Publications

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Currently 777 publications with reference to de.NBI Cloud are listed.

Recently added publication

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Multiplicity of <i>bla</i> <sub>KPC</sub> Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307
G. Arcari - R. Polani, S. Santilli, V. Capitani, et al. - Antimicrobial Agents and Chemotherapy, 2023 usegalaxy.eu

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

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

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

Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches
Z. Zinati - L. Nazari, - Scientific Reports, 2023 usegalaxy.eu

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

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

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

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

Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications
W. Lapadula - M. Juri Ayub, - Gene, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies
A. Pustam - J. Jayaraman, A. Ramsubhag, - PLOS ONE, 2023 usegalaxy.eu

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

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

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

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

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

Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of <i>Escherichia coli</i> towards interventive antibacterial therapy
J. Aribisala - K. Idowu, T. Makhanya, S. Sabiu, et al. - Molecular Simulation, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Proline and Silver Nitrate Promotes Multiple Shoot Induction from Mature Embryo and Shoot Tip Explants of Sorghum
B. Pawar - N. Markad, R. Wagh, M. Neumann, et al. - Sugar Tech, 2023

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

Genome-wide Identification of the Auxin Transporter Gene Families in Sweet Potato (Ipomoea batatas) and their Expression During Tuberization
S. Mathura - F. Sutton, V. Bowrin, - Tropical Plant Biology, 2023 usegalaxy.eu

In-silico transcriptome analysis of antibiotic-treated Mycobacterium tuberculosis identifies novel antibiotic resistance factors
S. Sundar - - Indian Journal of Tuberculosis, 2023 usegalaxy.eu

Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
M. Chanama - P. Prombutara, S. Chanama, - Scientific Reports, 2023 usegalaxy.eu

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

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

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

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

Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
V. Capitani - G. Arcari, A. Oliva, F. Sacco, et al. - Antibiotics, 2023 usegalaxy.eu

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

Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
S. Anbazhagan - K. Himani, R. Karthikeyan, L. Prakasan, et al. - International Microbiology, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

ODNA: identification of organellar DNA by machine learning
R. Martin - M. Nguyen, N. Lowack, D. Heider, et al. - Bioinformatics, 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections
R. Spanò - S. Fortunato, V. Linsalata, I. D’Antuono, et al. - Plants, 2023 usegalaxy.eu

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

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

The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops
J. Voelker - R. Mauleon, M. Shepherd, - Plant Systematics and Evolution, 2023 usegalaxy.eu

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

Proteome alterations in human autopsy tissues in relation to time after death
É. Kocsmár - M. Schmid, M. Cosenza-Contreras, I. Kocsmár, et al. - Cellular and Molecular Life Sciences, 2023 usegalaxy.eu

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

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

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

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

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

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

DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
H. Roux - S. Figueiredo, L. Sareoua, M. Salmona, et al. - Cell Reports Methods, 2023 usegalaxy.eu

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

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

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 - Research Square Platform LLC, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

Identification of Radiomic Biomarkers in a Set of Four Skeletal Muscle Groups on Dixon MRI of the NAKO MR study
M. Fischer - T. Küstner, S. Pappa, T. Niendorf, et al. - Research Square - Research Square Platform LLC, 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
A. Andersson - A. Behanova, C. Wählby, F. Malmberg, et al. - Springer Nature Switzerland, 2023

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

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

Development of Similarity Measures From Graph-Structured Bibliographic Metadata: An Application to Identify Scientific Convergence
T. Melnychuk - L. Galke, E. Seidlmayer, S. Bröring, et al. - IEEE Transactions on Engineering Management, 2023

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

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

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

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

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

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

Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
S. Bordel - D. Martín-González, R. Muñoz, F. Santos-Beneit, et al. - Molecular Genetics and Genomics, 2022 usegalaxy.eu

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
A. Kumar - G. Cuccuru, B. Grüning, R. Backofen, et al. - GigaScience, 2022 usegalaxy.eu

Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea
D. Lee - J. Kim, A. Park, D. Kim, et al. - Scientific Reports, 2022 usegalaxy.eu

Guiding the choice of informatics software and tools for lipidomics research applications
Z. Ni - M. Wölk, G. Jukes, K. Mendivelso Espinosa, et al. - Nature Methods, 2022

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

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

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

Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium
M. Dziuba - A. Paulus, L. Schramm, R. Awal, et al. - The ISME Journal, 2022 usegalaxy.eu

Points2Regions: Fast Interactive Clustering of<i>in Situ</i>Transcriptomics Data
A. Andersson - A. Behanova, C. Avenel, C. Wählby, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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. - bioRxiv - Cold Spring Harbor Laboratory, 2022

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
V. Atanasova - C. de Jesus Cardona, V. Hejret, A. Tiefenbacher, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Peakhood: individual site context extraction for CLIP-seq peak regions
M. Uhl - D. Rabsch, F. Eggenhofer, R. Backofen, et al. - Bioinformatics, 2021

The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
I. Phan - C. Rice, J. Craig, R. Noorai, et al. - Scientific Reports, 2021 usegalaxy.eu

The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
I. Dimkić - V. Bhardwaj, V. Carpentieri-Pipolo, N. Kuzmanović, et al. - PLOS ONE, 2021

Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
R. Rettenmaier - N. Thieme, J. Streubel, L. Di Bello, et al. - International Journal of Systematic and Evolutionary Microbiology, 2021

Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted <i>Arabidopsis halleri</i>
G. Lee - H. Ahmadi, J. Quintana, L. Syllwasschy, et al. - The Plant Journal, 2021

Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
J. Ma - J. Chen, B. Louro, R. Martins, et al. - Aquaculture and Fisheries, 2021 usegalaxy.eu

ARTS-DB: a database for antibiotic resistant targets
M. Mungan - K. Blin, N. Ziemert, - Nucleic Acids Research, 2021

Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
A. Page-Karjian - L. Whitmore, B. Stacy, J. Perrault, et al. - Animals, 2021 usegalaxy.eu

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

Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
C. Pessoa Rodrigues - A. Chatterjee, M. Wiese, T. Stehle, et al. - Nature Communications, 2021 usegalaxy.eu

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

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

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

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
J. Meier-Kolthoff - J. Carbasse, R. Peinado-Olarte, M. Göker, et al. - Nucleic Acids Research, 2021

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

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

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

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

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

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
K. Peters - S. Herman, P. Khoonsari, J. Burman, et al. - Scientific Reports, 2021 usegalaxy.eu

Genomic impact of stress-induced transposable element mobility in Arabidopsis
D. Roquis - M. Robertson, L. Yu, M. Thieme, et al. - Nucleic Acids Research, 2021 usegalaxy.eu

Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
O. Saleh - S. Dwiani, J. Rott, K. Kühn, et al. - Springer US, 2021 usegalaxy.eu

Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines
D. Brandt - M. Simunovic, T. Busche, M. Haak, et al. - Viruses, 2021

Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
A. Carattoli - G. Arcari, G. Bibbolino, F. Sacco, et al. - Antimicrobial Agents and Chemotherapy, 2021 usegalaxy.eu

FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
C. Fell - A. Hagelkruys, A. Cicvaric, M. Horrer, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
S. Hering - M. Jansson, M. Buhl, - International Journal of Systematic and Evolutionary Microbiology, 2021 usegalaxy.eu

The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
A. Migur - F. Heyl, J. Fuss, A. Srikumar, et al. - Journal of Experimental Botany, 2021 usegalaxy.eu

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
I. Apostolakos - A. Laconi, L. Mughini-Gras, Ö. Yapicier, et al. - Frontiers in Veterinary Science, 2021 usegalaxy.eu

First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
D. Chen - R. Zhang, X. Jin, J. Yang, et al. - Bulletin of Entomological Research, 2021 usegalaxy.eu

Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
O. Schwengers - L. Jelonek, M. Dieckmann, S. Beyvers, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
D. Katsanos - M. Ferrando-Marco, I. Razzaq, G. Aughey, et al. - Development, 2021 usegalaxy.eu

Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
T. Hepp - D. Blum, K. Armanious, B. Schölkopf, et al. - Computerized Medical Imaging and Graphics, 2021

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
V. Glaros - R. Rauschmeier, A. Artemov, A. Reinhardt, et al. - Immunity, 2021 usegalaxy.eu

Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
M. Kavas - K. Yıldırım, Z. Seçgin, M. Abdulla, et al. - Physiology and Molecular Biology of Plants, 2021 usegalaxy.eu

RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
J. Pérez-Schindler - B. Kohl, K. Schneider-Heieck, A. Leuchtmann, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
G. Cova - C. Taroni, M. Deau, Q. Cai, et al. - Journal of Experimental Medicine, 2021 usegalaxy.eu

Single‐cell omics: Overview, analysis, and application in biomedical science
C. Stein - R. Weiskirchen, F. Damm, P. Strzelecka, et al. - Journal of Cellular Biochemistry, 2021 usegalaxy.eu

Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
D. Vazquez - H. Schilbert, V. Dodero, - International Journal of Molecular Sciences, 2021

Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
J. Loske - J. Röhmel, S. Lukassen, S. Stricker, et al. - Nature Biotechnology, 2021

Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
S. Baron - O. Mediannikov, R. Abdallah, E. Kuete Yimagou, et al. - Antimicrobial Agents and Chemotherapy, 2021 usegalaxy.eu

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in <i>Arabidopsis</i>
A. Barragán-Rosillo - C. Peralta-Alvarez, J. Ojeda-Rivera, R. Arzate-Mejía, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
E. Musmeci - F. Candeliere, A. Amaretti, M. Rossi, et al. - Microbiology Resource Announcements, 2021 usegalaxy.eu

Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework
M. Föll - V. Volkmann, K. Enderle-Ammour, K. Wilhelm, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
S. Bandyopadhyay - O. Abiodun, B. Ogboo, A. Kola-Mustapha, et al. - Journal of Biomolecular Structure and Dynamics, 2021 usegalaxy.eu

A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass
J. Hölper - F. Grey, J. Baillie, T. Regan, et al. - Viruses, 2021 usegalaxy.eu

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
K. Mauer - H. Schmidt, M. Dittrich, A. Fröbius, et al. - BMC Genomics, 2021 usegalaxy.eu

A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species
J. Voelker - M. Shepherd, R. Mauleon, - Gigabyte, 2021 usegalaxy.eu

The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
M. Bartas - V. Brázda, A. Volná, J. Červeň, et al. - International Journal of Molecular Sciences, 2021 usegalaxy.eu

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.
L. Schaffert - M. Ruwe, J. Milse, K. Hanuschka, et al. - International Journal of Systematic and Evolutionary Microbiology, 2021

Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
A. Cvetkoska - E. Jovanovska, T. Hauffe, T. Donders, et al. - Quaternary Science Reviews, 2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
Y. Dorone - S. Boeynaems, E. Flores, B. Jin, et al. - Cell, 2021 usegalaxy.eu

Eplerenone Improves Pulmonary Vascular Remodeling and Hypertension by Inhibition of the Mineralocorticoid Receptor in Endothelial Cells
J. Kowalski - L. Deng, C. Suennen, D. Koca, et al. - Hypertension, 2021 usegalaxy.eu

A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
D. Pelletier - D. Roos, M. Bouchoucha, T. Schohn, et al. - Frontiers in Marine Science, 2021 usegalaxy.eu

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
T. Bauer - K. Collmar, T. Kaltofen, A. Loeffler, et al. - Cancers, 2021 usegalaxy.eu

Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
T. Spradling - A. Place, A. Campbell, J. Demastes, et al. - PLOS ONE, 2021 usegalaxy.eu

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

Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
S. Friedrich - H. Müller, C. Riesterer, H. Schüller, et al. - Scientific Reports, 2021 usegalaxy.eu

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
M. Hanussek - F. Bartusch, J. Krüger, - PLOS Computational Biology, 2021

Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
R. Pallares-Vega - G. Macedo, M. Brouwer, L. Hernandez Leal, et al. - Frontiers in Microbiology, 2021 usegalaxy.eu

Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
C. Bamford - L. Broadbent, E. Aranday-Cortes, M. McCabe, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

The complete mitochondrial genome of the wild silkmoth <i>Antheraea yamamai</i> from Heilongjiang, China (Lepidoptera: Saturniidae)
S. Sun - J. Huang, Y. Liu, - Mitochondrial DNA Part B, 2021 usegalaxy.eu

Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
J. Grzegorzewski - F. Bartsch, A. Köller, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time
J. Theine - D. Holtgräwe, K. Herzog, F. Schwander, et al. - BMC Plant Biology, 2021

Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis
M. Winkler - A. Pan, - Research Square - Research Square Platform LLC, 2021 usegalaxy.eu

ONT-Based Draft Genome Assembly and Annotation of <i>Alternaria atra</i>
B. Bonthala - C. Small, M. Lutz, A. Graf, et al. - Molecular Plant-Microbe Interactions®, 2021

Age-Net: An MRI-Based Iterative Framework for Brain Biological Age Estimation
K. Armanious - S. Abdulatif, W. Shi, S. Salian, et al. - IEEE Transactions on Medical Imaging, 2021

Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone
P. Volkova - G. Duarte, E. Kazakova, E. Makarenko, et al. - Science of The Total Environment, 2021 usegalaxy.eu

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
S. Oselusi - A. Christoffels, S. Egieyeh, - Molecules, 2021 usegalaxy.eu

Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
X. Zhuang - G. Schlunck, J. Wolf, D. Rosmus, et al. - Journal of Innate Immunity, 2021 usegalaxy.eu

Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
X. Zhuang - G. Schlunck, J. Wolf, D. Rosmus, et al. - Journal of Innate Immunity, 2021 usegalaxy.eu

Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon
B. Abanda - M. Schmid, A. Paguem, H. Iffland, et al. - Genes, 2021

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
M. Soares - D. Soares, V. Teixeira, A. Heskol, et al. - Genes &amp; Development, 2021 usegalaxy.eu

DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
L. Bichmann - S. Gupta, G. Rosenberger, L. Kuchenbecker, et al. - Journal of Proteome Research, 2021

SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction
A. Rempel - R. Wittler, - Bioinformatics, 2021

Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
M. Bleher - L. Hahn, M. Neumann, J. Patiño-Galindo, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021

Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy
K. Kimura - A. Ooms, K. Graf-Riesen, M. Kuppusamy, et al. - Nature Communications, 2021 usegalaxy.eu

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

Assessing the role of polygenic background on the penetrance of monogenic forms in Parkinson’s disease
E. Hassanin - P. May, R. Aldisi, P. Krawitz, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021

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

Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history
E. Hassanin - P. May, R. Aldisi, I. Spier, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021

AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
C. Vanni - M. Schechter, T. Delmont, A. Eren, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
M. Roncoroni - B. Droesbeke, I. Eguinoa, K. De Ruyck, et al. - Bioinformatics, 2021 usegalaxy.eu

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Q. Gu - A. Kumar, S. Bray, A. Creason, et al. - PLOS Computational Biology, 2021 usegalaxy.eu

A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame
E. Yol - M. Basak, S. Kızıl, S. Lucas, et al. - Frontiers in Plant Science, 2021 usegalaxy.eu

Going to extremes – a metagenomic journey into the dark matter of life
A. Aevarsson - A. Kaczorowska, B. Adalsteinsson, J. Ahlqvist, et al. - FEMS Microbiology Letters, 2021

Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells
S. Dvir - A. Argoetti, C. Lesnik, M. Roytblat, et al. - Cell Reports, 2021 usegalaxy.eu

CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification
C. Yanta - K. Bessonov, G. Robinson, K. Troell, et al. - Food and Waterborne Parasitology, 2021 usegalaxy.eu

Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis
Y. Yu - W. Fu, J. Xu, Y. Lei, et al. - Molecular Plant, 2021 usegalaxy.eu

COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints
L. Langnickel - R. Baum, J. Darms, S. Madan, et al. - IOS Press, 2021

A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines
M. Fahrner - L. Kook, K. Fröhlich, M. Biniossek, et al. - Proteomes, 2021 usegalaxy.eu

SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities
M. Macnee - E. Pérez-Palma, S. Schumacher-Bass, J. Dalton, et al. - Bioinformatics, 2021 usegalaxy.eu

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

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

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

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

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

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

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

Peptidotriazolamers Inhibit Aβ(1–42) Oligomerization and Cross a Blood‐Brain‐Barrier Model
N. Tonali - L. Hericks, D. Schröder, O. Kracker, et al. - ChemPlusChem, 2021

Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties
S. Oberbeckmann - D. Bartosik, S. Huang, J. Werner, et al. - Environmental Microbiology, 2021

Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants
S. Weigang - J. Fuchs, G. Zimmer, D. Schnepf, et al. - medRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

ZC3H4 restricts non-coding transcription in human cells
C. Estell - L. Davidson, P. Steketee, A. Monier, et al. - eLife, 2021 usegalaxy.eu

Common virulence gene expression in adult first-time infected malaria patients and severe cases
J. Wichers - G. Tonkin-Hill, T. Thye, R. Krumkamp, et al. - eLife, 2021 usegalaxy.eu

Draft genome of a biparental beetle species, Lethrus apterus
N. Nagy - R. Rácz, O. Rimington, S. Póliska, et al. - BMC Genomics, 2021 usegalaxy.eu

Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates
A. Klein - H. Solinski, N. Malewicz, H. Ieong, et al. - eLife, 2021 usegalaxy.eu

Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
O. Genolet - A. Monaco, I. Dunkel, M. Boettcher, et al. - Genome Biology, 2021 usegalaxy.eu

Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae)
J. Delroisse - L. Duchatelet, P. Flammang, J. Mallefet, et al. - Frontiers in Marine Science, 2021 usegalaxy.eu

A large-scale comparative study on peptide encodings for biomedical classification
S. Spänig - S. Mohsen, G. Hattab, A. Hauschild, et al. - NAR Genomics and Bioinformatics, 2021

Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies
R. Ali - J. Jayaraman, A. Mohammed, C. Chinnaraja, et al. - Research Square - Research Square Platform LLC, 2021 usegalaxy.eu

A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation
S. Pinter - F. Knodel, M. Choudalakis, P. Schnee, et al. - Nucleic Acids Research, 2021 usegalaxy.eu

Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels
A. Simon-Chica - M. Fernández, E. Wülfers, A. Lother, et al. - Cardiovascular Research, 2021 usegalaxy.eu

Haplotype-resolved diverse human genomes and integrated analysis of structural variation
P. Ebert - P. Audano, Q. Zhu, B. Rodriguez-Martin, et al. - Science, 2021

Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment
M. Cordellier - M. Wojewodzic, M. Wessels, C. Kuster, et al. - Zoology, 2021 usegalaxy.eu

Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds
I. Gessara - F. Dittrich, M. Hertel, S. Hildebrand, et al. - Stem Cell Reports, 2021 usegalaxy.eu

Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy
T. Villa - Y. Jaszczyszyn, D. Libri, - Data in Brief, 2021 usegalaxy.eu

The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures
T. Faddetta - L. Abbate, P. Alibrandi, W. Arancio, et al. - Scientific Reports, 2021 usegalaxy.eu

Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the<i>Xist</i>locus
R. Gjaltema - T. Schwämmle, P. Kautz, M. Robson, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
P. Moreno - N. Huang, J. Manning, S. Mohammed, et al. - Nature Methods, 2021 usegalaxy.eu

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
W. Maier - S. Bray, M. van den Beek, D. Bouvier, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Replication of a Novel Parkinson's Locus in a European Ancestry Population
S. Grover - A. Kumar‐Sreelatha, D. Bobbili, P. May, et al. - Movement Disorders, 2021

Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (<i>Pimephales promelas</i>)
A. Alcaraz - D. Potěšil, K. Mikulášek, D. Green, et al. - Environmental Science &amp; Technology, 2021 usegalaxy.eu

Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate
Z. Tu - P. Setlow, S. Brul, G. Kramer, et al. - Microorganisms, 2021 usegalaxy.eu

Direct impact of commonly used dietary emulsifiers on human gut microbiota
S. Naimi - E. Viennois, A. Gewirtz, B. Chassaing, et al. - Microbiome, 2021 usegalaxy.eu

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
A. Hoek - K. Maibach, E. Özmen, A. Vazquez-Armendariz, et al. - BMC Genomics, 2021

Single-Cell RNA Sequencing Procedures and Data Analysis
M. Wolfien - R. David, A. Galow, - Exon Publications, 2021 usegalaxy.eu

Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
K. Boulaassafer - M. Ghamizi, A. Machordom, C. Albrecht, et al. - Organisms Diversity &amp; Evolution, 2021

Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis
R. Rauschmeier - A. Reinhardt, C. Gustafsson, V. Glaros, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm, <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. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

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

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

AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
L. Kaindl - C. Small, R. Stam, - bioRxiv - Cold Spring Harbor Laboratory, 2021

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
F. Meyer - T. Lesker, D. Koslicki, A. Fritz, et al. - Nature Protocols, 2021

Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
M. Hesse - R. Bednarz, E. Carls, C. Becker, et al. - Journal of Molecular and Cellular Cardiology, 2021 usegalaxy.eu

Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
M. Hesse - R. Bednarz, E. Carls, C. Becker, et al. - Journal of Molecular and Cellular Cardiology, 2021 usegalaxy.eu

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

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

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

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

Decitabine Induces Gene Derepression on Monosomic Chromosomes: <i>In Vitro</i> and <i>In Vivo</i> Effects in Adverse-Risk Cytogenetics AML
G. Greve - J. Schüler, B. Grüning, B. Berberich, et al. - Cancer Research, 2021 usegalaxy.eu

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

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
W. Logroño - D. Popp, M. Nikolausz, P. Kluge, et al. - Frontiers in Microbiology, 2021

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
S. Mehta - M. Crane, E. Leith, B. Batut, et al. - F1000Research, 2021 usegalaxy.eu

Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra
S. Hetz - M. Horn, - Frontiers in Microbiology, 2021 usegalaxy.eu

Detecting high-scoring local alignments in pangenome graphs
T. Schulz - R. Wittler, S. Rahmann, F. Hach, et al. - Bioinformatics, 2021

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
A. Wittig - F. Miranda, M. Hölzer, T. Altenburg, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Interpretable detection of novel human viruses from genome sequencing data
J. Bartoszewicz - A. Seidel, B. Renard, - NAR Genomics and Bioinformatics, 2021

Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
C. Niemöller - J. Wehrle, J. Riba, R. Claus, et al. - Communications Biology, 2021 usegalaxy.eu

Diabetes changes gene expression but not DNA methylation in cardiac cells
A. Lother - O. Bondareva, A. Saadatmand, L. Pollmeier, et al. - Journal of Molecular and Cellular Cardiology, 2021 usegalaxy.eu

3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis
X. Luo - Y. Liu, D. Dang, T. Hu, et al. - Cell, 2021 usegalaxy.eu

Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
A. Ostrovsky - J. Hillman‐Jackson, D. Bouvier, D. Clements, et al. - Current Protocols, 2021 usegalaxy.eu

SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
M. Rogg - J. Maier, R. Dotzauer, N. Artelt, et al. - Journal of the American Society of Nephrology, 2021 usegalaxy.eu

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
P. Videm - A. Kumar, O. Zharkov, B. Grüning, et al. - GigaScience, 2021 usegalaxy.eu

Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences
G. Fiedler - A. Herbstmann, E. Doll, M. Wenning, et al. - Microorganisms, 2021 usegalaxy.eu

Scarless engineering of the<i>Drosophila</i>genome near any site-specific integration site
S. Feng - S. Lu, W. Grueber, R. Mann, et al. - Genetics, 2021 usegalaxy.eu

A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape
P. Vollrath - H. Chawla, S. Schiessl, I. Gabur, et al. - Theoretical and Applied Genetics, 2021

Congenital heart disease risk loci identified by genome-wide association study in European patients
H. Lahm - M. Jia, M. Dreßen, F. Wirth, et al. - Journal of Clinical Investigation, 2021 usegalaxy.eu

Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
O. Blifernez-Klassen - V. Klassen, D. Wibberg, E. Cebeci, et al. - Scientific Reports, 2021

Deep Learning‐Based Automated Abdominal Organ Segmentation in the UK Biobank and German National Cohort Magnetic Resonance Imaging Studies
T. Kart - M. Fischer, T. Küstner, T. Hepp, et al. - Investigative Radiology, 2021

On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
W. Zeng - A. Gautam, D. Huson, - Computation, 2021

ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
S. Hildebrandt - B. Kampfrath, K. Fischer, L. Hildebrand, et al. - Stem Cell Reviews and Reports, 2021 usegalaxy.eu

SANS serif: alignment-free, whole-genome based phylogenetic reconstruction
A. Rempel - R. Wittler, - bioRxiv - Cold Spring Harbor Laboratory, 2021

Electroactive microorganisms in mouse feces
L. Rago - D. Popp, J. Heiker, F. Harnisch, et al. - Electrochimica Acta, 2021

Current status of use of high throughput nucleotide sequencing in rheumatology
S. Boegel - J. Castle, A. Schwarting, - RMD Open, 2021

Tool recommender system in Galaxy using deep learning
A. Kumar - H. Rasche, B. Grüning, R. Backofen, et al. - GigaScience, 2021 usegalaxy.eu

The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry
L. Fernandez-Lopez - S. Sanchez-Carrillo, A. García-Moyano, E. Borchert, et al. - Computational and Structural Biotechnology Journal, 2021

Self-Supervised Learning for Automated Anatomical Tracking in Medical Image Data with Minimal Human Labeling Effort
M. Frueh - T. Kuestner, M. Nachbar, D. Thorwarth, et al. - SSRN Electronic Journal, 2021

MOSGA 2: Comparative genomics and validation tools
R. Martin - H. Dreßler, G. Hattab, T. Hackl, et al. - Computational and Structural Biotechnology Journal, 2021

RNA-Seq Data Analysis in Galaxy
B. Batut - M. van den Beek, M. Doyle, N. Soranzo, et al. - Springer US, 2021 usegalaxy.eu

RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
J. Tosar - F. Gámbaro, M. Castellano, A. Cayota, et al. - BIO-PROTOCOL, 2021 usegalaxy.eu

SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance
J. Stahlecker - E. Mingyar, N. Ziemert, M. Mungan, et al. - Molecules, 2020

Duration of Colonisation With Extended-spectrum Beta-lactamase-producing Escherichia Coli: Results of an Open Cohort Study With Dutch Nursing Home Residents (2013 – 2019)
V. Weterings - T. Goede, Y. Hendriks, L. Kilsdonk, et al. - Research Square - Research Square Platform LLC, 2020 usegalaxy.eu

Tuning the Biological Activity of RGD Peptides with Halotryptophans
I. Kemker - D. Schröder, R. Feiner, K. Müller, et al. - Journal of Medicinal Chemistry, 2020

Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
S. Trump - S. Lukassen, M. Anker, R. Chua, et al. - Nature Biotechnology, 2020

Population studies of the wild tomato species <i>Solanum chilense</i> reveal geographically structured major gene-mediated pathogen resistance
P. Kahlon - S. Seta, G. Zander, D. Scheikl, et al. - Proceedings of the Royal Society B: Biological Sciences, 2020

Genomic analysis provides novel insights into diversification and taxonomy of <i>Allorhizobium vitis</i> (i.e. <i>Agrobacterium vitis</i>)
N. Kuzmanović - E. Biondi, J. Overmann, J. Puławska, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Stable Protein Sialylation in Physcomitrella
L. Bohlender - J. Parsons, S. Hoernstein, C. Rempfer, et al. - Frontiers in Plant Science, 2020 usegalaxy.eu

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
I. Maus - T. Tubbesing, D. Wibberg, R. Heyer, et al. - Microorganisms, 2020

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
E. Redl - R. Sheibani-Tezerji, C. Cardona, P. Hamminger, et al. - Life Science Alliance, 2020

Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria
B. Liu - D. Popp, N. Müller, H. Sträuber, et al. - Microorganisms, 2020

Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
J. Broche - G. Kungulovski, P. Bashtrykov, P. Rathert, et al. - Nucleic Acids Research, 2020 usegalaxy.eu

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
D. Porubsky . - P. Ebert, P. Audano, M. Vollger, et al. - Nature Biotechnology, 2020

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
M. Chiara - A. D’Erchia, C. Gissi, C. Manzari, et al. - Briefings in Bioinformatics, 2020 usegalaxy.eu

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
M. Chiara - A. D’Erchia, C. Gissi, C. Manzari, et al. - Briefings in Bioinformatics, 2020 usegalaxy.eu

MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue
S. Boneva - A. Schlecht, P. Zhang, D. Boehringer, et al. - Scientific Reports, 2020 usegalaxy.eu

Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis
P. McErlean - C. Bell, R. Hewitt, Z. Busharat, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in<i>C. elegans</i>
W. Qi - E. Gromoff, F. Xu, Q. Zhao, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
M. Riediger - P. Spät, R. Bilger, K. Voigt, et al. - The Plant Cell, 2020 usegalaxy.eu

MOSGA: Modular Open-Source Genome Annotator
R. Martin - T. Hackl, G. Hattab, M. Fischer, et al. - Bioinformatics, 2020

Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
F. Stiehler - M. Steinborn, S. Scholz, D. Dey, et al. - Bioinformatics, 2020

A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
W. Liang - K. Yamahara, C. Hernando-Erhard, S. Lagies, et al. - Kidney International, 2020 usegalaxy.eu

De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
L. Marisaldi - D. Basili, G. Gioacchini, A. Canapa, et al. - Marine Genomics, 2020 usegalaxy.eu

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
J. Martinez-Fabregas - L. Wang, E. Pohler, A. Cozzani, et al. - Cell Reports, 2020 usegalaxy.eu

Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages
J. Wolf - X. Zhuang, A. Hildebrand, S. Boneva, et al. - Molecular Immunology, 2020 usegalaxy.eu

CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of<i>Coxiella burnetii</i>genomic sequences
A. Fasemore - A. Helbich, M. Walter, T. Dandekar, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
K. Dührkop - L. Nothias, M. Fleischauer, R. Reher, et al. - Nature Biotechnology, 2020

RNA nucleation by MSL2 induces selective X chromosome compartmentalization
C. Valsecchi - M. Basilicata, P. Georgiev, A. Gaub, et al. - Nature, 2020 usegalaxy.eu

Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
I. Meyer-Cifuentes - J. Werner, N. Jehmlich, S. Will, et al. - Nature Communications, 2020

Survey of metaproteomics software tools for functional microbiome analysis
R. Sajulga - C. Easterly, M. Riffle, B. Mesuere, et al. - PLOS ONE, 2020 usegalaxy.eu

PK-DB: pharmacokinetics database for individualized and stratified computational modeling
J. Grzegorzewski - J. Brandhorst, K. Green, D. Eleftheriadou, et al. - Nucleic Acids Research, 2020

Fully Automated and Standardized Segmentation of Adipose Tissue Compartments via Deep Learning in 3D Whole-Body MRI of Epidemiologic Cohort Studies
T. Küstner - T. Hepp, M. Fischer, M. Schwartz, et al. - Radiology: Artificial Intelligence, 2020

Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells
V. Čermák - D. Tyč, A. Přibylová, L. Fischer, et al. - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2020 usegalaxy.eu

Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues
F. Guendel - M. Kofoed-Branzk, K. Gronke, C. Tizian, et al. - Immunity, 2020 usegalaxy.eu

Next generation sequencing study on RNA viruses of<i>Vespa velutina</i>and<i>Apis mellifera</i>sharing the same foraging area
F. Marzoli - M. Forzan, L. Bortolotti, M. Pacini, et al. - Transboundary and Emerging Diseases, 2020 usegalaxy.eu

High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh
S. Ahmed - T. Das, M. Islam, A. Herrero-Fresno, et al. - Scientific Reports, 2020 usegalaxy.eu

Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets
Y. Gaafar - H. Ziebell, - PeerJ, 2020 usegalaxy.eu

The environment drives microbial trait variability in aquatic habitats
S. Beier - A. Andersson, P. Galand, C. Hochart, et al. - Molecular Ecology, 2020

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
T. Delmont - M. Gaia, D. Hinsinger, P. Fremont, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
A. Kumar - K. Kondhare, N. Malankar, A. Banerjee, et al. - Journal of Experimental Botany, 2020 usegalaxy.eu

The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
A. Kumar - K. Kondhare, N. Malankar, A. Banerjee, et al. - Journal of Experimental Botany, 2020 usegalaxy.eu

Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
J. Wolf - C. Auw-Haedrich, A. Schlecht, S. Boneva, et al. - Scientific Reports, 2020 usegalaxy.eu

Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
M. Bazzucchi - I. Pierini, M. Giammarioli, G. De Mia, et al. - Archives of Virology, 2020 usegalaxy.eu

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
C. Zavala-Alvarado - O. Sismeiro, R. Legendre, H. Varet, et al. - PLOS Pathogens, 2020 usegalaxy.eu

Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
P. Afouda - G. Dubourg, A. Levasseur, P. Fournier, et al. - Microorganisms, 2020 usegalaxy.eu

Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
T. Wilke - T. Hauffe, E. Jovanovska, A. Cvetkoska, et al. - Science Advances, 2020

3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
S. Boneva - A. Schlecht, D. Böhringer, H. Mittelviefhaus, et al. - Laboratory Investigation, 2020 usegalaxy.eu

Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay
A. Dad - V. Dobrovolsky, R. Heflich, J. Revollo, et al. - Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2020 usegalaxy.eu

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
M. Tekman - B. Batut, A. Ostrovsky, C. Antoniewski, et al. - GigaScience, 2020 usegalaxy.eu

Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
L. Estrada Mallarino - C. Engel, İ. Ilık, D. Maticzka, et al. - Scientific Reports, 2020 usegalaxy.eu

Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
L. Lezameta - D. Cuicapuza, A. Dávila-Barclay, S. Torres, et al. - Microbiology Resource Announcements, 2020 usegalaxy.eu

Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
R. Wirth - B. Pap, T. Böjti, P. Shetty, et al. - Frontiers in Bioengineering and Biotechnology, 2020 usegalaxy.eu

tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
S. Bose - A. Suescún, J. Song, C. Castillo-González, et al. - Plant Cell Reports, 2020 usegalaxy.eu

Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
G. Greenfield - S. McPherson, J. Smith, A. Mead, et al. - Cancers, 2020 usegalaxy.eu

Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
H. de Lastic - I. Liampa, A. Georgakilas, M. Zervakis, et al. - MDPI AG, 2020 usegalaxy.eu

An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
L. Morandi - S. Sabattini, A. Renzi, A. Rigillo, et al. - Cells, 2020 usegalaxy.eu

Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
S. Boneva - J. Wolf, D. Rosmus, A. Schlecht, et al. - Frontiers in Immunology, 2020 usegalaxy.eu

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
D. Wibberg - B. Batut, P. Belmann, J. Blom, et al. - F1000Research, 2020 usegalaxy.eu

Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
T. Wilke - J. Renz, T. Hauffe, D. Delicado, et al. - Malacologia, 2020

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
S. Bray - T. Senapathi, C. Barnett, B. Grüning, et al. - Journal of Cheminformatics, 2020

Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
C. Mootapally - M. Mahajan, N. Nathani, - Microbial Ecology, 2020 usegalaxy.eu

Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
M. Núñez-Sánchez - J. Colom, L. Walsh, C. Buttimer, et al. - Microorganisms, 2020 usegalaxy.eu

Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
H. Chawla - H. Lee, I. Gabur, P. Vollrath, et al. - Plant Biotechnology Journal, 2020

Deep learning-based diatom taxonomy on virtual slides
M. Kloster - D. Langenkämper, M. Zurowietz, B. Beszteri, et al. - Scientific Reports, 2020

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
H. Schiebenhoefer - K. Schallert, B. Renard, K. Trappe, et al. - Nature Protocols, 2020

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
M. Bentsen - P. Goymann, H. Schultheis, K. Klee, et al. - Nature Communications, 2020

DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
G. Di Dalmazi - L. Morandi, B. Rubin, C. Pilon, et al. - The Journal of Clinical Endocrinology &amp; Metabolism, 2020 usegalaxy.eu

Training Infrastructure as a Service
H. Rasche - B. Grüning, - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
D. Baker - M. van den Beek, D. Blankenberg, D. Bouvier, et al. - PLOS Pathogens, 2020 usegalaxy.eu

Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
P. Espíndola-Hernández - J. Mueller, M. Carrete, S. Boerno, et al. - Genome Biology and Evolution, 2020 usegalaxy.eu

Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease
A. Sauriol - K. Simeone, L. Portelance, L. Meunier, et al. - Cancers, 2020 usegalaxy.eu

Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
B. Liu - D. Popp, H. Sträuber, H. Harms, et al. - Microbiology Resource Announcements, 2020

Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health
R. Wirth - G. Maróti, L. Lipták, M. Mester, et al. - Research Square - Research Square Platform LLC, 2020 usegalaxy.eu

pyGenomeTracks: reproducible plots for multivariate genomic datasets 
L. Lopez-Delisle - L. Rabbani, J. Wolff, V. Bhardwaj, et al. - Bioinformatics, 2020 usegalaxy.eu

Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates
B. Liu - D. Popp, H. Sträuber, H. Harms, et al. - Research Square - Research Square Platform LLC, 2020

Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
M. Buhl - M. Marschal, - International Journal of Systematic and Evolutionary Microbiology, 2020 usegalaxy.eu

Ultrastructural, transcriptional, and functional differences between human reticulated and non‐reticulated platelets
L. Hille - M. Lenz, A. Vlachos, B. Grüning, et al. - Journal of Thrombosis and Haemostasis, 2020 usegalaxy.eu

SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
S. Müller - S. Wallner, G. Schmitz, T. Loew, et al. - Gene, 2020 usegalaxy.eu

Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration
A. Schlecht - S. Boneva, M. Gruber, P. Zhang, et al. - The American Journal of Pathology, 2020 usegalaxy.eu

A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
S. Dhamija - C. Yang, J. Seiler, K. Myacheva, et al. - Nature Cell Biology, 2020 usegalaxy.eu

Benchmarking challenging small variants with linked and long reads
J. Wagner - N. Olson, L. Harris, J. McDaniel, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

An Interactive Visualization for Feature Localization in Deep Neural Networks
M. Zurowietz - T. Nattkemper, - Frontiers in Artificial Intelligence, 2020

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
A. Hahn - D. Pensold, C. Bayer, J. Tittelmeier, et al. - Frontiers in Cell and Developmental Biology, 2020 usegalaxy.eu

Genome‐wide cooperation of <scp>EMT</scp> transcription factor <scp>ZEB</scp> 1 with <scp>YAP</scp> and <scp>AP</scp> ‐1 in breast cancer
N. Feldker - F. Ferrazzi, H. Schuhwerk, S. Widholz, et al. - The EMBO Journal, 2020 usegalaxy.eu

The landscape of SARS-CoV-2 RNA modifications
M. Miladi - J. Fuchs, W. Maier, S. Weigang, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
C. Lange - J. Wolf, C. Auw‐Haedrich, A. Schlecht, et al. - Journal of Medical Virology, 2020 usegalaxy.eu

Lake expansion elevates equilibrium diversity via increasing colonization
T. Hauffe - D. Delicado, R. Etienne, L. Valente, et al. - Journal of Biogeography, 2020

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
S. Mehta - C. Easterly, R. Sajulga, R. Millikin, et al. - Proteomes, 2020

Enhanced COVID-19 data for improved prediction of survival
W. Zeng - A. Gautam, D. Huson, - bioRxiv - Cold Spring Harbor Laboratory, 2020

Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
S. Roth - P. Bose, M. Alhamdani, S. Mustafa, et al. - Annals of Surgery, 2020

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
V. Piro - T. Dadi, E. Seiler, K. Reinert, et al. - Bioinformatics, 2020

Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
T. Villa - M. Barucco, M. Martin-Niclos, A. Jacquier, et al. - Cell Reports, 2020 usegalaxy.eu

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve, et al. - Antibiotics, 2020 usegalaxy.eu

Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve, et al. - Antibiotics, 2020 usegalaxy.eu

Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart
H. Lahm - M. Jia, M. Dreßen, F. Wirth, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research
R. Rajan - K. Divya, R. Kandadai, R. Yadav, et al. - Frontiers in Neurology, 2020

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
R. Rettenmaier - M. Schneider, B. Munk, M. Lebuhn, et al. - Microorganisms, 2020

Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
M. Foschini - L. Morandi, A. Sanchez, A. Santoro, et al. - Frontiers in Oncology, 2020 usegalaxy.eu

Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
R. Zhang - J. Gehlen, A. Kawalia, M. Melissari, et al. - PLOS ONE, 2020

Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
H. Nützmann - D. Doerr, A. Ramírez-Colmenero, J. Sotelo-Fonseca, et al. - Proceedings of the National Academy of Sciences, 2020

<scp>GLASSgo</scp> in <scp>Galaxy</scp>: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
R. Schäfer - S. Lott, J. Georg, B. Grüning, et al. - Bioinformatics, 2020 usegalaxy.eu

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
V. Jalili E. Afgan Q. Gu D. Clements D. Blankenberg J. Goecks J. Taylor A. Nekrutenko - - Nucleic Acids Research, 2020

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
S. Bray - X. Lucas, A. Kumar, B. Grüning, et al. - Journal of Cheminformatics, 2020 usegalaxy.eu

Galactic Circos: User-friendly Circos plots within the Galaxy platform
H. Rasche S. Hiltemann - - GigaScience, 2020 usegalaxy.eu

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
A. Busch - M. Brüggemann, S. Ebersberger, K. Zarnack, et al. - Methods, 2020 usegalaxy.eu

Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus
N. Yoshida - C. Kaito, - Data in Brief, 2020 usegalaxy.eu

Independent attenuation correction of whole body [18F]FDG-PET using a deep learning approach with Generative Adversarial Networks
K. Armanious - T. Hepp, T. Küstner, H. Dittmann, et al. - EJNMMI Research, 2020

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
J. Oeyen - P. Baa-Puyoulet, J. Benoit, L. Beukeboom, et al. - Genome Biology and Evolution, 2020 usegalaxy.eu

AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
T. Altenburg - S. Giese, S. Wang, T. Muth, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020

Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server
A. Kumar - A. Bangash, B. Gruening, - MDPI AG, 2020 usegalaxy.eu

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
M. Mungan M. Alanjary K. Blin T. Weber M. Medema N. Ziemert - - Nucleic Acids Research, 2020

Two new genera and three new subterranean species of Hydrobiidae (Caenogastropoda: Truncatelloidea) from Tunisia
N. Khalloufi - M. Béjaoui, D. Delicado, - European Journal of Taxonomy, 2020

Phylogenetic relationships within <i>Pseudamnicola</i> Paulucci, 1878 (Caenogastropoda: Truncatelloidea) indicate two independent dispersal events from different continents to the Balearic Islands
K. Boulaassafer - M. Ghamizi, A. Machordom, D. Delicado, et al. - Systematics and Biodiversity, 2020

Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
R. Winkler - I. Rosas-Román, - American Chemical Society (ACS), 2020 usegalaxy.eu

A framework for designing miRNA-based distributed cell classifier circuits
M. Nowicka - H. Siebert, - bioRxiv - Cold Spring Harbor Laboratory, 2020

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
N. Blomberg - K. Lauer, - European Journal of Human Genetics, 2020 usegalaxy.eu

LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity
A. Dorn - M. Glaß, C. Neu, B. Heydel, et al. - Cancers, 2020 usegalaxy.eu

A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases
P. Kumar - J. Johnson, C. Easterly, S. Mehta, et al. - Journal of Proteome Research, 2020

A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
D. Becker - D. Popp, H. Harms, F. Centler, et al. - Microorganisms, 2020

Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
B. Öztürk J. Werner J. Meier-Kolthoff B. Bunk C. Spröer D. Springael - - Genome Biology and Evolution, 2020

The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
M. McGill - B. Sabikunnahar, Q. Fang, C. Teuscher, et al. - Journal of Neuroimmunology, 2020 usegalaxy.eu

MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome
I. Parenti - F. Diab, S. Gil, E. Mulugeta, et al. - Cell Reports, 2020 usegalaxy.eu

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
S. Chen - G. Sun, Y. Yan, K. Konstantinidis, et al. - Proceedings of the National Academy of Sciences, 2020

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive<i>de novo</i>DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
H. Lee - H. Chawla, C. Obermeier, F. Dreyer, et al. - Frontiers in Plant Science, 2020

Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
T. Hepp - M. Fischer, M. Winkelmann, S. Baldenhofer, et al. - Journal of Thoracic Imaging, 2020

Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
W. Logroño - D. Popp, S. Kleinsteuber, H. Sträuber, et al. - Microorganisms, 2020

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
G. Lodewijk - D. Fernandes, I. Vretzakis, J. Savage, et al. - Molecular Biology and Evolution, 2020 usegalaxy.eu

An epigenetic map of malaria parasite development from host to vector
K. Witmer - S. Fraschka, D. Vlachou, R. Bártfai, et al. - Scientific Reports, 2020 usegalaxy.eu

Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
M. Tangaro G. Donvito M. Antonacci M. Chiara P. Mandreoli G. Pesole F. Zambelli - - GigaScience, 2020 usegalaxy.eu

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
T. McGowan J. Johnson P. Kumar R. Sajulga 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
F. Uellendahl-Werth - M. Wolfien, A. Franke, O. Wolkenhauer, et al. - Scientific Reports, 2020 usegalaxy.eu

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
S. Kumaran - A. Ngo, F. Schultes, D. Tischler, et al. - 3 Biotech, 2020 usegalaxy.eu

Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
I. Hernández - C. Sant, R. Martínez, C. Fernández, et al. - Frontiers in Microbiology, 2020 usegalaxy.eu

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells
O. Genolet - A. Monaco, I. Dunkel, M. Boettcher, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
O. Schwengers - A. Hoek, M. Fritzenwanker, L. Falgenhauer, et al. - PLOS Computational Biology, 2020

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
I. Maus - M. Klocke, J. Derenkó, Y. Stolze, et al. - Environmental Microbiome, 2020

Effects of simulated dose variation on contrast-enhanced CT-based radiomic analysis for Non-Small Cell Lung Cancer
T. Hepp - A. Othman, A. Liebgott, J. Kim, et al. - European Journal of Radiology, 2020

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
J. Werner - E. Nour, B. Bunk, C. Spröer, et al. - Frontiers in Microbiology, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
J. Garrido - M. Aguilar, P. Prieto, - Scientific Reports, 2020 usegalaxy.eu

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
B. Stelbrink - R. Richter, F. Köhler, F. Riedel, et al. - Systematic Biology, 2020

Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann, et al. - Scientific Reports, 2020 usegalaxy.eu

Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
G. Farmiloe - G. Lodewijk, S. Robben, E. van Bree, et al. - Philosophical Transactions of the Royal Society B: Biological Sciences, 2020 usegalaxy.eu

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
D. Hofacker - J. Broche, L. Laistner, S. Adam, et al. - International Journal of Molecular Sciences, 2020 usegalaxy.eu

Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages
F. Candeliere - S. Raimondi, G. Spampinato, M. Tay, et al. - Microbiology Resource Announcements, 2020 usegalaxy.eu

BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
M. Hanussek - F. Bartusch, J. Krüger, - Future Generation Computer Systems, 2020

MedGAN: Medical image translation using GANs
K. Armanious - C. Jiang, M. Fischer, T. Küstner, et al. - Computerized Medical Imaging and Graphics, 2020

Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye, et al. - Springer International Publishing, 2020

Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
M. Zurowietz - T. Nattkemper, - IEEE Access, 2020

GLP: A requirement in cell therapies - perspectives for the cardiovascular field
U. Müller-Ruch - A. Skorska, H. Lemcke, G. Steinhoff, et al. - Advanced Drug Delivery Reviews, 2020 usegalaxy.eu

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

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
G. Sevillya D. Doerr Y. Lerner J. Stoye M. Steel S. Snir - - Molecular Biology and Evolution, 2019

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Y. Perez‐Riverol - P. Moreno, - PROTEOMICS, 2019 usegalaxy.eu

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
M. Lewinski - Y. Bramkamp, T. Köster, D. Staiger, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2019

A Glyphosate Pulse to Brackish Long-Term Microcosms Has a Greater Impact on the Microbial Diversity and Abundance of Planktonic Than of Biofilm Assemblages
R. Janßen - W. Skeff, J. Werner, M. Wirth, et al. - Frontiers in Marine Science, 2019

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
D. Gissi - A. Tarsitano, A. Gabusi, R. Rossi, et al. - Journal of Clinical Medicine, 2019 usegalaxy.eu

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger, et al. - GigaScience, 2019

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
G. Etherington - N. Soranzo, S. Mohammed, W. Haerty, et al. - GigaScience, 2019 usegalaxy.eu

An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts
R. Janßen - J. Zabel, U. von Lukas, M. Labrenz, et al. - Marine Pollution Bulletin, 2019

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata, - bioRxiv - Cold Spring Harbor Laboratory, 2019 usegalaxy.eu

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
J. Werner - A. Géron, J. Kerssemakers, S. Matallana-Surget, et al. - Biology Direct, 2019

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
I. Papatheodorou - P. Moreno, J. Manning, A. Fuentes, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
A. Géron - J. Werner, R. Wattiez, P. Lebaron, et al. - Frontiers in Microbiology, 2019

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
M. Emperle - S. Adam, S. Kunert, M. Dukatz, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage
R. Wirth - T. Böjti, G. Lakatos, G. Maróti, et al. - Frontiers in Energy Research, 2019 usegalaxy.eu

An intrinsically disordered proteins community for ELIXIR
N. Davey - M. Babu, M. Blackledge, A. Bridge, et al. - F1000Research, 2019 usegalaxy.eu

Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
S. Lambrecht - Y. Kanesaki, J. Fuss, B. Huettel, et al. - Scientific Reports, 2019 usegalaxy.eu

Development of novel microsatellite markers for <i>Alkanna tinctoria</i> by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer, et al. - Applications in Plant Sciences, 2019 usegalaxy.eu

Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies
F. Larsen - B. Bed’Hom, B. Guldbrandtsen, T. Dalgaard, et al. - Molecular Immunology, 2019 usegalaxy.eu

ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
M. Haas - J. Gómez Vázquez, D. Sun, H. Tran, et al. - Cell Reports, 2019 usegalaxy.eu

<i>Candida auris</i> in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen, et al. - Emerging Infectious Diseases, 2019 usegalaxy.eu

Historical faunal exchange between the Pontocaspian Basin and North America
J. Vandendorpe - C. van Baak, B. Stelbrink, D. Delicado, et al. - Ecology and Evolution, 2019

Draft Genome Sequence of a <i>Chitinimonas</i> Species from Hudson Valley Waterways That Expresses Violacein Pigment
B. Jude - - Microbiology Resource Announcements, 2019 usegalaxy.eu

Pheno-seq – linking visual features and gene expression in 3D cell culture systems
S. Tirier - J. Park, F. Preußer, L. Amrhein, et al. - Scientific Reports, 2019

Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
R. Rauschmeier - C. Gustafsson, A. Reinhardt, N. A‐Gonzalez, et al. - The EMBO Journal, 2019 usegalaxy.eu

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
T. Wollmann - M. Gunkel, I. Chung, H. Erfle, et al. - Medical Image Analysis, 2019

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
L. Sánchez - B. Burger, C. Horro, A. Fabregat, et al. - GigaScience, 2019 usegalaxy.eu

Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion, et al. - Journal of Medicinal Chemistry, 2019

U2 <scp>AF</scp> <sup>65</sup> assemblies drive sequence‐specific splice site recognition
M. Tari - V. Manceau, J. de Matha Salone, A. Kobayashi, et al. - EMBO reports, 2019 usegalaxy.eu

Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis
I. Lengfelder - I. Sava, J. Hansen, K. Kleigrewe, et al. - Frontiers in Immunology, 2019 usegalaxy.eu

A pan-cancer analysis of synonymous mutations
Y. Sharma - M. Miladi, S. Dukare, K. Boulay, et al. - Nature Communications, 2019 usegalaxy.eu

de.NBI Cloud federation through ELIXIR AAI
P. Belmann - B. Fischer, J. Krüger, M. Procházka, et al. - F1000Research, 2019

Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells
C. Ritter - T. Wollmann, P. Bernhard, M. Gunkel, et al. - International Journal of Computer Assisted Radiology and Surgery, 2019

Versatile interactions and bioinformatics analysis of noncoding RNAs
Q. Chen - X. Meng, Q. Liao, M. Chen, et al. - Briefings in Bioinformatics, 2019 usegalaxy.eu

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
J. Nelkner - C. Henke, T. Lin, W. Pätzold, et al. - Genes, 2019

RNApolis: Computational Platform for RNA Structure Analysis
M. Szachniuk - - Foundations of Computing and Decision Sciences, 2019 usegalaxy.eu

BIIGLE2Go—A scalable image annotation system for easy deployment on cruises
M. Zurowietz - D. Langenkamper, T. Nattkemper, - IEEE, 2019

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
B. Pucker - D. Holtgräwe, K. Stadermann, K. Frey, et al. - PLOS ONE, 2019

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
J. Meier-Kolthoff - M. Göker, - Nature Communications, 2019

The RNA workbench 2.0: next generation RNA data analysis
J. Fallmann - P. Videm, A. Bagnacani, B. Batut, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Reproducible Scientific Workflows for High Performance and Cloud Computing
F. Bartusch - M. Hanussek, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

BOOTABLE: Bioinformatics Benchmark Tool Suite
M. Hanussek - F. Bartusch, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
M. Brunet X. Roucou - - Journal of Visualized Experiments, 2019 usegalaxy.eu

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
J. Espenshade - S. Thijs, S. Gawronski, H. Bové, et al. - Frontiers in Microbiology, 2019 usegalaxy.eu

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

1,4-Disubstituted 1H-1,2,3-Triazole Containing Peptidotriazolamers: A New Class of Peptidomimetics With Interesting Foldamer Properties
D. Schröder - O. Kracker, T. Fröhr, J. Góra, et al. - Frontiers in Chemistry, 2019

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
J. Teikari - R. Popin, S. Hou, M. Wahlsten, et al. - Scientific Reports, 2019 usegalaxy.eu

Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus
D. Delicado - B. Arconada, A. Aguado, M. Ramos, et al. - Zoological Journal of the Linnean Society, 2019

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

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

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

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

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

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

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

Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
A. Kalmbach - C. Schröder, L. Klein-Hitpass, K. Nordström, et al. - Cytogenetic and Genome Research, 2019 usegalaxy.eu

Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
I. Prislan - S. Sajko, N. Ulrih, L. Fürst, et al. - RSC Advances, 2019 usegalaxy.eu

Workflow Development for the Functional Characterization of ncRNAs
M. Wolfien - D. Brauer, A. Bagnacani, O. Wolkenhauer, et al. - Springer New York, 2019 usegalaxy.eu

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
P. Kumar - P. Panigrahi, J. Johnson, W. Weber, et al. - Journal of Proteome Research, 2018 usegalaxy.eu

Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
S. Matallana-Surget - J. Werner, R. Wattiez, K. Lebaron, et al. - Frontiers in Microbiology, 2018

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
S. Weise - G. Arumugam, A. Villarreal, P. Videm, et al. - Molecular Neurobiology, 2018 usegalaxy.eu

Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation
N. Blagitko-Dorfs - P. Schlosser, G. Greve, D. Pfeifer, et al. - Leukemia, 2018 usegalaxy.eu

MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
M. Zurowietz - D. Langenkämper, B. Hosking, H. Ruhl, et al. - PLOS ONE, 2018

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J. Huerta-Cepas - D. Szklarczyk, D. Heller, A. Hernández-Plaza, et al. - Nucleic Acids Research, 2018

Aequatus: an open-source homology browser
A. Thanki - N. Soranzo, J. Herrero, W. Haerty, et al. - GigaScience, 2018 usegalaxy.eu

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
P. Bovio - H. Franz, S. Heidrich, T. Rauleac, et al. - Molecular Neurobiology, 2018 usegalaxy.eu

Common ELIXIR Service for Researcher Authentication and Authorisation
M. Linden - M. Prochazka, I. Lappalainen, D. Bucik, et al. - F1000Research, 2018

Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium
G. Retamal-Morales - T. Heine, J. Tischler, B. Erler, et al. - Journal of Biotechnology, 2018 usegalaxy.eu

Ultrastructural alterations in the retinal pigment epithelium and photoreceptors of a Stargardt patient and three Stargardt mouse models: indication for the central role of RPE melanin in oxidative stress
T. Taubitz - A. Tschulakow, M. Tikhonovich, B. Illing, et al. - PeerJ, 2018

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors