Publications

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Currently 314 publications with reference to de.NBI Cloud are listed.

Recently added publication

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
M. Dieckmann - S. Beyvers, R. Nkouamedjo-Fankep, P. Hanel, et al. - Oxford University Press (OUP), 2021


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

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

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

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

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

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

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

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

Trait-trait relationships and functional tradeoffs vary with genome size in prokaryotes
S. Beier - J. Werner, T. Bouvier, N. Mouquet, et al. - Cold Spring Harbor Laboratory, 2021

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

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

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. - Cold Spring Harbor Laboratory, 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

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

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

Topology identifies emerging adaptive mutations in SARS-CoV-2
M. Bleher - L. Hahn, J. Patiño-Galindo, M. Carrière, et al. - Cold Spring Harbor Laboratory, 2021

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

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

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

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

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. - Cold Spring Harbor Laboratory, 2021

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

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

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

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

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 & Environment, 2021

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

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

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

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

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

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

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

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

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

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

Updates on metaQuantome Software for Quantitative Metaproteomics
S. Mehta - P. Kumar, M. Crane, J. Johnson, et al. - Journal of Proteome Research, 2021 usegalaxy.eu

Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
T. Van Den Bossche - B. Kunath, K. Schallert, S. Schäpe, et al. - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

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

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

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

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

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

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

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

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

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. - 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

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

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

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, - Cold Spring Harbor Laboratory, 2021

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

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

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

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

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

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

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

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

A secreted endoribonuclease ENDU-2 from the soma protects germline immortality inC. elegans
W. Qi - E. Gromoff, F. Xu, Q. Zhao, et al. - Cold Spring Harbor Laboratory, 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

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

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 Coxiella burnetii genomic sequences
A. Fasemore - A. Helbich, M. Walter, T. Dandekar, et al. - 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

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

Next generation sequencing study on RNA viruses of Vespa velutina and Apis mellifera 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

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

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

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

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

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

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

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

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

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

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

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

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

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 & Metabolism, 2020 usegalaxy.eu

Training Infrastructure as a Service
H. Rasche - B. Grüning, - 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

Draft Genome Sequences of Three Clostridia 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 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

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

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

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. - 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 EMT transcription factor ZEB 1 with YAP and AP ‐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. - Cold Spring Harbor Laboratory, 2020

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

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

Enhanced COVID-19 data for improved prediction of survival
W. Zeng - A. Gautam, D. Huson, - 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
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Unifying the known and unknown microbial coding sequence space
C. Vanni - M. Schechter, S. Acinas, A. Barberán, et al. - Cold Spring Harbor Laboratory, 2020

Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve, et al. - Antibiotics, 2020 usegalaxy.eu

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

GLASSgo in Galaxy: 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

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

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

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

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, - 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

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 de novo DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm, et al. - 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

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
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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

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

Pluripotency factors determine gene expression repertoire at zygotic genome activation
M. Gao - M. Veil, M. Rosenblatt, A. Gebhard, et al. - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

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

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

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

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

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata, - 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

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 Alkanna tinctoria  by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer, et al. - Applications in Plant Sciences, 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

Candida auris in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen, et al. - Emerging Infectious Diseases, 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 AF 65 assemblies drive sequence‐specific splice site recognition
M. Tari - V. Manceau, J. 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

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

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

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

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

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

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

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

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

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

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J. Wolff - V. Bhardwaj, S. Nothjunge, G. Richard, et al. - Nucleic Acids Research, 2018 usegalaxy.eu

Community-Driven Data Analysis Training for Biology
B. Batut - S. Hiltemann, A. Bagnacani, D. Baker, et al. - Cell Systems, 2018 usegalaxy.eu

ASaiM: a Galaxy-based framework to analyze microbiota data
B. Batut - K. Gravouil, C. Defois, S. Hiltemann, et al. - GigaScience, 2018 usegalaxy.eu

Biology Needs Evolutionary Software Tools: Let’s Build Them Right
A. Nekrutenko - G. Team, J. Goecks, J. Taylor, et al. - Molecular Biology and Evolution, 2018 usegalaxy.eu

Structure and Interaction Prediction in Prokaryotic RNA Biology
P. Wright* - M. Mann*, R. Backofen*, - Microbiology Spectrum, 2018 usegalaxy.eu

CMV: visualization for RNA and protein family models and their comparisons
F. Eggenhofer - I. Hofacker, R. Backofen, C. Höner zu Siederdissen, et al. - Bioinformatics, 2018 usegalaxy.eu

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
Y. Stolze - A. Bremges, I. Maus, A. Pühler, et al. - Microbial Biotechnology, 2017

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
I. Maus - A. Bremges, Y. Stolze, S. Hahnke, et al. - Biotechnology for Biofuels, 2017

Bioinformatics for NGS-based metagenomics and the application to biogas research
S. Jünemann - N. Kleinbölting, S. Jaenicke, C. Henke, et al. - Journal of Biotechnology, 2017

Workflows for microscopy image analysis and cellular phenotyping
T. Wollmann - H. Erfle, R. Eils, K. Rohr, et al. - Journal of Biotechnology, 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
B. Grüning - J. Fallmann, D. Yusuf, S. Will, et al. - Nucleic Acids Research, 2017 usegalaxy.eu

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper, et al. - Frontiers in Marine Science, 2017