stich, - Frontiers in Plant Science, 2022

Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
G. Silva - A. Gautam, I. Duarte, T. Delforno, et al. - Scientific Reports, 2022

Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021
K. Subramoney - N. Mtileni, A. Bharuthram, A. Davis, et al. - Journal of Medical Virology, 2022 usegalaxy.eu

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
N. Pinter - D. Glätzer, M. Fahrner, K. Fröhlich, et al. - Journal of Proteome Research, 2022 usegalaxy.eu

The potential of bacterial key species as a tool for monitoring peatland quality
F. Saragih - . Nelvia, N. Pratiwi, D. Zul, et al. - IOP Conference Series: Earth and Environmental Science, 2022 usegalaxy.eu

Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau
P. Zebua - . Nelvia, N. Pratiwi, D. Zul, et al. - IOP Conference Series: Earth and Environmental Science, 2022 usegalaxy.eu

Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum)
J. Puławska - N. Kuzmanović, P. Trzciński, - Systematic and Applied Microbiology, 2022

Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds
G. Semenzato - T. Alonso-Vásquez, S. Del Duca, A. Vassallo, et al. - Microorganisms, 2022 usegalaxy.eu

Computational identification and characterization of vascular wilt pathogen (<i>Fusarium oxysporum f. sp. lycopersici</i>) CAZymes in tomato xylem sap
A. Roy - B. Kalita, A. Jayaprakash, A. Kumar, et al. - Journal of Biomolecular Structure and Dynamics, 2022 usegalaxy.eu

Age-related brain deviations and aggression
N. Holz - D. Floris, A. Llera, P. Aggensteiner, et al. - Psychological Medicine, 2022

Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water
J. Farrell - L. Whitmore, N. Mashkour, D. Rollinson Ramia, et al. - Molecular Ecology Resources, 2022 usegalaxy.eu

A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
T. Hauffe - M. Pires, T. Quental, T. Wilke, et al. - Methods in Ecology and Evolution, 2022

Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
A. Eisenhardt - Z. Brugger, U. Lausch, J. Kiefer, et al. - Cancers, 2022 usegalaxy.eu

Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2
V. Mevada - R. Patel, P. Dudhagara, H. Gandhi, et al. - COVID, 2022 usegalaxy.eu

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
S. Bray - T. Dudgeon, R. Skyner, R. Backofen, et al. - Journal of Cheminformatics, 2022 usegalaxy.eu

Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
D. Kopczynski - N. Hoffmann, B. Peng, G. Liebisch, et al. - Analytical Chemistry, 2022

Identification and annotation of peptide allergens in Prunus dulcis
A. Singh - A. Upadhyay, - Research Square - Research Square Platform LLC, 2022 usegalaxy.eu

Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
T. Altenburg - S. Giese, S. Wang, T. Muth, et al. - Nature Machine Intelligence, 2022

NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
M. Latif - G. Schmidt, S. Mercan, R. Rahman, et al. - Gut, 2022 usegalaxy.eu

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
J. Ebler - P. Ebert, W. Clarke, T. Rausch, et al. - Nature Genetics, 2022

Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
J. Beinecke - P. Anders, T. Schurrat, D. Heider, et al. - Computers in Biology and Medicine, 2022

Critical Assessment of Metagenome Interpretation: the second round of challenges
F. Meyer - A. Fritz, Z. Deng, D. Koslicki, et al. - Nature Methods, 2022

Enabling technologies towards personalization of scaffolds for large bone defect regeneration
P. Poh - T. Lingner, S. Kalkhof, S. Märdian, et al. - Current Opinion in Biotechnology, 2022

Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration
J. Wolf - A. Schlecht, D. Rosmus, S. Boneva, et al. - Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2022 usegalaxy.eu

Unifying the known and unknown microbial coding sequence space
C. Vanni - M. Schechter, S. Acinas, A. Barberán, et al. - eLife, 2022

Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
A. Borchel - A. Komisarczuk, F. Nilsen, - PLOS ONE, 2022 usegalaxy.eu

Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture
B. Liu - H. Sträuber, J. Saraiva, H. Harms, et al. - Microbiome, 2022

Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
N. Kuzmanović - C. Fagorzi, A. Mengoni, F. Lassalle, et al. - International Journal of Systematic and Evolutionary Microbiology, 2022

Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation
Y. Liu - S. Wagner, T. Peng, - Journal of Imaging, 2022

Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
J. Wolf - S. Boneva, D. Rosmus, H. Agostini, et al. - Investigative Opthalmology &amp; Visual Science, 2022 usegalaxy.eu

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. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Genome and proteome analyses show the gaseous alkane degrader <i>Desulfosarcina</i> sp. strain <scp>BuS5</scp> as an extreme metabolic specialist
S. Chen - J. Ji, D. Popp, U. Jaekel, et al. - Environmental Microbiology, 2022

Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
D. Muehler - X. Mao, S. Czemmel, J. Geißert, et al. - Microorganisms, 2022

Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis)
J. Tregear - F. Richaud, M. Collin, J. Esbelin, et al. - Plants, 2022 usegalaxy.eu

Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
D. Dias - S. Costa, C. Fonseca, R. Baraúna, et al. - Science of The Total Environment, 2022 usegalaxy.eu

In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
S. Kumaran - A. Ngo, F. Schultes, V. Saravanan, et al. - Genomics, 2022 usegalaxy.eu

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
O. Mossad - B. Batut, B. Yilmaz, N. Dokalis, et al. - Nature Neuroscience, 2022 usegalaxy.eu

The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue
J. Wolf - S. Boneva, A. Schlecht, T. Lapp, et al. - Genomics, 2022 usegalaxy.eu

SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
S. Tiesmeyer - S. Sahay, N. Müller-Bötticher, R. Eils, et al. - Frontiers in Genetics, 2022

Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
M. Klaas - K. Mäemets-Allas, E. Heinmäe, H. Lagus, et al. - Cellular and Molecular Life Sciences, 2022 usegalaxy.eu

Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
E. Jovanovska - T. Hauffe, B. Stelbrink, A. Cvetkoska, et al. - Global Ecology and Biogeography, 2022

Shell features and anatomy of the springsnail genus <i>Radomaniola</i> (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years
D. Delicado - T. Hauffe, - Zoological Journal of the Linnean Society, 2022

Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
A. Gautam - H. Felderhoff, C. Bağci, D. Huson, et al. - mSystems, 2022

Onset of Late Cretaceous diversification in Europe’s freshwater gastropod fauna links to global climatic and biotic events
T. Neubauer - M. Harzhauser, - Scientific Reports, 2022

Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
D. Wulf - J. Arndt, I. Bleile, C. Bramers, et al. - Microbiology Resource Announcements, 2022

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
K. Sielemann - B. Pucker, N. Schmidt, P. Viehöver, et al. - BMC Genomics, 2022

Pluripotency factors determine gene expression repertoire at zygotic genome activation
M. Gao - M. Veil, M. Rosenblatt, A. Riesle, et al. - Nature Communications, 2022 usegalaxy.eu

Unsupervised encoding selection through ensemble pruning for biomedical classification
S. Spänig - A. Michel, D. Heider, - bioRxiv - Cold Spring Harbor Laboratory, 2022

STENCIL: A web templating engine for visualizing and sharing life science datasets
Q. Sun - A. Nematbakhsh, P. Kuntala, G. Kellogg, et al. - PLOS Computational Biology, 2022 usegalaxy.eu

Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage
D. Verma - P. Bagchi, S. IA, - Research Square - Research Square Platform LLC, 2022 usegalaxy.eu

Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
C. Bamford - L. Broadbent, E. Aranday-Cortes, M. McCabe, et al. - Viruses, 2022 usegalaxy.eu

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
K. Willenbücher - D. Wibberg, L. Huang, M. Conrady, et al. - Microorganisms, 2022

Targeted DamID in <i>C. elegans</i> reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate
D. Katsanos - M. Barkoulas, - Science Advances, 2022 usegalaxy.eu

Drivers of diversification in freshwater gastropods vary over deep time
T. Neubauer - T. Hauffe, D. Silvestro, C. Scotese, et al. - Proceedings of the Royal Society B: Biological Sciences, 2022

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
D. Aggarwal - R. Myers, W. Hamilton, T. Bharucha, et al. - The Lancet Microbe, 2022 usegalaxy.eu

Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
T. Nührenberg - J. Stöckle, F. Marini, M. Zurek, et al. - PLOS ONE, 2022 usegalaxy.eu

sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
R. Nasirigerdeh - R. Torkzadehmahani, J. Matschinske, T. Frisch, et al. - Genome Biology, 2022

Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
M. McDonald - S. Palecanda, J. Cohen, M. Porter, et al. - Journal of Experimental Biology, 2022 usegalaxy.eu

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning
S. Krakau - D. Straub, H. Gourlé, G. Gabernet, et al. - NAR Genomics and Bioinformatics, 2022

TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens
M. do Amaral - A. Freitas, A. Santos, E. dos Santos, et al. - Scientific Reports, 2022 usegalaxy.eu

What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach
L. Colin - D. Abed-Navandi, D. Conde, J. Craggs, et al. - Conservation Genetics Resources, 2022 usegalaxy.eu

SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
K. Koeppel - A. Mendes, A. Strydom, L. Rotherham, et al. - Viruses, 2022 usegalaxy.eu

<i>Saccharomyces boulardii</i> CNCM I‐745 supplementation modifies the fecal resistome during <i>Helicobacter pylori</i> eradication therapy
S. Cifuentes - M. Prado, M. Fornasini, H. Cohen, et al. - Helicobacter, 2022

Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
G. Arcari - A. Oliva, F. Sacco, F. Di Lella, et al. - European Journal of Clinical Microbiology &amp; Infectious Diseases, 2022 usegalaxy.eu

Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
H. Mack - J. Kremer, E. Albertini, E. Mack, et al. - BMC Genomics, 2022 usegalaxy.eu

LAMP Assay for Distinguishing <i>Fusarium oxysporum</i> and <i>Fusarium commune</i> in Lotus (<i>Nelumbo nucifera</i>) Rhizomes
S. Deng - X. Ma, Y. Chen, H. Feng, et al. - Plant Disease, 2022 usegalaxy.eu

Expanding the Galaxy’s reference data
N. VijayKrishna - J. Joshi, N. Coraor, J. Hillman-Jackson, et al. - Bioinformatics Advances, 2022 usegalaxy.eu

Multi-label classification for multi-drug resistance prediction of Escherichia coli
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Computational and Structural Biotechnology Journal, 2022

Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
M. Fahrner - M. Föll, B. Grüning, M. Bernt, et al. - GigaScience, 2022 usegalaxy.eu

A Tetragenococcus halophilus human gut isolate
C. Guindo - M. Morsli, S. Bellali, M. Drancourt, et al. - Current Research in Microbial Sciences, 2022 usegalaxy.eu

Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of<i>Acinetobacter baumannii</i>
S. Halder - M. Mim, M. Alif, J. Shathi, et al. - RSC Advances, 2022 usegalaxy.eu

Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
S. Shi - M. Verstegen, H. Roest, A. Ardisasmita, et al. - Cellular and Molecular Gastroenterology and Hepatology, 2022 usegalaxy.eu

Canonical Workflows to Make Data FAIR
P. Wittenburg - A. Hardisty, Y. Le Franc, A. Mozaffari, et al. - Data Intelligence, 2022 usegalaxy.eu

Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
M. Gaïa - L. Meng, E. Pelletier, P. Forterre, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Taxonomic transfer of two species of hydrobiid snails from western Anatolia (Caenogastropoda, Truncatelloidea) to two new genera, based on molecular and morphological evidence
D. Delicado - M. Gürlek, - Archiv für Molluskenkunde International Journal of Malacology, 2021

CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences
A. Fasemore - A. Helbich, M. Walter, T. Dandekar, et al. - mSystems, 2021

Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
A. Géron - J. Werner, P. Lebaron, R. Wattiez, et al. - Microorganisms, 2021

COVID-19++: A Citation-Aware Covid-19 Dataset for the Analysis of Research Dynamics
L. Galke - E. Seidlmayer, G. Ludemann, L. Langnickel, et al. - IEEE, 2021

PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
S. Patz - A. Gautam, M. Becker, S. Ruppel, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

An ecological perspective on microbial genes of unknown function in soil
H. Holland-Moritz - C. Vanni, A. Fernandez-Guerra, A. Bissett, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
D. Aciole Barbosa - B. Araújo, G. Branco, A. Simeone, et al. - Marine Biotechnology, 2021 usegalaxy.eu

Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
M. Achom - P. Roy, B. Lagunas, E. Picot, et al. - Journal of Experimental Botany, 2021 usegalaxy.eu

LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
T. Kustner - J. Pan, H. Qi, G. Cruz, et al. - IEEE Transactions on Medical Imaging, 2021

Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
S. Gilbertson - A. Weinmann, - Trends in Immunology, 2021 usegalaxy.eu

Current Trends and Future Directions of Large Scale Image and Video Annotation: Observations From Four Years of BIIGLE 2.0
M. Zurowietz - T. Nattkemper, - Frontiers in Marine Science, 2021

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
A. Gautam - H. Felderhoff, C. Bağci, D. Huson, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Expression Atlas update: gene and protein expression in multiple species
P. Moreno - S. Fexova, N. George, J. Manning, et al. - Nucleic Acids Research, 2021 usegalaxy.eu

Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
P. Vollrath - H. Chawla, D. Alnajar, I. Gabur, et al. - Frontiers in Plant Science, 2021

New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
D. Barbosa - A. Simeone, A. Humberto, Y. de Maria, et al. - Research Square - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
G. da Silva - A. Gautam, I. Silveira Duarte, T. Delforno, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Peakhood: individual site context extraction for CLIP-seq peak regions
M. Uhl - D. Rabsch, F. Eggenhofer, R. Backofen, et al. - Bioinformatics, 2021

The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
I. Phan - C. Rice, J. Craig, R. Noorai, et al. - Scientific Reports, 2021 usegalaxy.eu

Viral suppressor of <scp>RNA</scp> silencing in vascular plants also interferes with the development of the bryophyte <scp><i>Physcomitrella patens</i></scp>
E. Marttinen - M. Lehtonen, N. van Gessel, R. Reski, et al. - Plant, Cell &amp; Environment, 2021

The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
I. Dimkić - V. Bhardwaj, V. Carpentieri-Pipolo, N. Kuzmanović, et al. - PLOS ONE, 2021

Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
R. Rettenmaier - N. Thieme, J. Streubel, L. Di Bello, et al. - International Journal of Systematic and Evolutionary Microbiology, 2021

Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted <i>Arabidopsis halleri</i>
G. Lee - H. Ahmadi, J. Quintana, L. Syllwasschy, et al. - The Plant Journal, 2021

Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
J. Ma - J. Chen, B. Louro, R. Martins, et al. - Aquaculture and Fisheries, 2021 usegalaxy.eu

ARTS-DB: a database for antibiotic resistant targets
M. Mungan - K. Blin, N. Ziemert, - Nucleic Acids Research, 2021

Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
A. Page-Karjian - L. Whitmore, B. Stacy, J. Perrault, et al. - Animals, 2021 usegalaxy.eu

From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
M. Lauxmann - D. Vazquez, H. Schilbert, P. Neubauer, et al. - BioEssays, 2021

Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
C. Pessoa Rodrigues - A. Chatterjee, M. Wiese, T. Stehle, et al. - Nature Communications, 2021 usegalaxy.eu

Automatic identification and annotation of MYB gene family members in plants
B. Pucker - - bioRxiv - Cold Spring Harbor Laboratory, 2021

Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
M. Früh - M. Fischer, A. Schilling, S. Gatidis, et al. - Journal of Medical Imaging, 2021

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
M. Ranchou-Peyruse - M. Guignard, F. Casteran, M. Abadie, et al. - Frontiers in Microbiology, 2021 usegalaxy.eu

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
J. Meier-Kolthoff - J. Carbasse, R. Peinado-Olarte, M. Göker, et al. - Nucleic Acids Research, 2021

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Bioinformatics, 2021

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
C. Cantalapiedra - A. Hernández-Plaza, I. Letunic, P. Bork, et al. - Molecular Biology and Evolution, 2021

Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
T. Stachurová - H. Piková, M. Bartas, J. Semerád, et al. - Chemosphere, 2021 usegalaxy.eu

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
W. Maier - S. Bray, M. van den Beek, D. Bouvier, et al. - Nature Biotechnology, 2021

Screening of<i>Azadirachta indica</i>phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study
S. Chandel - R. Singh, A. Gautam, V. Ravichandiran, et al. - Journal of Biomolecular Structure and Dynamics, 2021

OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
J. Saraiva - A. Bartholomäus, R. Kallies, M. Gomes, et al. - Life Science Alliance, 2021

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
K. Peters - S. Herman, P. Khoonsari, J. Burman, et al. - Scientific Reports, 2021 usegalaxy.eu

Genomic impact of stress-induced transposable element mobility in Arabidopsis
D. Roquis - M. Robertson, L. Yu, M. Thieme, et al. - Nucleic Acids Research, 2021 usegalaxy.eu

Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
O. Saleh - S. Dwiani, J. Rott, K. Kühn, et al. - Springer US, 2021 usegalaxy.eu

Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines
D. Brandt - M. Simunovic, T. Busche, M. Haak, et al. - Viruses, 2021

Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
A. Carattoli - G. Arcari, G. Bibbolino, F. Sacco, et al. - Antimicrobial Agents and Chemotherapy, 2021 usegalaxy.eu

FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
C. Fell - A. Hagelkruys, A. Cicvaric, M. Horrer, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
S. Hering - M. Jansson, M. Buhl, - International Journal of Systematic and Evolutionary Microbiology, 2021 usegalaxy.eu

The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
A. Migur - F. Heyl, J. Fuss, A. Srikumar, et al. - Journal of Experimental Botany, 2021 usegalaxy.eu

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
I. Apostolakos - A. Laconi, L. Mughini-Gras, Ö. Yapicier, et al. - Frontiers in Veterinary Science, 2021 usegalaxy.eu

First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
D. Chen - R. Zhang, X. Jin, J. Yang, et al. - Bulletin of Entomological Research, 2021 usegalaxy.eu

Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
O. Schwengers - L. Jelonek, M. Dieckmann, S. Beyvers, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
D. Katsanos - M. Ferrando-Marco, I. Razzaq, G. Aughey, et al. - Development, 2021 usegalaxy.eu

Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
T. Hepp - D. Blum, K. Armanious, B. Schölkopf, et al. - Computerized Medical Imaging and Graphics, 2021

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
V. Glaros - R. Rauschmeier, A. Artemov, A. Reinhardt, et al. - Immunity, 2021 usegalaxy.eu

Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
M. Kavas - K. Yıldırım, Z. Seçgin, M. Abdulla, et al. - Physiology and Molecular Biology of Plants, 2021 usegalaxy.eu

RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
J. Pérez-Schindler - B. Kohl, K. Schneider-Heieck, A. Leuchtmann, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
G. Cova - C. Taroni, M. Deau, Q. Cai, et al. - Journal of Experimental Medicine, 2021 usegalaxy.eu

Single‐cell omics: Overview, analysis, and application in biomedical science
C. Stein - R. Weiskirchen, F. Damm, P. Strzelecka, et al. - Journal of Cellular Biochemistry, 2021 usegalaxy.eu

Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
D. Vazquez - H. Schilbert, V. Dodero, - International Journal of Molecular Sciences, 2021

Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
J. Loske - J. Röhmel, S. Lukassen, S. Stricker, et al. - Nature Biotechnology, 2021

Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
S. Baron - O. Mediannikov, R. Abdallah, E. Kuete Yimagou, et al. - Antimicrobial Agents and Chemotherapy, 2021 usegalaxy.eu

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in<i>Arabidopsis</i>
A. Barragán-Rosillo - C. Peralta-Alvarez, J. Ojeda-Rivera, R. Arzate-Mejía, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
E. Musmeci - F. Candeliere, A. Amaretti, M. Rossi, et al. - Microbiology Resource Announcements, 2021 usegalaxy.eu

Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework
M. Föll - V. Volkmann, K. Enderle-Ammour, K. Wilhelm, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
S. Bandyopadhyay - O. Abiodun, B. Ogboo, A. Kola-Mustapha, et al. - Journal of Biomolecular Structure and Dynamics, 2021 usegalaxy.eu

A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass
J. Hölper - F. Grey, J. Baillie, T. Regan, et al. - Viruses, 2021 usegalaxy.eu

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
K. Mauer - H. Schmidt, M. Dittrich, A. Fröbius, et al. - BMC Genomics, 2021 usegalaxy.eu

A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species
J. Voelker - M. Shepherd, R. Mauleon, - Gigabyte, 2021 usegalaxy.eu

The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
M. Bartas - V. Brázda, A. Volná, J. Červeň, et al. - International Journal of Molecular Sciences, 2021 usegalaxy.eu

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.
L. Schaffert - M. Ruwe, J. Milse, K. Hanuschka, et al. - International Journal of Systematic and Evolutionary Microbiology, 2021

Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
A. Cvetkoska - E. Jovanovska, T. Hauffe, T. Donders, et al. - Quaternary Science Reviews, 2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
Y. Dorone - S. Boeynaems, E. Flores, B. Jin, et al. - Cell, 2021 usegalaxy.eu

Eplerenone Improves Pulmonary Vascular Remodeling and Hypertension by Inhibition of the Mineralocorticoid Receptor in Endothelial Cells
J. Kowalski - L. Deng, C. Suennen, D. Koca, et al. - Hypertension, 2021 usegalaxy.eu

De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
L. Marisaldi - D. Basili, G. Gioacchini, A. Canapa, et al. - Marine Genomics, 2021 usegalaxy.eu

A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
D. Pelletier - D. Roos, M. Bouchoucha, T. Schohn, et al. - Frontiers in Marine Science, 2021 usegalaxy.eu

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
T. Bauer - K. Collmar, T. Kaltofen, A. Loeffler, et al. - Cancers, 2021 usegalaxy.eu

Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
T. Spradling - A. Place, A. Campbell, J. Demastes, et al. - PLOS ONE, 2021 usegalaxy.eu

Deep learning-based real-time detection of novel pathogens during sequencing
J. Bartoszewicz - U. Genske, B. Renard, - Briefings in Bioinformatics, 2021

Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
S. Friedrich - H. Müller, C. Riesterer, H. Schüller, et al. - Scientific Reports, 2021 usegalaxy.eu

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
M. Hanussek - F. Bartusch, J. Krüger, - PLOS Computational Biology, 2021

Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
R. Pallares-Vega - G. Macedo, M. Brouwer, L. Hernandez Leal, et al. - Frontiers in Microbiology, 2021 usegalaxy.eu

Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
C. Bamford - L. Broadbent, E. Aranday-Cortes, M. McCabe, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

The complete mitochondrial genome of the wild silkmoth <i>Antheraea yamamai</i> from Heilongjiang, China (Lepidoptera: Saturniidae)
S. Sun - J. Huang, Y. Liu, - Mitochondrial DNA Part B, 2021 usegalaxy.eu

Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
J. Grzegorzewski - F. Bartsch, A. Köller, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time
J. Theine - D. Holtgräwe, K. Herzog, F. Schwander, et al. - BMC Plant Biology, 2021

Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis
M. Winkler - A. Pan, - Research Square - Research Square Platform LLC, 2021 usegalaxy.eu

ONT-Based Draft Genome Assembly and Annotation of <i>Alternaria atra</i>
B. Bonthala - C. Small, M. Lutz, A. Graf, et al. - Molecular Plant-Microbe Interactions®, 2021

Age-Net: An MRI-Based Iterative Framework for Brain Biological Age Estimation
K. Armanious - S. Abdulatif, W. Shi, S. Salian, et al. - IEEE Transactions on Medical Imaging, 2021

Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone
P. Volkova - G. Duarte, E. Kazakova, E. Makarenko, et al. - Science of The Total Environment, 2021 usegalaxy.eu

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
S. Oselusi - A. Christoffels, S. Egieyeh, - Molecules, 2021 usegalaxy.eu

Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
X. Zhuang - G. Schlunck, J. Wolf, D. Rosmus, et al. - Journal of Innate Immunity, 2021 usegalaxy.eu

Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon
B. Abanda - M. Schmid, A. Paguem, H. Iffland, et al. - Genes, 2021

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
M. Soares - D. Soares, V. Teixeira, A. Heskol, et al. - Genes &amp; Development, 2021 usegalaxy.eu

DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
L. Bichmann - S. Gupta, G. Rosenberger, L. Kuchenbecker, et al. - Journal of Proteome Research, 2021

SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction
A. Rempel - R. Wittler, - Bioinformatics, 2021

Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
M. Bleher - L. Hahn, M. Neumann, J. Patiño-Galindo, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021

Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy
K. Kimura - A. Ooms, K. Graf-Riesen, M. Kuppusamy, et al. - Nature Communications, 2021 usegalaxy.eu

Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
V. Kaiser - L. Talmane, Y. Kumar, F. Semple, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history
E. Hassanin - P. May, R. Aldisi, I. Spier, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
R. Gelhausen - T. Müller, S. Svensson, O. Alkhnbashi, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Assessing the role of polygenic background on the penetrance of monogenic forms in Parkinson’s disease
E. Hassanin - P. May, R. Aldisi, P. Krawitz, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021

AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
C. Vanni - M. Schechter, T. Delmont, A. Eren, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
M. Roncoroni - B. Droesbeke, I. Eguinoa, K. De Ruyck, et al. - Bioinformatics, 2021 usegalaxy.eu

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Q. Gu - A. Kumar, S. Bray, A. Creason, et al. - PLOS Computational Biology, 2021 usegalaxy.eu

A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame
E. Yol - M. Basak, S. Kızıl, S. Lucas, et al. - Frontiers in Plant Science, 2021 usegalaxy.eu

Going to extremes – a metagenomic journey into the dark matter of life
A. Aevarsson - A. Kaczorowska, B. Adalsteinsson, J. Ahlqvist, et al. - FEMS Microbiology Letters, 2021

Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells
S. Dvir - A. Argoetti, C. Lesnik, M. Roytblat, et al. - Cell Reports, 2021 usegalaxy.eu

CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification
C. Yanta - K. Bessonov, G. Robinson, K. Troell, et al. - Food and Waterborne Parasitology, 2021 usegalaxy.eu

Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis
Y. Yu - W. Fu, J. Xu, Y. Lei, et al. - Molecular Plant, 2021 usegalaxy.eu

COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints
L. Langnickel - R. Baum, J. Darms, S. Madan, et al. - IOS Press, 2021

A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines
M. Fahrner - L. Kook, K. Fröhlich, M. Biniossek, et al. - Proteomes, 2021 usegalaxy.eu

SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities
M. Macnee - E. Pérez-Palma, S. Schumacher-Bass, J. Dalton, et al. - Bioinformatics, 2021 usegalaxy.eu

Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
M. Friedrich - R. Sankowski, L. Bunse, M. Kilian, et al. - Nature Cancer, 2021 usegalaxy.eu

Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction
T. Neubauer - T. Hauffe, D. Silvestro, J. Schauer, et al. - Communications Earth &amp; Environment, 2021

Arganiella Giusti &amp; Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?
D. Delicado - V. Pešić, M. Ramos, - European Journal of Taxonomy, 2021

Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing
M. Morsli - C. Zandotti, A. Morand, P. Colson, et al. - Pathogens, 2021 usegalaxy.eu

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
M. Dieckmann - S. Beyvers, R. Nkouamedjo-Fankep, P. Hanel, et al. - Nucleic Acids Research, 2021

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts
A. Bayona-Feliu - S. Barroso, S. Muñoz, A. Aguilera, et al. - Nature Genetics, 2021 usegalaxy.eu

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
A. Rajczewski - S. Mehta, D. Nguyen, B. Grüning, et al. - Clinical Proteomics, 2021 usegalaxy.eu

Peptidotriazolamers Inhibit Aβ(1–42) Oligomerization and Cross a Blood‐Brain‐Barrier Model
N. Tonali - L. Hericks, D. Schröder, O. Kracker, et al. - ChemPlusChem, 2021

Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties
S. Oberbeckmann - D. Bartosik, S. Huang, J. Werner, et al. - Environmental Microbiology, 2021

Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants
S. Weigang - J. Fuchs, G. Zimmer, D. Schnepf, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

ZC3H4 restricts non-coding transcription in human cells
C. Estell - L. Davidson, P. Steketee, A. Monier, et al. - eLife, 2021 usegalaxy.eu

Common virulence gene expression in adult first-time infected malaria patients and severe cases
J. Wichers - G. Tonkin-Hill, T. Thye, R. Krumkamp, et al. - eLife, 2021 usegalaxy.eu

Draft genome of a biparental beetle species, Lethrus apterus
N. Nagy - R. Rácz, O. Rimington, S. Póliska, et al. - BMC Genomics, 2021 usegalaxy.eu

Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates
A. Klein - H. Solinski, N. Malewicz, H. Ieong, et al. - eLife, 2021 usegalaxy.eu

Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
O. Genolet - A. Monaco, I. Dunkel, M. Boettcher, et al. - Genome Biology, 2021 usegalaxy.eu

Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae)
J. Delroisse - L. Duchatelet, P. Flammang, J. Mallefet, et al. - Frontiers in Marine Science, 2021 usegalaxy.eu

A large-scale comparative study on peptide encodings for biomedical classification
S. Spänig - S. Mohsen, G. Hattab, A. Hauschild, et al. - NAR Genomics and Bioinformatics, 2021

Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies
R. Ali - J. Jayaraman, A. Mohammed, C. Chinnaraja, et al. - Research Square - Research Square Platform LLC, 2021 usegalaxy.eu

A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation
S. Pinter - F. Knodel, M. Choudalakis, P. Schnee, et al. - Nucleic Acids Research, 2021 usegalaxy.eu

Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels
A. Simon-Chica - M. Fernández, E. Wülfers, A. Lother, et al. - Cardiovascular Research, 2021 usegalaxy.eu

Haplotype-resolved diverse human genomes and integrated analysis of structural variation
P. Ebert - P. Audano, Q. Zhu, B. Rodriguez-Martin, et al. - Science, 2021

Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment
M. Cordellier - M. Wojewodzic, M. Wessels, C. Kuster, et al. - Zoology, 2021 usegalaxy.eu

Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds
I. Gessara - F. Dittrich, M. Hertel, S. Hildebrand, et al. - Stem Cell Reports, 2021 usegalaxy.eu

Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy
T. Villa - Y. Jaszczyszyn, D. Libri, - Data in Brief, 2021 usegalaxy.eu

The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures
T. Faddetta - L. Abbate, P. Alibrandi, W. Arancio, et al. - Scientific Reports, 2021 usegalaxy.eu

Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the<i>Xist</i>locus
R. Gjaltema - T. Schwämmle, P. Kautz, M. Robson, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
P. Moreno - N. Huang, J. Manning, S. Mohammed, et al. - Nature Methods, 2021 usegalaxy.eu

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
W. Maier - S. Bray, M. van den Beek, D. Bouvier, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Replication of a Novel Parkinson's Locus in a European Ancestry Population
S. Grover - A. Kumar‐Sreelatha, D. Bobbili, P. May, et al. - Movement Disorders, 2021

Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (<i>Pimephales promelas</i>)
A. Alcaraz - D. Potěšil, K. Mikulášek, D. Green, et al. - Environmental Science &amp; Technology, 2021 usegalaxy.eu

Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate
Z. Tu - P. Setlow, S. Brul, G. Kramer, et al. - Microorganisms, 2021 usegalaxy.eu

Direct impact of commonly used dietary emulsifiers on human gut microbiota
S. Naimi - E. Viennois, A. Gewirtz, B. Chassaing, et al. - Microbiome, 2021 usegalaxy.eu

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
A. Hoek - K. Maibach, E. Özmen, A. Vazquez-Armendariz, et al. - BMC Genomics, 2021

Single-Cell RNA Sequencing Procedures and Data Analysis
M. Wolfien - R. David, A. Galow, - Exon Publications, 2021 usegalaxy.eu

Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
K. Boulaassafer - M. Ghamizi, A. Machordom, C. Albrecht, et al. - Organisms Diversity &amp; Evolution, 2021

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
R. Rauschmeier - A. Reinhardt, C. Gustafsson, V. Glaros, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm,Antheraea pernyi (Lepidoptera: Saturniidae)
X. Li - Y. Liu, R. Zhang, D. Chen, et al. - Journal of Insects as Food and Feed, 2021 usegalaxy.eu

Updates on metaQuantome Software for Quantitative Metaproteomics
S. Mehta - P. Kumar, M. Crane, J. Johnson, et al. - Journal of Proteome Research, 2021 usegalaxy.eu

Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
T. Van Den Bossche - B. Kunath, K. Schallert, S. Schäpe, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
P. Verschaffelt - T. Van Den Bossche, W. Gabriel, M. Burdukiewicz, et al. - Journal of Proteome Research, 2021

Large scale genomic rearrangements in selected<i>Arabidopsis thaliana</i>T-DNA lines are caused by T-DNA insertion mutagenesis
B. Pucker - N. Kleinbölting, B. Weisshaar, - bioRxiv - Cold Spring Harbor Laboratory, 2021

AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
L. Kaindl - C. Small, R. Stam, - bioRxiv - Cold Spring Harbor Laboratory, 2021

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
F. Meyer - T. Lesker, D. Koslicki, A. Fritz, et al. - Nature Protocols, 2021

Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
M. Hesse - R. Bednarz, E. Carls, C. Becker, et al. - Journal of Molecular and Cellular Cardiology, 2021 usegalaxy.eu

Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa
T. King - S. Schmidt, S. Thakur, P. Fedorka-Cray, et al. - Journal of Global Antimicrobial Resistance, 2021 usegalaxy.eu

VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
N. Poulose - N. Forsythe, A. Polonski, G. Gregg, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring
K. Wüllems - A. Zurowietz, M. Zurowietz, R. Schneider, et al. - Scientific Reports, 2021

Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture
S. Tabacchioni - S. Passato, P. Ambrosino, L. Huang, et al. - Microorganisms, 2021

Decitabine Induces Gene Derepression on Monosomic Chromosomes: <i>In Vitro</i> and <i>In Vivo</i> Effects in Adverse-Risk Cytogenetics AML
G. Greve - J. Schüler, B. Grüning, B. Berberich, et al. - Cancer Research, 2021 usegalaxy.eu

DenovoProfiling: a webserver for de novo generated molecule library profiling
Z. Liu - J. Du, B. Liu, Z. Cui, et al. - Research Square - Springer Science and Business Media LLC, 2021 usegalaxy.eu

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
W. Logroño - D. Popp, M. Nikolausz, P. Kluge, et al. - Frontiers in Microbiology, 2021

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
S. Mehta - M. Crane, E. Leith, B. Batut, et al. - F1000Research, 2021 usegalaxy.eu

Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra
S. Hetz - M. Horn, - Frontiers in Microbiology, 2021 usegalaxy.eu

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
A. Wittig - F. Miranda, M. Hölzer, T. Altenburg, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Detecting high-scoring local alignments in pangenome graphs
T. Schulz - R. Wittler, S. Rahmann, F. Hach, et al. - Bioinformatics, 2021

Interpretable detection of novel human viruses from genome sequencing data
J. Bartoszewicz - A. Seidel, B. Renard, - NAR Genomics and Bioinformatics, 2021

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
C. Niemöller - J. Wehrle, J. Riba, R. Claus, et al. - Communications Biology, 2021 usegalaxy.eu

Diabetes changes gene expression but not DNA methylation in cardiac cells
A. Lother - O. Bondareva, A. Saadatmand, L. Pollmeier, et al. - Journal of Molecular and Cellular Cardiology, 2021 usegalaxy.eu

3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis
X. Luo - Y. Liu, D. Dang, T. Hu, et al. - Cell, 2021 usegalaxy.eu

Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
A. Ostrovsky - J. Hillman‐Jackson, D. Bouvier, D. Clements, et al. - Current Protocols, 2021 usegalaxy.eu

SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
M. Rogg - J. Maier, R. Dotzauer, N. Artelt, et al. - Journal of the American Society of Nephrology, 2021 usegalaxy.eu

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
P. Videm - A. Kumar, O. Zharkov, B. Grüning, et al. - GigaScience, 2021 usegalaxy.eu

Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences
G. Fiedler - A. Herbstmann, E. Doll, M. Wenning, et al. - Microorganisms, 2021 usegalaxy.eu

Scarless engineering of the<i>Drosophila</i>genome near any site-specific integration site
S. Feng - S. Lu, W. Grueber, R. Mann, et al. - Genetics, 2021 usegalaxy.eu

A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape
P. Vollrath - H. Chawla, S. Schiessl, I. Gabur, et al. - Theoretical and Applied Genetics, 2021

Congenital heart disease risk loci identified by genome-wide association study in European patients
H. Lahm - M. Jia, M. Dreßen, F. Wirth, et al. - Journal of Clinical Investigation, 2021 usegalaxy.eu

Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
O. Blifernez-Klassen - V. Klassen, D. Wibberg, E. Cebeci, et al. - Scientific Reports, 2021

Deep Learning‐Based Automated Abdominal Organ Segmentation in the UK Biobank and German National Cohort Magnetic Resonance Imaging Studies
T. Kart - M. Fischer, T. Küstner, T. Hepp, et al. - Investigative Radiology, 2021

On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
W. Zeng - A. Gautam, D. Huson, - Computation, 2021

ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
S. Hildebrandt - B. Kampfrath, K. Fischer, L. Hildebrand, et al. - Stem Cell Reviews and Reports, 2021 usegalaxy.eu

SANS serif: alignment-free, whole-genome based phylogenetic reconstruction
A. Rempel - R. Wittler, - bioRxiv - Cold Spring Harbor Laboratory, 2021

Electroactive microorganisms in mouse feces
L. Rago - D. Popp, J. Heiker, F. Harnisch, et al. - Electrochimica Acta, 2021

Current status of use of high throughput nucleotide sequencing in rheumatology
S. Boegel - J. Castle, A. Schwarting, - RMD Open, 2021

Tool recommender system in Galaxy using deep learning
A. Kumar - H. Rasche, B. Grüning, R. Backofen, et al. - GigaScience, 2021 usegalaxy.eu

The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry
L. Fernandez-Lopez - S. Sanchez-Carrillo, A. García-Moyano, E. Borchert, et al. - Computational and Structural Biotechnology Journal, 2021

Self-Supervised Learning for Automated Anatomical Tracking in Medical Image Data with Minimal Human Labeling Effort
M. Frueh - T. Kuestner, M. Nachbar, D. Thorwarth, et al. - SSRN Electronic Journal, 2021

MOSGA 2: Comparative genomics and validation tools
R. Martin - H. Dreßler, G. Hattab, T. Hackl, et al. - Computational and Structural Biotechnology Journal, 2021

RNA-Seq Data Analysis in Galaxy
B. Batut - M. van den Beek, M. Doyle, N. Soranzo, et al. - Springer US, 2021 usegalaxy.eu

RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
J. Tosar - F. Gámbaro, M. Castellano, A. Cayota, et al. - BIO-PROTOCOL, 2021 usegalaxy.eu

SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance
J. Stahlecker - E. Mingyar, N. Ziemert, M. Mungan, et al. - Molecules, 2020

Duration of Colonisation With Extended-spectrum Beta-lactamase-producing Escherichia Coli: Results of an Open Cohort Study With Dutch Nursing Home Residents (2013 – 2019)
V. Weterings - T. Goede, Y. Hendriks, L. Kilsdonk, et al. - Research Square - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
S. Trump - S. Lukassen, M. Anker, R. Chua, et al. - Nature Biotechnology, 2020

Tuning the Biological Activity of RGD Peptides with Halotryptophans
I. Kemker - D. Schröder, R. Feiner, K. Müller, et al. - Journal of Medicinal Chemistry, 2020

Population studies of the wild tomato species <i>Solanum chilense</i> reveal geographically structured major gene-mediated pathogen resistance
P. Kahlon - S. Seta, G. Zander, D. Scheikl, et al. - Proceedings of the Royal Society B: Biological Sciences, 2020

Genomic analysis provides novel insights into diversification and taxonomy of<i>Allorhizobium vitis</i>(i.e.<i>Agrobacterium vitis</i>)
N. Kuzmanović - E. Biondi, J. Overmann, J. Puławska, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Stable Protein Sialylation in Physcomitrella
L. Bohlender - J. Parsons, S. Hoernstein, C. Rempfer, et al. - Frontiers in Plant Science, 2020 usegalaxy.eu

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
I. Maus - T. Tubbesing, D. Wibberg, R. Heyer, et al. - Microorganisms, 2020

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
E. Redl - R. Sheibani-Tezerji, C. Cardona, P. Hamminger, et al. - Life Science Alliance, 2020

Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria
B. Liu - D. Popp, N. Müller, H. Sträuber, et al. - Microorganisms, 2020

Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
J. Broche - G. Kungulovski, P. Bashtrykov, P. Rathert, et al. - Nucleic Acids Research, 2020 usegalaxy.eu

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
. D. Porubsky - P. Ebert, P. Audano, M. Vollger, et al. - Nature Biotechnology, 2020

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
M. Chiara - A. D’Erchia, C. Gissi, C. Manzari, et al. - Briefings in Bioinformatics, 2020 usegalaxy.eu

MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue
S. Boneva - A. Schlecht, P. Zhang, D. Boehringer, et al. - Scientific Reports, 2020 usegalaxy.eu

Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis
P. McErlean - C. Bell, R. Hewitt, Z. Busharat, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in<i>C. elegans</i>
W. Qi - E. Gromoff, F. Xu, Q. Zhao, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
M. Riediger - P. Spät, R. Bilger, K. Voigt, et al. - The Plant Cell, 2020 usegalaxy.eu

MOSGA: Modular Open-Source Genome Annotator
R. Martin - T. Hackl, G. Hattab, M. Fischer, et al. - Bioinformatics, 2020

Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
F. Stiehler - M. Steinborn, S. Scholz, D. Dey, et al. - Bioinformatics, 2020

A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
W. Liang - K. Yamahara, C. Hernando-Erhard, S. Lagies, et al. - Kidney International, 2020 usegalaxy.eu

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
J. Martinez-Fabregas - L. Wang, E. Pohler, A. Cozzani, et al. - Cell Reports, 2020 usegalaxy.eu

Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages
J. Wolf - X. Zhuang, A. Hildebrand, S. Boneva, et al. - Molecular Immunology, 2020 usegalaxy.eu

CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of<i>Coxiella burnetii</i>genomic sequences
A. Fasemore - A. Helbich, M. Walter, T. Dandekar, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
K. Dührkop - L. Nothias, M. Fleischauer, R. Reher, et al. - Nature Biotechnology, 2020

RNA nucleation by MSL2 induces selective X chromosome compartmentalization
C. Valsecchi - M. Basilicata, P. Georgiev, A. Gaub, et al. - Nature, 2020 usegalaxy.eu

Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
I. Meyer-Cifuentes - J. Werner, N. Jehmlich, S. Will, et al. - Nature Communications, 2020

Survey of metaproteomics software tools for functional microbiome analysis
R. Sajulga - C. Easterly, M. Riffle, B. Mesuere, et al. - PLOS ONE, 2020 usegalaxy.eu

PK-DB: pharmacokinetics database for individualized and stratified computational modeling
J. Grzegorzewski - J. Brandhorst, K. Green, D. Eleftheriadou, et al. - Nucleic Acids Research, 2020

Fully Automated and Standardized Segmentation of Adipose Tissue Compartments via Deep Learning in 3D Whole-Body MRI of Epidemiologic Cohort Studies
T. Küstner - T. Hepp, M. Fischer, M. Schwartz, et al. - Radiology: Artificial Intelligence, 2020

Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells
V. Čermák - D. Tyč, A. Přibylová, L. Fischer, et al. - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2020 usegalaxy.eu

Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues
F. Guendel - M. Kofoed-Branzk, K. Gronke, C. Tizian, et al. - Immunity, 2020 usegalaxy.eu

Next generation sequencing study on RNA viruses of<i>Vespa velutina</i>and<i>Apis mellifera</i>sharing the same foraging area
F. Marzoli - M. Forzan, L. Bortolotti, M. Pacini, et al. - Transboundary and Emerging Diseases, 2020 usegalaxy.eu

High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh
S. Ahmed - T. Das, M. Islam, A. Herrero-Fresno, et al. - Scientific Reports, 2020 usegalaxy.eu

Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets
Y. Gaafar - H. Ziebell, - PeerJ, 2020 usegalaxy.eu

The environment drives microbial trait variability in aquatic habitats
S. Beier - A. Andersson, P. Galand, C. Hochart, et al. - Molecular Ecology, 2020

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
T. Delmont - M. Gaia, D. Hinsinger, P. Fremont, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
A. Kumar - K. Kondhare, N. Malankar, A. Banerjee, et al. - Journal of Experimental Botany, 2020 usegalaxy.eu

Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
J. Wolf - C. Auw-Haedrich, A. Schlecht, S. Boneva, et al. - Scientific Reports, 2020 usegalaxy.eu

Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
M. Bazzucchi - I. Pierini, M. Giammarioli, G. De Mia, et al. - Archives of Virology, 2020 usegalaxy.eu

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
C. Zavala-Alvarado - O. Sismeiro, R. Legendre, H. Varet, et al. - PLOS Pathogens, 2020 usegalaxy.eu

Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
P. Afouda - G. Dubourg, A. Levasseur, P. Fournier, et al. - Microorganisms, 2020 usegalaxy.eu

Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
T. Wilke - T. Hauffe, E. Jovanovska, A. Cvetkoska, et al. - Science Advances, 2020

3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
S. Boneva - A. Schlecht, D. Böhringer, H. Mittelviefhaus, et al. - Laboratory Investigation, 2020 usegalaxy.eu

Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay
A. Dad - V. Dobrovolsky, R. Heflich, J. Revollo, et al. - Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2020 usegalaxy.eu

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
M. Tekman - B. Batut, A. Ostrovsky, C. Antoniewski, et al. - GigaScience, 2020 usegalaxy.eu

Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
L. Estrada Mallarino - C. Engel, İ. Ilık, D. Maticzka, et al. - Scientific Reports, 2020 usegalaxy.eu

Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
L. Lezameta - D. Cuicapuza, A. Dávila-Barclay, S. Torres, et al. - Microbiology Resource Announcements, 2020 usegalaxy.eu

Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
R. Wirth - B. Pap, T. Böjti, P. Shetty, et al. - Frontiers in Bioengineering and Biotechnology, 2020 usegalaxy.eu

tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
S. Bose - A. Suescún, J. Song, C. Castillo-González, et al. - Plant Cell Reports, 2020 usegalaxy.eu

Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
G. Greenfield - S. McPherson, J. Smith, A. Mead, et al. - Cancers, 2020 usegalaxy.eu

Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
H. de Lastic - I. Liampa, A. Georgakilas, M. Zervakis, et al. - MDPI AG, 2020 usegalaxy.eu

An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
L. Morandi - S. Sabattini, A. Renzi, A. Rigillo, et al. - Cells, 2020 usegalaxy.eu

Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
S. Boneva - J. Wolf, D. Rosmus, A. Schlecht, et al. - Frontiers in Immunology, 2020 usegalaxy.eu

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
D. Wibberg - B. Batut, P. Belmann, J. Blom, et al. - F1000Research, 2020 usegalaxy.eu

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
S. Bray - T. Senapathi, C. Barnett, B. Grüning, et al. - Journal of Cheminformatics, 2020

Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
T. Wilke - J. Renz, T. Hauffe, D. Delicado, et al. - Malacologia, 2020

Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
C. Mootapally - M. Mahajan, N. Nathani, - Microbial Ecology, 2020 usegalaxy.eu

Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
M. Núñez-Sánchez - J. Colom, L. Walsh, C. Buttimer, et al. - Microorganisms, 2020 usegalaxy.eu

Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
H. Chawla - H. Lee, I. Gabur, P. Vollrath, et al. - Plant Biotechnology Journal, 2020

Deep learning-based diatom taxonomy on virtual slides
M. Kloster - D. Langenkämper, M. Zurowietz, B. Beszteri, et al. - Scientific Reports, 2020

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
H. Schiebenhoefer - K. Schallert, B. Renard, K. Trappe, et al. - Nature Protocols, 2020

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
M. Bentsen - P. Goymann, H. Schultheis, K. Klee, et al. - Nature Communications, 2020

DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
G. Di Dalmazi - L. Morandi, B. Rubin, C. Pilon, et al. - The Journal of Clinical Endocrinology &amp; Metabolism, 2020 usegalaxy.eu

Training Infrastructure as a Service
H. Rasche - B. Grüning, - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
D. Baker - M. van den Beek, D. Blankenberg, D. Bouvier, et al. - PLOS Pathogens, 2020 usegalaxy.eu

Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
P. Espíndola-Hernández - J. Mueller, M. Carrete, S. Boerno, et al. - Genome Biology and Evolution, 2020 usegalaxy.eu

Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease
S. Sauriol - K. Simeone, L. Portelance, L. Meunier, et al. - Cancers, 2020 usegalaxy.eu

Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
B. Liu - D. Popp, H. Sträuber, H. Harms, et al. - Microbiology Resource Announcements, 2020

Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health
R. Wirth - G. Maróti, L. Lipták, M. Mester, et al. - Research Square - Springer Science and Business Media LLC, 2020 usegalaxy.eu

pyGenomeTracks: reproducible plots for multivariate genomic datasets 
L. Lopez-Delisle - L. Rabbani, J. Wolff, V. Bhardwaj, et al. - Bioinformatics, 2020 usegalaxy.eu

Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates
B. Liu - D. Popp, H. Sträuber, H. Harms, et al. - Research Square - Springer Science and Business Media LLC, 2020

Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
M. Buhl - M. Marschal, - International Journal of Systematic and Evolutionary Microbiology, 2020 usegalaxy.eu

Ultrastructural, transcriptional, and functional differences between human reticulated and non‐reticulated platelets
L. Hille - M. Lenz, A. Vlachos, B. Grüning, et al. - Journal of Thrombosis and Haemostasis, 2020 usegalaxy.eu

SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
S. Müller - S. Wallner, G. Schmitz, T. Loew, et al. - Gene, 2020 usegalaxy.eu

Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration
A. Schlecht - S. Boneva, M. Gruber, P. Zhang, et al. - The American Journal of Pathology, 2020 usegalaxy.eu

A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
S. Dhamija - C. Yang, J. Seiler, K. Myacheva, et al. - Nature Cell Biology, 2020 usegalaxy.eu

Benchmarking challenging small variants with linked and long reads
J. Wagner - N. Olson, L. Harris, J. McDaniel, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

An Interactive Visualization for Feature Localization in Deep Neural Networks
M. Zurowietz - T. Nattkemper, - Frontiers in Artificial Intelligence, 2020

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
A. Hahn - D. Pensold, C. Bayer, J. Tittelmeier, et al. - Frontiers in Cell and Developmental Biology, 2020 usegalaxy.eu

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
N. Feldker - F. Ferrazzi, H. Schuhwerk, S. Widholz, et al. - The EMBO Journal, 2020 usegalaxy.eu

The landscape of SARS-CoV-2 RNA modifications
M. Miladi - J. Fuchs, W. Maier, S. Weigang, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
C. Lange - J. Wolf, C. Auw‐Haedrich, A. Schlecht, et al. - Journal of Medical Virology, 2020 usegalaxy.eu

Lake expansion elevates equilibrium diversity via increasing colonization
T. Hauffe - D. Delicado, R. Etienne, L. Valente, et al. - Journal of Biogeography, 2020

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
S. Mehta - C. Easterly, R. Sajulga, R. Millikin, et al. - Proteomes, 2020

Enhanced COVID-19 data for improved prediction of survival
W. Zeng - A. Gautam, D. Huson, - bioRxiv - Cold Spring Harbor Laboratory, 2020

Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
S. Roth - P. Bose, M. Alhamdani, S. Mustafa, et al. - Annals of Surgery, 2020

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
V. Piro - T. Dadi, E. Seiler, K. Reinert, et al. - Bioinformatics, 2020

Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
T. Villa - M. Barucco, M. Martin-Niclos, A. Jacquier, et al. - Cell Reports, 2020 usegalaxy.eu

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve, et al. - Antibiotics, 2020 usegalaxy.eu

Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart
H. Lahm - M. Jia, M. Dreßen, F. Wirth, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research
R. Rajan - K. Divya, R. Kandadai, R. Yadav, et al. - Frontiers in Neurology, 2020

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
R. Rettenmaier - M. Schneider, B. Munk, M. Lebuhn, et al. - Microorganisms, 2020

Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
M. Foschini - L. Morandi, A. Sanchez, A. Santoro, et al. - Frontiers in Oncology, 2020 usegalaxy.eu

Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
R. Zhang - J. Gehlen, A. Kawalia, M. Melissari, et al. - PLOS ONE, 2020

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
H. Nützmann - D. Doerr, A. Ramírez-Colmenero, J. Sotelo-Fonseca, et al. - Proceedings of the National Academy of Sciences, 2020

<scp>GLASSgo</scp> in <scp>Galaxy</scp>: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
R. Schäfer - S. Lott, J. Georg, B. Grüning, et al. - Bioinformatics, 2020 usegalaxy.eu

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
V. Jalili E. Afgan Q. Gu D. Clements D. Blankenberg J. Goecks J. Taylor A. Nekrutenko - - Nucleic Acids Research, 2020

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
S. Bray - X. Lucas, A. Kumar, B. Grüning, et al. - Journal of Cheminformatics, 2020 usegalaxy.eu

Galactic Circos: User-friendly Circos plots within the Galaxy platform
H. Rasche - S. Hiltemann, - GigaScience, 2020 usegalaxy.eu

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
A. Busch - M. Brüggemann, S. Ebersberger, K. Zarnack, et al. - Methods, 2020 usegalaxy.eu

Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus
N. Yoshida - C. Kaito, - Data in Brief, 2020 usegalaxy.eu

Independent attenuation correction of whole body [18F]FDG-PET using a deep learning approach with Generative Adversarial Networks
K. Armanious - T. Hepp, T. Küstner, H. Dittmann, et al. - EJNMMI Research, 2020

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
J. Oeyen - P. Baa-Puyoulet, J. Benoit, L. Beukeboom, et al. - Genome Biology and Evolution, 2020 usegalaxy.eu

AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
T. Altenburg - S. Giese, S. Wang, T. Muth, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server
A. Kumar - A. Bangash, B. Gruening, - MDPI AG, 2020 usegalaxy.eu

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
M. Mungan M. Alanjary K. Blin T. Weber M. Medema N. Ziemert - - Nucleic Acids Research, 2020

Two new genera and three new subterranean species of Hydrobiidae (Caenogastropoda: Truncatelloidea) from Tunisia
N. Khalloufi - M. Béjaoui, D. Delicado, - European Journal of Taxonomy, 2020

Phylogenetic relationships within <i>Pseudamnicola</i> Paulucci, 1878 (Caenogastropoda: Truncatelloidea) indicate two independent dispersal events from different continents to the Balearic Islands
K. Boulaassafer - M. Ghamizi, A. Machordom, D. Delicado, et al. - Systematics and Biodiversity, 2020

Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
R. Winkler - I. Rosas-Román, - American Chemical Society (ACS), 2020 usegalaxy.eu

A framework for designing miRNA-based distributed cell classifier circuits
M. Nowicka - H. Siebert, - bioRxiv - Cold Spring Harbor Laboratory, 2020

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
N. Blomberg - K. Lauer, - European Journal of Human Genetics, 2020 usegalaxy.eu

LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity
A. Dorn - M. Glaß, C. Neu, B. Heydel, et al. - Cancers, 2020 usegalaxy.eu

A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases
P. Kumar - J. Johnson, C. Easterly, S. Mehta, et al. - Journal of Proteome Research, 2020

A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
D. Becker - D. Popp, H. Harms, F. Centler, et al. - Microorganisms, 2020

Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
B. Öztürk J. Werner J. Meier-Kolthoff B. Bunk C. Spröer D. Springael - - Genome Biology and Evolution, 2020

The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
M. McGill - B. Sabikunnahar, Q. Fang, C. Teuscher, et al. - Journal of Neuroimmunology, 2020 usegalaxy.eu

MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome
I. Parenti - F. Diab, S. Gil, E. Mulugeta, et al. - Cell Reports, 2020 usegalaxy.eu

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
S. Chen - G. Sun, Y. Yan, K. Konstantinidis, et al. - Proceedings of the National Academy of Sciences, 2020

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive<i>de novo</i>DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
T. Hepp - M. Fischer, M. Winkelmann, S. Baldenhofer, et al. - Journal of Thoracic Imaging, 2020

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
H. Lee - H. Chawla, C. Obermeier, F. Dreyer, et al. - Frontiers in Plant Science, 2020

Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
W. Logroño - D. Popp, S. Kleinsteuber, H. Sträuber, et al. - Microorganisms, 2020

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
G. Lodewijk - D. Fernandes, I. Vretzakis, J. Savage, et al. - Molecular Biology and Evolution, 2020 usegalaxy.eu

An epigenetic map of malaria parasite development from host to vector
K. Witmer - S. Fraschka, D. Vlachou, R. Bártfai, et al. - Scientific Reports, 2020 usegalaxy.eu

Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
M. Tangaro - G. Donvito, M. Antonacci, M. Chiara, et al. - GigaScience, 2020 usegalaxy.eu

The importance of incorporating transcript information in CLIP-seq data analysis
M. Uhl - D. Tran, R. Backofen, - Springer Science and Business Media LLC, 2020 usegalaxy.eu

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
T. McGowan - J. Johnson, P. Kumar, R. Sajulga, et al. - GigaScience, 2020 usegalaxy.eu

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
F. Uellendahl-Werth - M. Wolfien, A. Franke, O. Wolkenhauer, et al. - Scientific Reports, 2020 usegalaxy.eu

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
S. Kumaran - A. Ngo, F. Schultes, D. Tischler, et al. - 3 Biotech, 2020 usegalaxy.eu

Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
I. Hernández - C. Sant, R. Martínez, C. Fernández, et al. - Frontiers in Microbiology, 2020 usegalaxy.eu

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells
O. Genolet - A. Monaco, I. Dunkel, M. Boettcher, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
O. Schwengers - A. Hoek, M. Fritzenwanker, L. Falgenhauer, et al. - PLOS Computational Biology, 2020

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
I. Maus - M. Klocke, J. Derenkó, Y. Stolze, et al. - Environmental Microbiome, 2020

Effects of simulated dose variation on contrast-enhanced CT-based radiomic analysis for Non-Small Cell Lung Cancer
T. Hepp - A. Othman, A. Liebgott, J. Kim, et al. - European Journal of Radiology, 2020

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
J. Werner - E. Nour, B. Bunk, C. Spröer, et al. - Frontiers in Microbiology, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
J. Garrido - M. Aguilar, P. Prieto, - Scientific Reports, 2020 usegalaxy.eu

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
B. Stelbrink - R. Richter, F. Köhler, F. Riedel, et al. - Systematic Biology, 2020

Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann, et al. - Scientific Reports, 2020 usegalaxy.eu

Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
G. Farmiloe - G. Lodewijk, S. Robben, E. van Bree, et al. - Philosophical Transactions of the Royal Society B: Biological Sciences, 2020 usegalaxy.eu

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
D. Hofacker - J. Broche, L. Laistner, S. Adam, et al. - International Journal of Molecular Sciences, 2020 usegalaxy.eu

Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages
F. Candeliere - S. Raimondi, G. Spampinato, M. Tay, et al. - Microbiology Resource Announcements, 2020 usegalaxy.eu

BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
M. Hanussek - F. Bartusch, J. Krüger, - Future Generation Computer Systems, 2020

MedGAN: Medical image translation using GANs
K. Armanious - C. Jiang, M. Fischer, T. Küstner, et al. - Computerized Medical Imaging and Graphics, 2020

Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye, et al. - Springer International Publishing, 2020

Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
M. Zurowietz - T. Nattkemper, - IEEE Access, 2020

GLP: A requirement in cell therapies - perspectives for the cardiovascular field
U. Müller-Ruch - A. Skorska, H. Lemcke, G. Steinhoff, et al. - Advanced Drug Delivery Reviews, 2020 usegalaxy.eu

BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
T. Senapathi - C. Barnett, K. Naidoo, - BIO-PROTOCOL, 2020 usegalaxy.eu

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
G. Sevillya D. Doerr Y. Lerner J. Stoye M. Steel S. Snir - - Molecular Biology and Evolution, 2019

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Y. Perez‐Riverol - P. Moreno, - PROTEOMICS, 2019 usegalaxy.eu

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
M. Lewinski - Y. Bramkamp, T. Köster, D. Staiger, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2019

A Glyphosate Pulse to Brackish Long-Term Microcosms Has a Greater Impact on the Microbial Diversity and Abundance of Planktonic Than of Biofilm Assemblages
R. Janßen - W. Skeff, J. Werner, M. Wirth, et al. - Frontiers in Marine Science, 2019

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
D. Gissi - A. Tarsitano, A. Gabusi, R. Rossi, et al. - Journal of Clinical Medicine, 2019 usegalaxy.eu

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger, et al. - GigaScience, 2019

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
G. Etherington - N. Soranzo, S. Mohammed, W. Haerty, et al. - GigaScience, 2019 usegalaxy.eu

An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts
R. Janßen - J. Zabel, U. von Lukas, M. Labrenz, et al. - Marine Pollution Bulletin, 2019

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata, - bioRxiv - Cold Spring Harbor Laboratory, 2019 usegalaxy.eu

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
J. Werner - A. Géron, J. Kerssemakers, S. Matallana-Surget, et al. - Biology Direct, 2019

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
J. Torres-Paz - J. Leclercq, S. Rétaux, - eLife, 2019 usegalaxy.eu

Expression Atlas update: from tissues to single cells
I. Papatheodorou - P. Moreno, J. Manning, A. Fuentes, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
A. Géron - J. Werner, R. Wattiez, P. Lebaron, et al. - Frontiers in Microbiology, 2019

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
M. Emperle - S. Adam, S. Kunert, M. Dukatz, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Highly Efficient Library Preparation for Ion Torrent Sequencing Using Y-Adapters
L. Forth - D. Höper, - BioTechniques, 2019 usegalaxy.eu

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage
R. Wirth - T. Böjti, G. Lakatos, G. Maróti, et al. - Frontiers in Energy Research, 2019 usegalaxy.eu

An intrinsically disordered proteins community for ELIXIR
N. Davey - M. Babu, M. Blackledge, A. Bridge, et al. - F1000Research, 2019 usegalaxy.eu

Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
S. Lambrecht - Y. Kanesaki, J. Fuss, B. Huettel, et al. - Scientific Reports, 2019 usegalaxy.eu

Development of novel microsatellite markers for <i>Alkanna tinctoria</i> by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer, et al. - Applications in Plant Sciences, 2019 usegalaxy.eu

Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies
F. Larsen - B. Bed’Hom, B. Guldbrandtsen, T. Dalgaard, et al. - Molecular Immunology, 2019 usegalaxy.eu

ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
M. Haas - J. Gómez Vázquez, D. Sun, H. Tran, et al. - Cell Reports, 2019 usegalaxy.eu

<i>Candida auris</i> in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen, et al. - Emerging Infectious Diseases, 2019 usegalaxy.eu

Historical faunal exchange between the Pontocaspian Basin and North America
J. Vandendorpe - C. van Baak, B. Stelbrink, D. Delicado, et al. - Ecology and Evolution, 2019

Draft Genome Sequence of a <i>Chitinimonas</i> Species from Hudson Valley Waterways That Expresses Violacein Pigment
B. Jude - - Microbiology Resource Announcements, 2019 usegalaxy.eu

Pheno-seq – linking visual features and gene expression in 3D cell culture systems
S. Tirier - J. Park, F. Preußer, L. Amrhein, et al. - Scientific Reports, 2019

Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
R. Rauschmeier - C. Gustafsson, A. Reinhardt, N. A‐Gonzalez, et al. - The EMBO Journal, 2019 usegalaxy.eu

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
T. Wollmann - M. Gunkel, I. Chung, H. Erfle, et al. - Medical Image Analysis, 2019

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
L. Sánchez - B. Burger, C. Horro, A. Fabregat, et al. - GigaScience, 2019 usegalaxy.eu

Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion, et al. - Journal of Medicinal Chemistry, 2019

U2 <scp>AF</scp> <sup>65</sup> assemblies drive sequence‐specific splice site recognition
M. Tari - V. Manceau, J. de Matha Salone, A. Kobayashi, et al. - EMBO reports, 2019 usegalaxy.eu

Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis
I. Lengfelder - I. Sava, J. Hansen, K. Kleigrewe, et al. - Frontiers in Immunology, 2019 usegalaxy.eu

A pan-cancer analysis of synonymous mutations
Y. Sharma - M. Miladi, S. Dukare, K. Boulay, et al. - Nature Communications, 2019 usegalaxy.eu

de.NBI Cloud federation through ELIXIR AAI
P. Belmann - B. Fischer, J. Krüger, M. Procházka, et al. - F1000Research, 2019

Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells
C. Ritter - T. Wollmann, P. Bernhard, M. Gunkel, et al. - International Journal of Computer Assisted Radiology and Surgery, 2019

Versatile interactions and bioinformatics analysis of noncoding RNAs
Q. Chen - X. Meng, Q. Liao, M. Chen, et al. - Briefings in Bioinformatics, 2019 usegalaxy.eu

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
J. Nelkner - C. Henke, T. Lin, W. Pätzold, et al. - Genes, 2019

RNApolis: Computational Platform for RNA Structure Analysis
M. Szachniuk - - Foundations of Computing and Decision Sciences, 2019 usegalaxy.eu

BIIGLE2Go—A scalable image annotation system for easy deployment on cruises
M. Zurowietz - D. Langenkamper, T. Nattkemper, - IEEE, 2019

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
B. Pucker - D. Holtgräwe, K. Stadermann, K. Frey, et al. - PLOS ONE, 2019

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
J. Meier-Kolthoff - M. Göker, - Nature Communications, 2019

The RNA workbench 2.0: next generation RNA data analysis
J. Fallmann - P. Videm, A. Bagnacani, B. Batut, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

BOOTABLE: Bioinformatics Benchmark Tool Suite
M. Hanussek - F. Bartusch, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

Reproducible Scientific Workflows for High Performance and Cloud Computing
F. Bartusch - M. Hanussek, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

Mapping-based Genome Size Estimation
S. Natarajan - J. Gehrke, B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2019

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
M. Brunet X. Roucou - - Journal of Visualized Experiments, 2019 usegalaxy.eu

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
J. Espenshade - S. Thijs, S. Gawronski, H. Bové, et al. - Frontiers in Microbiology, 2019 usegalaxy.eu

Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
L. Youssar - V. Wernet, N. Hensel, X. Yu, et al. - PLOS Genetics, 2019 usegalaxy.eu

1,4-Disubstituted 1H-1,2,3-Triazole Containing Peptidotriazolamers: A New Class of Peptidomimetics With Interesting Foldamer Properties
D. Schröder - O. Kracker, T. Fröhr, J. Góra, et al. - Frontiers in Chemistry, 2019

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
J. Teikari - R. Popin, S. Hou, M. Wahlsten, et al. - Scientific Reports, 2019 usegalaxy.eu

Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus
D. Delicado - B. Arconada, A. Aguado, M. Ramos, et al. - Zoological Journal of the Linnean Society, 2019

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi - S. Bray, C. Barnett, B. Grüning, et al. - Bioinformatics, 2019 usegalaxy.eu

CAMISIM: simulating metagenomes and microbial communities
A. Fritz - P. Hofmann, S. Majda, E. Dahms, et al. - Microbiome, 2019

Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
K. Wylie - T. Wylie, P. Minx, D. Rosen, et al. - Frontiers in Cellular and Infection Microbiology, 2019 usegalaxy.eu

Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms
D. Kolosov - M. O'Donnell, - Journal of Experimental Biology, 2019 usegalaxy.eu

Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis
A. Lother - L. Deng, M. Huck, D. Fürst, et al. - Journal of Endocrinology, 2019 usegalaxy.eu

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
N. Owen - M. Moosajee, - Therapeutic Advances in Ophthalmology, 2019 usegalaxy.eu

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
A. Bagnacani - M. Wolfien, O. Wolkenhauer, - Springer New York, 2019 usegalaxy.eu

Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
A. Kalmbach - C. Schröder, L. Klein-Hitpass, K. Nordström, et al. - Cytogenetic and Genome Research, 2019 usegalaxy.eu

Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
I. Prislan - S. Sajko, N. Ulrih, L. Fürst, et al. - RSC Advances, 2019 usegalaxy.eu

Workflow Development for the Functional Characterization of ncRNAs
M. Wolfien - D. Brauer, A. Bagnacani, O. Wolkenhauer, et al. - Springer New York, 2019 usegalaxy.eu

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
P. Kumar - P. Panigrahi, J. Johnson, W. Weber, et al. - Journal of Proteome Research, 2018 usegalaxy.eu

Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
S. Matallana-Surget - J. Werner, R. Wattiez, K. Lebaron, et al. - Frontiers in Microbiology, 2018

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
S. Weise - G. Arumugam, A. Villarreal, P. Videm, et al. - Molecular Neurobiology, 2018 usegalaxy.eu

Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation
N. Blagitko-Dorfs - P. Schlosser, G. Greve, D. Pfeifer, et al. - Leukemia, 2018 usegalaxy.eu

MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
M. Zurowietz - D. Langenkämper, B. Hosking, H. Ruhl, et al. - PLOS ONE, 2018

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J. Huerta-Cepas - D. Szklarczyk, D. Heller, A. Hernández-Plaza, et al. - Nucleic Acids Research, 2018

Aequatus: an open-source homology browser
A. Thanki - N. Soranzo, J. Herrero, W. Haerty, et al. - GigaScience, 2018 usegalaxy.eu

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
P. Bovio - H. Franz, S. Heidrich, T. Rauleac, et al. - Molecular Neurobiology, 2018 usegalaxy.eu

Common ELIXIR Service for Researcher Authentication and Authorisation
M. Linden - M. Prochazka, I. Lappalainen, D. Bucik, et al. - F1000Research, 2018

Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium
G. Retamal-Morales - T. Heine, J. Tischler, B. Erler, et al. - Journal of Biotechnology, 2018 usegalaxy.eu

Ultrastructural alterations in the retinal pigment epithelium and photoreceptors of a Stargardt patient and three Stargardt mouse models: indication for the central role of RPE melanin in oxidative stress
T. Taubitz - A. Tschulakow, M. Tikhonovich, B. Illing, et al. - PeerJ, 2018

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
I. Maus - M. Rumming, I. Bergmann, K. Heeg, et al. - Biotechnology for Biofuels, 2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J. Wolff - V. Bhardwaj, S. Nothjunge, G. Richard, et al. - Nucleic Acids Research, 2018 usegalaxy.eu

Community-Driven Data Analysis Training for Biology
B. Batut - S. Hiltemann, A. Bagnacani, D. Baker, et al. - Cell Systems, 2018 usegalaxy.eu

ASaiM: a Galaxy-based framework to analyze microbiota data
B. Batut - K. Gravouil, C. Defois, S. Hiltemann, et al. - GigaScience, 2018 usegalaxy.eu

Biology Needs Evolutionary Software Tools: Let’s Build Them Right
A. Nekrutenko - G. Team, J. Goecks, J. Taylor, et al. - Molecular Biology and Evolution, 2018 usegalaxy.eu

Structure and Interaction Prediction in Prokaryotic RNA Biology
P. Wright* - M. Mann*, R. Backofen*, - Microbiology Spectrum, 2018 usegalaxy.eu

CMV: visualization for RNA and protein family models and their comparisons
F. Eggenhofer - I. Hofacker, R. Backofen, C. Höner zu Siederdissen, et al. - Bioinformatics, 2018 usegalaxy.eu

Targeted <i>in situ</i> metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
Y. Stolze - A. Bremges, I. Maus, A. Pühler, et al. - Microbial Biotechnology, 2017

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
I. Maus - A. Bremges, Y. Stolze, S. Hahnke, et al. - Biotechnology for Biofuels, 2017

The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
T. Wołkowicz - - Briefings in Functional Genomics, 2017 usegalaxy.eu

Bioinformatics for NGS-based metagenomics and the application to biogas research
S. Jünemann - N. Kleinbölting, S. Jaenicke, C. Henke, et al. - Journal of Biotechnology, 2017

Workflows for microscopy image analysis and cellular phenotyping
T. Wollmann - H. Erfle, R. Eils, K. Rohr, et al. - Journal of Biotechnology, 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
B. Grüning - J. Fallmann, D. Yusuf, S. Will, et al. - Nucleic Acids Research, 2017 usegalaxy.eu

Deep residual Hough voting for mitotic cell detection in histopathology images
T. Wollmann - K. Rohr, - IEEE, 2017

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper, et al. - Frontiers in Marine Science, 2017

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Y. Stolze - A. Bremges, M. Rumming, C. Henke, et al. - Biotechnology for Biofuels, 2016