Publications

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Currently 909 publications with reference to de.NBI Cloud are listed.

Recently added publication

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
R. Gelhausen - T. Müller, S. Svensson, O. Alkhnbashi, et al. - Cold Spring Harbor Laboratory, 2021

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Developmental pathways underlying sexual differentiation in a U/V sex chromosome system
D. Liesner - G. Cossard, M. Zheng, O. Godfroy, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

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

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

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

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

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
D. Larivière - L. Abueg, N. Brajuka, C. Gallardo-Alba, et al. - Nature Biotechnology, 2024 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Construction and analysis of pseudogene-related ceRNA network in breast cancer
H. Mohebifar - A. Sabbaghian, T. Farazmandfar, M. Golalipour, et al. - Scientific Reports, 2023 usegalaxy.eu

Resin acids play key roles in shaping microbial communities during degradation of spruce bark
A. Ristinmaa - A. Tafur Rangel, A. Idström, S. Valenzuela, et al. - Nature Communications, 2023 usegalaxy.eu

Environmental regulation of male fertility is mediated through Arabidopsis transcription factors bHLH89, 91, and 10
J. Robson - A. Tidy, S. Thomas, Z. Wilson, et al. - Journal of Experimental Botany, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana
P. Goossens - J. Spooren, K. Baremans, A. Andel, et al. - Nature Microbiology, 2023 usegalaxy.eu

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

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

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

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

Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases
F. Ratajczak - M. Joblin, M. Hildebrandt, M. Ringsquandl, et al. - Nature Communications, 2023

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

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

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

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

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

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

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

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

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

Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins
G. Farmiloe - E. van Bree, S. Robben, L. Janssen, et al. - Genome Biology and Evolution, 2023 usegalaxy.eu

Spitting in the wind?—The challenges of RNA sequencing for biomarker discovery from saliva
A. Gosch - R. Banemann, G. Dørum, C. Haas, et al. - International Journal of Legal Medicine, 2023 usegalaxy.eu

Interaction of Mesonivirus and Negevirus with arboviruses and the RNAi response in Culex tarsalis-derived cells
E. Agboli - J. Schulze, S. Jansen, D. Cadar, et al. - Parasites &amp; Vectors, 2023 usegalaxy.eu

SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
M. Yousif - S. Rachida, S. Taukobong, N. Ndlovu, et al. - Nature Communications, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The design of functional proteins using tensorized energy calculations
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Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications
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BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa
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Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of <i>Rhizobium</i> spp. and Their Differentiation from Other Ti and Ri Plasmids
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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
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Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes
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Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans
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Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil
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Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies
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Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil
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Integrative meta-omics in Galaxy and beyond
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Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of <i>Escherichia coli</i> towards interventive antibacterial therapy
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The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses
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Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48
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Genome-wide identification and comparative in-silico characterization of β-galactosidase (GH-35) in ascomycetes and its role in germ tube development of Aspergillus fumigatus via RNA-seq analysis
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Genome-wide Identification of the Auxin Transporter Gene Families in Sweet Potato (Ipomoea batatas) and their Expression During Tuberization
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The autoPET challenge: Towards fully automated lesion segmentation in oncologic PET/CT imaging
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Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone
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A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland
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In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut
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Genetic factors explaining anthocyanin pigmentation differences
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MR-DNA: Flexible 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification
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Ribosome profiling reveals the fine-tuned response of<i>Escherichia coli</i>to mild and severe acid stress
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Proline and Silver Nitrate Promotes Multiple Shoot Induction from Mature Embryo and Shoot Tip Explants of Sorghum
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In-silico transcriptome analysis of antibiotic-treated Mycobacterium tuberculosis identifies novel antibiotic resistance factors
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Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
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A Roadmap for the Human Gut Cell Atlas
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Species Delineation and Comparative Genomics within the<i>Campylobacter ureolyticus</i>Complex
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Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
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β-Cell–Specific <i>E2f1</i> Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
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Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
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<i>De Novo</i> Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte -<i>Alternaria burnsii</i>NCIM 1409
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Single‐heartbeat cardiac cine imaging via jointly regularized nonrigid motion‐corrected reconstruction
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Mapping cells through time and space with moscot
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MpoxRadar: a worldwide MPXV genomic surveillance dashboard
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Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
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Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge
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Genetic architecture of brain age and its causal relations with brain and mental disorders
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A draft human pangenome reference
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Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
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Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
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Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia
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Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition
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Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum
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Automatic annotation of the bHLH gene family in plants
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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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ODNA: identification of organellar DNA by machine learning
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Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
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Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
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Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
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Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
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Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium
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Increasing complexity of opsin expression across stomatopod development
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How does particulate matter affect plant transcriptome and microbiome?
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DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate
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Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
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Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
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Mapping lineage-traced cells across time points with moslin
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A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
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Aircraft surveys for air eDNA: probing biodiversity in the sky
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Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion
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Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient
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Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections
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Building pangenome graphs
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The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops
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Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
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Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
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Proteome alterations in human autopsy tissues in relation to time after death
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The complete reference genome for grapevine (<i>Vitis vinifera</i>L.) genetics and breeding
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mlf-core: a framework for deterministic machine learning
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Mapping Normative Trajectories of Cognitive Function and Its Relation to Psychopathology Symptoms and Genetic Risk in Youth
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Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)
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Identification of a Czc-like operon of the periodontal pathobiont Porphyromonas gingivalis involved in metal ion efflux
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A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages
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DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
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Genomics of the “tumorigenes” clade of the family <i>Rhizobiaceae</i> and description of <i>Rhizobium rhododendri</i> sp. nov.
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Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
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Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
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Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin
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Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
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External <scp>DNA</scp> contamination and efficiency of bleach decontamination for arthropod diet analysis
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An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
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Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes
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Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses
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The giant diploid faba genome unlocks variation in a global protein crop
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IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides
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Sex-biased gene expression in nutrient-sensing pathways
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Sex-biased gene expression in nutrient-sensing pathways
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Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
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Identification of Radiomic Biomarkers in a Set of Four Skeletal Muscle Groups on Dixon MRI of the NAKO MR study
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Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness
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Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L.
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Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022)
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Evaluating Tuning Strategies for Sequence Generation with Protein Language Models
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Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43
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Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease
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Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region
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A comprehensive review of bioinformatics tools for chromatin loop calling
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MeganServer: facilitating interactive access to metagenomic data on a server
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Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint
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Co‐action of <scp>COP1</scp>, <scp>SPA</scp> and cryptochrome in light signal transduction and photomorphogenesis of the moss <i>Physcomitrium patens</i>
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Pilot Study on the Action of Thymus vulgaris Essential Oil in Treating the Most Common Bacterial Contaminants and Salmonella enterica subsp. enterica Serovar Derby in Poultry Litter
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Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru
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S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
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Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
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Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples
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Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution
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Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources
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DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage
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MpoxRadar: a worldwide Mpox genomic surveillance dashboard
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Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera
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Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach
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Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression
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Biodegradable microplastic increases CO2 emission and alters microbial biomass and bacterial community composition in different soil types
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Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents
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Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling
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A Physcomitrella <scp>PIN</scp> protein acts in spermatogenesis and sporophyte retention
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Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
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The Full Genome Sequences of Pseudomonas sp. Strain MM221 and <i>Pseudoarthrobacter</i> sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
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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
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Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue
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Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine
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Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study
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Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat
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nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plant root tissue
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Apiaceae FNS I originated from F3H through tandem gene duplication
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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
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A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis
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Genome-wide characterization of Ficus carica MADS-box transcription factors with a focus on their roles during fruit development
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Endosomal vesicle fusion machinery is involved with the contractile vacuole in <i>Dictyostelium discoideum</i>
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Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia
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Azithromycin Susceptibility Testing and Molecular Investigation of Neisseria gonorrhoeae Isolates Collected in Russia, 2020–2021
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Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge
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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
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A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
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MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments
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Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma
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MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
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Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome
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Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
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Physics-Driven Deep Learning for Computational Magnetic Resonance Imaging: Combining physics and machine learning for improved medical imaging
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CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway
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RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.
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The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves
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Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation
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Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
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Unraveling the small proteome of the plant symbiont<i>Sinorhizobium meliloti</i>by ribosome profiling and proteogenomics
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A bibliometric analysis and visualization of spatially resolved transcriptomics
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Revealing the small proteome of<i>Haloferax volcanii</i>by combining ribosome profiling and small-protein optimized mass spectrometry
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Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
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Avoiding Shortcut-Learning by Mutual Information Minimization in Deep Learning-Based Image Processing
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DIAMOND +  MEGAN Microbiome Analysis
A. Gautam - W. Zeng, D. Huson, - Springer US, 2023

Unraveling the small proteome of the plant symbiont<i>Sinorhizobium meliloti</i>by ribosome profiling and proteogenomics
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Characterization of mercury species and microbial communities in sediments and suspended particulate matter from historically contaminated river systems
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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

Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland
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Hybrid Genome Assembly of Short and Long Reads in Galaxy
T. Ohta - Y. Shiwa, - Springer US, 2023 usegalaxy.eu

Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan
H. SAKAMOTO - G. ITO, Y. GOTO-KOSHINO, M. SAKAMOTO, et al. - Journal of Veterinary Medical Science, 2023 usegalaxy.eu

Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
M. Suzuki - Y. Hashimoto, A. Hirabayashi, K. Yahara, et al. - Springer US, 2023 usegalaxy.eu

Analysis of RNA Sequences and Modifications Using NASE
S. Wein - - Springer US, 2023 usegalaxy.eu

Exploring Scutellaria baicalensis bioactives as EGFR tyrosine kinase inhibitors: Cheminformatics and molecular docking studies
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NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming
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Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
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Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
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An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
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Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea
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Guiding the choice of informatics software and tools for lipidomics research applications
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The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
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Better Together
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Better Together
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Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
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Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium
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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
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STAT3 signaling induced by IL-6 family cytokines modulates angiogenesis
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Rapid detection and online analysis of microbial changes through flow cytometry
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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
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Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
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MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
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Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink
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Complete Genome Sequence of Terrisporobacter glycolicus Strain WW3900, Isolated from Influent Wastewater at a Research Center with Multiple-Species Research Animal Facilities
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Revisiting pangenome openness with k-mers
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Replication collisions induced by de-repressed S-phase transcription are connected with malignant transformation of adult stem cells
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Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics
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Small proteome of the nitrogen-fixing plant symbiont<i>Sinorhizobium meliloti</i>
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Further Extension of Lifespan by Unc-43/CaMKII and Egl-8/PLCβ Mutations in Germline-Deficient Caenorhabditis elegans
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Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
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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
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Two New <i>Rhizobiales</i> Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies
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Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism
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Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan
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

Multi-histone ChIP-Seq Analysis with DecoDen
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Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower
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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
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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
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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
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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
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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
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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
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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
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The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation
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

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

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

An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
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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
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Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
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Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
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Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat
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A Draft Human Pangenome Reference
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MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
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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>
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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
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Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
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Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
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KIPEs3: Automatic annotation of biosynthesis pathways
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Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response
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Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
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A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
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Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)
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MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
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Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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Sequence-based pangenomic core detection
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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.
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AB12PHYLO: An Integrated Pipeline for Maximum Likelihood Phylogenetic Inference from ABI Trace Data
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Structural analysis of microbiomes from salt caverns used for underground gas storage
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Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
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Association of DNA methylation and genetic variations of the <i>APOE</i> gene with the risk of diabetic dyslipidemia
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A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
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Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
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Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
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Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
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Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation
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ODGI: understanding pangenome graphs
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Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
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Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes
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Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
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Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021
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MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
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The potential of bacterial key species as a tool for monitoring peatland quality
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Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau
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Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum)
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Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds
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Age-related brain deviations and aggression
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Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water
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A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
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Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
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Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
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Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
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Identification and annotation of peptide allergens in Prunus dulcis
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Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
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NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
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Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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Critical Assessment of Metagenome Interpretation: the second round of challenges
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Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration
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Unifying the known and unknown microbial coding sequence space
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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
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Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture
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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation
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Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
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Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
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Genome and proteome analyses show the gaseous alkane degrader <i>Desulfosarcina</i> sp. strain <scp>BuS5</scp> as an extreme metabolic specialist
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Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue
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SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
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Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
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Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
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Shell features and anatomy of the springsnail genus <i>Radomaniola</i> (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years
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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
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Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
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Onset of Late Cretaceous diversification in Europe’s freshwater gastropod fauna links to global climatic and biotic events
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Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
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Pluripotency factors determine gene expression repertoire at zygotic genome activation
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Unsupervised encoding selection through ensemble pruning for biomedical classification
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STENCIL: A web templating engine for visualizing and sharing life science datasets
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Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage
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Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
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Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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Targeted DamID in <i>C. elegans</i> reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate
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Drivers of diversification in freshwater gastropods vary over deep time
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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
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Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
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sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens
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What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach
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SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
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<i>Saccharomyces boulardii</i> CNCM I‐745 supplementation modifies the fecal resistome during <i>Helicobacter pylori</i> eradication therapy
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Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
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Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
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LAMP Assay for Distinguishing <i>Fusarium oxysporum</i> and <i>Fusarium commune</i> in Lotus (<i>Nelumbo nucifera</i>) Rhizomes
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Expanding the Galaxy’s reference data
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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A Tetragenococcus halophilus human gut isolate
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Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of<i>Acinetobacter baumannii</i>
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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Canonical Workflows to Make Data FAIR
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
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CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences
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Taxonomic transfer of two species of hydrobiid snails from western Anatolia (Caenogastropoda, Truncatelloidea) to two new genera, based on molecular and morphological evidence
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Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
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PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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An ecological perspective on microbial genes of unknown function in soil
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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
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LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
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Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
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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
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Expression Atlas update: gene and protein expression in multiple species
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Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
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New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
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Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
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Peakhood: individual site context extraction for CLIP-seq peak regions
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The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted <i>Arabidopsis halleri</i>
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
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ARTS-DB: a database for antibiotic resistant targets
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Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
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Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
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Automatic identification and annotation of MYB gene family members in plants
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Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
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

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

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

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

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

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

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

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

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

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

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

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
C. Cantalapiedra - A. Hernández-Plaza, I. Letunic, P. Bork, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

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

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

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

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

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

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

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

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
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VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
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Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture
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Decitabine Induces Gene Derepression on Monosomic Chromosomes: <i>In Vitro</i> and <i>In Vivo</i> Effects in Adverse-Risk Cytogenetics AML
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DenovoProfiling: a webserver for de novo generated molecule library profiling
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Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
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Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
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Detecting high-scoring local alignments in pangenome graphs
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Interpretable detection of novel human viruses from genome sequencing data
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Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
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Diabetes changes gene expression but not DNA methylation in cardiac cells
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3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis
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Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
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SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
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ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
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Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences
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Scarless engineering of the<i>Drosophila</i>genome near any site-specific integration site
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A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape
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Congenital heart disease risk loci identified by genome-wide association study in European patients
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Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
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Deep Learning‐Based Automated Abdominal Organ Segmentation in the UK Biobank and German National Cohort Magnetic Resonance Imaging Studies
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On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
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ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
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SANS serif: alignment-free, whole-genome based phylogenetic reconstruction
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Electroactive microorganisms in mouse feces
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Tool recommender system in Galaxy using deep learning
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The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry
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MOSGA 2: Comparative genomics and validation tools
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Self-Supervised Learning for Automated Anatomical Tracking in Medical Image Data with Minimal Human Labeling Effort
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RNA-Seq Data Analysis in Galaxy
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RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
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SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance
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Duration of Colonisation With Extended-spectrum Beta-lactamase-producing Escherichia Coli: Results of an Open Cohort Study With Dutch Nursing Home Residents (2013 – 2019)
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Tuning the Biological Activity of RGD Peptides with Halotryptophans
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Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
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Population studies of the wild tomato species <i>Solanum chilense</i> reveal geographically structured major gene-mediated pathogen resistance
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Genomic analysis provides novel insights into diversification and taxonomy of<i>Allorhizobium vitis</i>(i.e.<i>Agrobacterium vitis</i>)
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Stable Protein Sialylation in Physcomitrella
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The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
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Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria
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Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
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Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue
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Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis
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A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in<i>C. elegans</i>
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Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
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MOSGA: Modular Open-Source Genome Annotator
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Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
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A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
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CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
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Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages
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CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of<i>Coxiella burnetii</i>genomic sequences
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
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RNA nucleation by MSL2 induces selective X chromosome compartmentalization
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Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
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Survey of metaproteomics software tools for functional microbiome analysis
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PK-DB: pharmacokinetics database for individualized and stratified computational modeling
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Fully Automated and Standardized Segmentation of Adipose Tissue Compartments via Deep Learning in 3D Whole-Body MRI of Epidemiologic Cohort Studies
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Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells
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Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues
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Next generation sequencing study on RNA viruses of<i>Vespa velutina</i>and<i>Apis mellifera</i>sharing the same foraging area
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High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh
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Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets
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The environment drives microbial trait variability in aquatic habitats
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Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
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The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
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The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
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Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
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Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
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The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
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Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
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Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
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3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
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Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay
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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
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Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
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Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
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Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
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tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
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Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
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Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
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An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
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Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
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Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
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Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
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Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
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Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
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Deep learning-based diatom taxonomy on virtual slides
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
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
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Training Infrastructure as a Service
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No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
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Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
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Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease
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Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
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Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health
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pyGenomeTracks: reproducible plots for multivariate genomic datasets 
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Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates
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Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
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Ultrastructural, transcriptional, and functional differences between human reticulated and non‐reticulated platelets
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SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
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Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration
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A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
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Benchmarking challenging small variants with linked and long reads
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An Interactive Visualization for Feature Localization in Deep Neural Networks
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DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
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Genome‐wide cooperation of <scp>EMT</scp> transcription factor <scp>ZEB</scp> 1 with <scp>YAP</scp> and <scp>AP</scp> ‐1 in breast cancer
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The landscape of SARS-CoV-2 RNA modifications
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Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
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Lake expansion elevates equilibrium diversity via increasing colonization
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Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
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Enhanced COVID-19 data for improved prediction of survival
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Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
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ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
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Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
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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
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Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research
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Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
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Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
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Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
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<scp>GLASSgo</scp> in <scp>Galaxy</scp>: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
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The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
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Galactic Circos: User-friendly Circos plots within the Galaxy platform
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iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
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Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus
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Independent attenuation correction of whole body [18F]FDG-PET using a deep learning approach with Generative Adversarial Networks
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Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
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AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
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Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server
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Two new genera and three new subterranean species of Hydrobiidae (Caenogastropoda: Truncatelloidea) from Tunisia
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ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
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Phylogenetic relationships within <i>Pseudamnicola</i> Paulucci, 1878 (Caenogastropoda: Truncatelloidea) indicate two independent dispersal events from different continents to the Balearic Islands
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Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
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A framework for designing miRNA-based distributed cell classifier circuits
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Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
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LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity
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A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases
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A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
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Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
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The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
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MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome
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The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
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Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive<i>de novo</i>DNA methylation mechanisms
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Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
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Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
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Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
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Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
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An epigenetic map of malaria parasite development from host to vector
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Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
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The importance of incorporating transcript information in CLIP-seq data analysis
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Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
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A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
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Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
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Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
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Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells
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ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
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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
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Effects of simulated dose variation on contrast-enhanced CT-based radiomic analysis for Non-Small Cell Lung Cancer
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PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
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Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
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Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
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Gene expression in immortalized versus primary isolated cardiac endothelial cells
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Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
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Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
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Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages
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MedGAN: Medical image translation using GANs
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BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
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Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
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Computing the Rearrangement Distance of Natural Genomes
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GLP: A requirement in cell therapies - perspectives for the cardiovascular field
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BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
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Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
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Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
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SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
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A Glyphosate Pulse to Brackish Long-Term Microcosms Has a Greater Impact on the Microbial Diversity and Abundance of Planktonic Than of Biofilm Assemblages
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13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
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Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
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A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
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An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts
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Full-coverage native RNA sequencing of HIV-1 viruses
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mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
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Highly efficient library preparation for Ion Torrent sequencing using Y-adapters
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Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
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Expression Atlas update: from tissues to single cells
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Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
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Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
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Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage
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An intrinsically disordered proteins community for ELIXIR
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Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
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Development of novel microsatellite markers for <i>Alkanna tinctoria</i> by comparative transcriptomics
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Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies
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ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
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<i>Candida auris</i> in Germany and Previous Exposure to Foreign Healthcare
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Historical faunal exchange between the Pontocaspian Basin and North America
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Draft Genome Sequence of a <i>Chitinimonas</i> Species from Hudson Valley Waterways That Expresses Violacein Pigment
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Pheno-seq – linking visual features and gene expression in 3D cell culture systems
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Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
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GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
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PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
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Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
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U2 <scp>AF</scp> <sup>65</sup> assemblies drive sequence‐specific splice site recognition
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Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis
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A pan-cancer analysis of synonymous mutations
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de.NBI Cloud federation through ELIXIR AAI
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Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells
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Versatile interactions and bioinformatics analysis of noncoding RNAs
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Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
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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
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A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
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TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
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The RNA workbench 2.0: next generation RNA data analysis
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BOOTABLE: Bioinformatics Benchmark Tool Suite
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Reproducible Scientific Workflows for High Performance and Cloud Computing
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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
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Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
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1,4-Disubstituted 1H-1,2,3-Triazole Containing Peptidotriazolamers: A New Class of Peptidomimetics With Interesting Foldamer Properties
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Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
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Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus
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Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
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CAMISIM: simulating metagenomes and microbial communities
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Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
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Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms
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Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis
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RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
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Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
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Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
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Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
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Workflow Development for the Functional Characterization of ncRNAs
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QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
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Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
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FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
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Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation
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MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
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eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
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Aequatus: an open-source homology browser
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Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
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Common ELIXIR Service for Researcher Authentication and Authorisation
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Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium
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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
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Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
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Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
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Community-Driven Data Analysis Training for Biology
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ASaiM: a Galaxy-based framework to analyze microbiota data
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Biology Needs Evolutionary Software Tools: Let’s Build Them Right
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Structure and Interaction Prediction in Prokaryotic RNA Biology
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CMV: visualization for RNA and protein family models and their comparisons
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Targeted <i>in situ</i> metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
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Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
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The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
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Bioinformatics for NGS-based metagenomics and the application to biogas research
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Workflows for microscopy image analysis and cellular phenotyping
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The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
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Deep residual Hough voting for mitotic cell detection in histopathology images
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