Publications

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Currently 647 publications with reference to de.NBI Cloud are listed.

Recently added publication

The RNA workbench 2.0: next generation RNA data analysis
J. Fallmann - P. Videm, A. Bagnacani, B. Batut, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu


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

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

Mapping lineage-traced cells across time points with moslin
M. Lange - Z. Piran, M. Klein, B. Spanjaard, et al. - Cold Spring Harbor Laboratory, 2023

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

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification
A. Gautam - D. Bhowmik, S. Basu, A. Lahiri, et al. - Cold Spring Harbor Laboratory, 2023

Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
L. Schwab - L. Prinsen, G. Nowack, D. Popp, et al. - Frontiers in Energy Research, 2023

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

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

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

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

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

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

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

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

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

IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides
M. Amundarain - A. Vietri, V. Dodero, M. Costabel, et al. - The Journal of Physical Chemistry B, 2023

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

The giant diploid faba genome unlocks variation in a global protein crop
M. Jayakodi - A. Golicz, J. Kreplak, L. Fechete, et al. - Nature, 2023

Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
P. Siatra - G. Vatsellas, A. Chatzianastasiou, E. Balafas, et al. - npj Regenerative Medicine, 2023 usegalaxy.eu

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

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

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

Evaluating Prompt Tuning for Conditional Protein Sequence Generation
A. Nathansen - K. Klein, B. Renard, M. Nowicka, et al. - Cold Spring Harbor Laboratory, 2023

Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region
M. Figiel - F. Szubert, E. Luchinat, P. Bonarek, et al. - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2023 usegalaxy.eu

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

A comprehensive review of bioinformatics tools for chromatin loop calling
L. Liu - K. Han, H. Sun, L. Han, et al. - Briefings in Bioinformatics, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources
D. Becker - D. Popp, F. Bonk, S. Kleinsteuber, et al. - Microorganisms, 2023

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage
M. Welzel - P. Schwarz, H. Löchel, T. Kabdullayeva, et al. - Nature Communications, 2023

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

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

Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression
J. Broche - A. Köhler, F. Kühnel, B. Osteresch, et al. - Communications Biology, 2023 usegalaxy.eu

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

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

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

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

Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine
C. Nielsen - J. Barrett, C. Davis, J. Fallon, et al. - JCI Insight, 2023 usegalaxy.eu

Complete Genome Sequences of Pseudomonas sp. Strains MM223 and MM227 and <i>Rheinheimera</i> sp. Strain MM224, Isolated from a Pond Edge in Bielefeld, Germany
B. Frommer - T. Folchert, A. Witschel, M. Reddeker, et al. - Microbiology Resource Announcements, 2023

Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue
M. Sulyok - J. Luibrand, J. Strohäker, P. Karacsonyi, et al. - Parasites &amp; Vectors, 2023

Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study
S. Phillip - M. Mushi, A. Decano, J. Seni, et al. - Pathogens, 2023 usegalaxy.eu

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

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

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

nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plant root tissue
J. Wanner - L. Cuellar, L. Rausch, K. Berendzen, et al. - Cold Spring Harbor Laboratory, 2023

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

Genome-wide characterization of Ficus carica MADS-box transcription factors with a focus on their roles during fruit development
N. Kmeli - J. Hamdi, D. Bouktila, - Horticulture, Environment, and Biotechnology, 2023 usegalaxy.eu

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

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

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

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

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge
N. Abdulkadir - J. Saraiva, F. Schattenberg, R. Toscan, et al. - Microorganisms, 2023

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

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

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

Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome
I. Akol - A. Izzo, F. Gather, S. Strack, et al. - Proceedings of the National Academy of Sciences, 2023 usegalaxy.eu

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
A. Soorni - M. Karimi, B. Al Sharif, K. Habibi, et al. - BMC Plant Biology, 2023 usegalaxy.eu

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

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

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

Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation
M. Zirngibl - G. Araguirang, A. Kitashova, K. Jahnke, et al. - Plant Communications, 2023 usegalaxy.eu

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

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

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

Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland
L. Andrade - M. Ryan, L. Burke, P. Hynds, et al. - Elsevier BV, 2023 usegalaxy.eu

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

NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming
Z. Zhang - X. Wang, F. Hamdan, A. Likhobabina, et al. - Cellular and Molecular Gastroenterology and Hepatology, 2023 usegalaxy.eu

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

Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
V. Atanasova - C. de Jesus Cardona, V. Hejret, A. Tiefenbacher, et al. - Cellular and Molecular Gastroenterology and Hepatology, 2023

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

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

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
L. Weber - Y. Jia, B. Stielow, S. Gisselbrecht, et al. - Nucleic Acids Research, 2022 usegalaxy.eu

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

Megan Server: facilitating interactive access to metagenomic data on a server
A. Gautam - W. Zeng, D. Huson, - Cold Spring Harbor Laboratory, 2022

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

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

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

Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov
K. Gašić - N. Zlatković, N. Kuzmanović, - Frontiers in Plant Science, 2022

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

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

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

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

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

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

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

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

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

Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
T. Kart - M. Fischer, S. Winzeck, B. Glocker, et al. - Scientific Reports, 2022

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

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

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

Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan
J. Grzegorzewski - J. Brandhorst, M. König, - Frontiers in Pharmacology, 2022

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

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

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

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

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

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

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

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

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

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

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

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

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. - 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. - 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

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

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

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

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

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

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

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

Phased grapevine genome sequence of an<i>Rpv12</i>carrier for biotechnological exploration of resistance to<i>Plasmopara viticola</i>
B. Frommer - S. Müllner, D. Holtgräwe, P. Viehöver, et al. - 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)
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An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
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Delineating genome-wide alternative splicing landscapes and their functional significance in orchids
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Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges
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Genetic and genomic diversity in the sorghum gene bank collection of Uganda
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Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
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Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
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Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat
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A Draft Human Pangenome Reference
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MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
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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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Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
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CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
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Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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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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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
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Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)
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Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
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MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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AB12PHYLO: An Integrated Pipeline for Maximum Likelihood Phylogenetic Inference from ABI Trace Data
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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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Sequence-based pangenomic core detection
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Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
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Association of DNA methylation and genetic variations of the <i>APOE</i> gene with the risk of diabetic dyslipidemia
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A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
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Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
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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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Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
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Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes
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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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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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Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes
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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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Critical Assessment of Metagenome Interpretation: the second round of challenges
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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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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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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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
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Unifying the known and unknown microbial coding sequence space
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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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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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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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In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
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Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
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Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
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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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Onset of Late Cretaceous diversification in Europe’s freshwater gastropod fauna links to global climatic and biotic events
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Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
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Pluripotency factors determine gene expression repertoire at zygotic genome activation
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Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
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Unsupervised encoding selection through ensemble pruning for biomedical classification
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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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STENCIL: A web templating engine for visualizing and sharing life science datasets
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Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
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Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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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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Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
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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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Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
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Expanding the Galaxy’s reference data
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LAMP Assay for Distinguishing <i>Fusarium oxysporum</i> and <i>Fusarium commune</i> in Lotus (<i>Nelumbo nucifera</i>) Rhizomes
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Canonical Workflows to Make Data FAIR
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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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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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A Tetragenococcus halophilus human gut isolate
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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Computational and Structural Biotechnology Journal, 2022

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

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
A. Géron - J. Werner, P. Lebaron, R. Wattiez, et al. - Microorganisms, 2021

PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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An ecological perspective on microbial genes of unknown function in soil
H. Holland-Moritz - C. Vanni, A. Fernandez-Guerra, A. Bissett, et al. - Cold Spring Harbor Laboratory, 2021

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
T. Kustner - J. Pan, H. Qi, G. Cruz, et al. - IEEE Transactions on Medical Imaging, 2021

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

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

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

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
M. Uhl - D. Rabsch, F. Eggenhofer, R. Backofen, et al. - Bioinformatics, 2021

The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
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Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted <i>Arabidopsis halleri</i>
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Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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ARTS-DB: a database for antibiotic resistant targets
M. Mungan - K. Blin, N. Ziemert, - Nucleic Acids Research, 2021

From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
M. Lauxmann - D. Vazquez, H. Schilbert, P. Neubauer, et al. - BioEssays, 2021

Automatic identification and annotation of MYB gene family members in plants
B. Pucker - - Cold Spring Harbor Laboratory, 2021

Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
M. Früh - M. Fischer, A. Schilling, S. Gatidis, et al. - Journal of Medical Imaging, 2021

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
M. Ranchou-Peyruse - M. Guignard, F. Casteran, M. Abadie, et al. - Frontiers in Microbiology, 2021 usegalaxy.eu

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Bioinformatics, 2021

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
C. Cantalapiedra - A. Hernández-Plaza, I. Letunic, P. Bork, et al. - Molecular Biology and Evolution, 2021

Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
T. Stachurová - H. Piková, M. Bartas, J. Semerád, et al. - Chemosphere, 2021 usegalaxy.eu

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
W. Maier - S. Bray, M. van den Beek, D. Bouvier, et al. - Nature Biotechnology, 2021

Screening of <i>Azadirachta indica</i> phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study
S. Chandel - R. Singh, A. Gautam, V. Ravichandiran, et al. - Journal of Biomolecular Structure and Dynamics, 2021

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

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

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. - 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. - 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

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

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

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. - Cold Spring Harbor Laboratory, 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

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 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

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

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

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

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
S. Beier - J. Werner, T. Bouvier, N. Mouquet, et al. - Cold Spring Harbor Laboratory, 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

Deep learning-based real-time detection of novel pathogens during sequencing
J. Bartoszewicz - U. Genske, B. Renard, - Briefings in Bioinformatics, 2021

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. - 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. - 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 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

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

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

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, J. Patiño-Galindo, M. Carrière, et al. - Cold Spring Harbor Laboratory, 2021

Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
V. Kaiser - L. Talmane, Y. Kumar, F. Semple, et al. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

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. - Cold Spring Harbor Laboratory, 2021

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

AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
C. Vanni - M. Schechter, T. Delmont, A. Eren, et al. - 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

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

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

Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
M. Friedrich - R. Sankowski, L. Bunse, M. Kilian, et al. - Nature Cancer, 2021 usegalaxy.eu

Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction
T. Neubauer - T. Hauffe, D. Silvestro, J. Schauer, et al. - Communications Earth &amp; Environment, 2021

Arganiella Giusti &amp; Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?
D. Delicado - V. Pešić, M. Ramos, - European Journal of Taxonomy, 2021

Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing
M. Morsli - C. Zandotti, A. Morand, P. Colson, et al. - Pathogens, 2021 usegalaxy.eu

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
M. Dieckmann - S. Beyvers, R. Nkouamedjo-Fankep, P. Hanel, et al. - Nucleic Acids Research, 2021

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts
A. Bayona-Feliu - S. Barroso, S. Muñoz, A. Aguilera, et al. - Nature Genetics, 2021 usegalaxy.eu

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
A. Rajczewski - S. Mehta, D. Nguyen, B. Grüning, et al. - Clinical Proteomics, 2021 usegalaxy.eu

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

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

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. - 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 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

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

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

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. - 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. - 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

Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
J. Pérez-Schindler - E. Vargas-Fernández, B. Karrer-Cardel, D. Ritz, et al. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

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

Single-Cell RNA Sequencing Procedures and Data Analysis
M. Wolfien - R. David, A. Galow, - Exon Publications, 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

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. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm, <i>Antheraea pernyi</i> (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. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
P. Verschaffelt - T. Van Den Bossche, W. Gabriel, M. Burdukiewicz, et al. - Journal of Proteome Research, 2021

Large scale genomic rearrangements in selected <i>Arabidopsis thaliana</i> T-DNA lines are caused by T-DNA insertion mutagenesis
B. Pucker - N. Kleinbölting, B. Weisshaar, - Cold Spring Harbor Laboratory, 2021

AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
L. Kaindl - C. Small, R. Stam, - 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

Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa
T. King - S. Schmidt, S. Thakur, P. Fedorka-Cray, et al. - Journal of Global Antimicrobial Resistance, 2021 usegalaxy.eu

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

VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
N. Poulose - N. Forsythe, A. Polonski, G. Gregg, et al. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring
K. Wüllems - A. Zurowietz, M. Zurowietz, R. Schneider, et al. - Scientific Reports, 2021

Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture
S. Tabacchioni - S. Passato, P. Ambrosino, L. Huang, et al. - Microorganisms, 2021

DenovoProfiling: a webserver for de novo generated molecule library profiling
Z. Liu - J. Du, B. Liu, Z. Cui, et al. - Research Square Platform LLC, 2021 usegalaxy.eu

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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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
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Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
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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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Interpretable detection of novel human viruses from genome sequencing data
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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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Diabetes changes gene expression but not DNA methylation in cardiac cells
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SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
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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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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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On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
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SANS serif: alignment-free, whole-genome based phylogenetic reconstruction
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RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
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Self-Supervised Learning for Automated Anatomical Tracking in Medical Image Data with Minimal Human Labeling Effort
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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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Tuning the Biological Activity of RGD Peptides with Halotryptophans
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Stable Protein Sialylation in Physcomitrella
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The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
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Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
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Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria
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Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in<i>C. elegans</i>
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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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Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
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Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
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MOSGA: Modular Open-Source Genome Annotator
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De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
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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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A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
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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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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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3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
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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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Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
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Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
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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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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
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Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
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Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
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Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
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Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
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Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
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Deep learning-based diatom taxonomy on virtual slides
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
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DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
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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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Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease
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Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
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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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Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
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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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Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration
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Ultrastructural, transcriptional, and functional differences between human reticulated and non‐reticulated platelets
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SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
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A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
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Benchmarking challenging small variants with linked and long reads
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An Interactive Visualization for Feature Localization in Deep Neural Networks
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DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
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Genome‐wide cooperation of <scp>EMT</scp> transcription factor <scp>ZEB</scp> 1 with <scp>YAP</scp> and <scp>AP</scp> ‐1 in breast cancer
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The landscape of SARS-CoV-2 RNA modifications
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Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
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Lake expansion elevates equilibrium diversity via increasing colonization
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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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Unifying the known and unknown microbial coding sequence space
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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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Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
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Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
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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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Galactic Circos: User-friendly Circos plots within the Galaxy platform
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The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
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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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Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server
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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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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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Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
R. Winkler - I. Rosas-Román, - American Chemical Society (ACS), 2020 usegalaxy.eu

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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Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
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A framework for designing miRNA-based distributed cell classifier circuits
M. Nowicka - H. Siebert, - Cold Spring Harbor Laboratory, 2020

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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Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive<i>de novo</i>DNA methylation mechanisms
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The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
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Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
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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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Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
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Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
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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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Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
T. McGowan J. Johnson P. Kumar R. Sajulga S. Mehta P. Jagtap T. Griffin - - GigaScience, 2020 usegalaxy.eu

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
J. Werner - E. Nour, B. Bunk, C. Spröer, et al. - Frontiers in Microbiology, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
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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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Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
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Gene expression in immortalized versus primary isolated cardiac endothelial cells
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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
M. Zurowietz - T. Nattkemper, - IEEE Access, 2020

BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
T. Senapathi - C. Barnett, K. Naidoo, - BIO-PROTOCOL, 2020 usegalaxy.eu

GLP: A requirement in cell therapies - perspectives for the cardiovascular field
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Computing the Rearrangement Distance of Natural Genomes
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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
Y. Perez‐Riverol - P. Moreno, - PROTEOMICS, 2019 usegalaxy.eu

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
R. Janßen - W. Skeff, J. Werner, M. Wirth, et al. - Frontiers in Marine Science, 2019

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
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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
L. Forth - D. Höper, - BioTechniques, 2019 usegalaxy.eu

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
J. Torres-Paz - J. Leclercq, S. Rétaux, - eLife, 2019 usegalaxy.eu

Expression Atlas update: from tissues to single cells
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Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
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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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Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
M. Emperle - S. Adam, S. Kunert, M. Dukatz, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

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
B. Jude - - Microbiology Resource Announcements, 2019 usegalaxy.eu

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
I. Kemker - C. Schnepel, D. Schröder, A. Marion, et al. - Journal of Medicinal Chemistry, 2019

U2 <scp>AF</scp> <sup>65</sup> assemblies drive sequence‐specific splice site recognition
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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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The RNA workbench 2.0: next generation RNA data analysis
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Reproducible Scientific Workflows for High Performance and Cloud Computing
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BOOTABLE: Bioinformatics Benchmark Tool Suite
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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
J. Espenshade - S. Thijs, S. Gawronski, H. Bové, et al. - Frontiers in Microbiology, 2019 usegalaxy.eu

Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
L. Youssar - V. Wernet, N. Hensel, X. Yu, et al. - PLOS Genetics, 2019 usegalaxy.eu

1,4-Disubstituted 1H-1,2,3-Triazole Containing Peptidotriazolamers: A New Class of Peptidomimetics With Interesting Foldamer Properties
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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
D. Delicado - B. Arconada, A. Aguado, M. Ramos, et al. - Zoological Journal of the Linnean Society, 2019

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi - S. Bray, C. Barnett, B. Grüning, et al. - Bioinformatics, 2019 usegalaxy.eu

CAMISIM: simulating metagenomes and microbial communities
A. Fritz - P. Hofmann, S. Majda, E. Dahms, et al. - Microbiome, 2019

Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
K. Wylie - T. Wylie, P. Minx, D. Rosen, et al. - Frontiers in Cellular and Infection Microbiology, 2019 usegalaxy.eu

Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms
D. Kolosov - M. O'Donnell, - Journal of Experimental Biology, 2019 usegalaxy.eu

Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis
A. Lother - L. Deng, M. Huck, D. Fürst, et al. - Journal of Endocrinology, 2019 usegalaxy.eu

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
N. Owen - M. Moosajee, - Therapeutic Advances in Ophthalmology, 2019 usegalaxy.eu

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
A. Bagnacani - M. Wolfien, O. Wolkenhauer, - Springer New York, 2019 usegalaxy.eu

Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
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Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
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Workflow Development for the Functional Characterization of ncRNAs
M. Wolfien - D. Brauer, A. Bagnacani, O. Wolkenhauer, et al. - Springer New York, 2019 usegalaxy.eu

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
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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
I. Maus - M. Rumming, I. Bergmann, K. Heeg, et al. - Biotechnology for Biofuels, 2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
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Community-Driven Data Analysis Training for Biology
B. Batut - S. Hiltemann, A. Bagnacani, D. Baker, et al. - Cell Systems, 2018 usegalaxy.eu

ASaiM: a Galaxy-based framework to analyze microbiota data
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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
P. Wright* - M. Mann*, R. Backofen*, - Microbiology Spectrum, 2018 usegalaxy.eu

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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Workflows for microscopy image analysis and cellular phenotyping
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Bioinformatics for NGS-based metagenomics and the application to biogas research
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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
T. Wollmann - K. Rohr, - IEEE, 2017

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
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Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Y. Stolze - A. Bremges, M. Rumming, C. Henke, et al. - Biotechnology for Biofuels, 2016