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

Currently 238 publications with reference to de.NBI Cloud are listed.

Recently added publication

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. - American Chemical Society (ACS), 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

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Q. Gu - A. Kumar, S. Bray, A. Creason et al. - Public Library of Science (PLoS), 2021usegalaxy.eu

Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
M. Friedrich - R. Sankowski, L. Bunse, M. Kilian et al. - Springer Science and Business Media LLC, 2021usegalaxy.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. - Springer Science and Business Media LLC, 2021usegalaxy.eu

A large-scale comparative study on peptide encodings for biomedical classification
S. Spänig - S. Mohsen, G. Hattab, A. Hauschild et al. - Oxford University Press (OUP), 2021

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. - Oxford University Press (OUP), 2021usegalaxy.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, 2021usegalaxy.eu

Updates on metaQuantome Software for Quantitative Metaproteomics
S. Mehta - P. Kumar, M. Crane, J. Johnson et al. - American Chemical Society (ACS), 2021usegalaxy.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, 2021usegalaxy.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. - American Chemical Society (ACS), 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

Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring
K. Wüllems - A. Zurowietz, M. Zurowietz, R. Schneider et al. - Springer Science and Business Media LLC, 2021

Haplotype-resolved diverse human genomes and integrated analysis of structural variation
P. Ebert - P. Audano, Q. Zhu, B. Rodriguez-Martin et al. - American Association for the Advancement of Science (AAAS), 2021

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
W. Logroño - D. Popp, M. Nikolausz, P. Kluge et al. - Frontiers Media SA, 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. - F1000 Research Ltd, 2021usegalaxy.eu

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 - Oxford University Press (OUP), 2021

Diabetes changes gene expression but not DNA methylation in cardiac cells
A. Lother - O. Bondareva, A. Saadatmand, L. Pollmeier et al. - Elsevier BV, 2021usegalaxy.eu

Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
A. Ostrovsky - J. Hillman‐Jackson, D. Bouvier, D. Clements et al. - Wiley, 2021usegalaxy.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. - Oxford University Press (OUP), 2021usegalaxy.eu

Deep learning-based real-time detection of novel pathogens during sequencing
J. Bartoszewicz - U. Genske, B. Renard - Cold Spring Harbor Laboratory, 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. - American Society for Clinical Investigation, 2021usegalaxy.eu

Electroactive microorganisms in mouse feces
L. Rago - D. Popp, J. Heiker, F. Harnisch - Elsevier BV, 2021

Tool recommender system in Galaxy using deep learning
A. Kumar - H. Rasche, B. Grüning, R. Backofen - Oxford University Press (OUP), 2021usegalaxy.eu

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

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

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, LLC, 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. - Oxford University Press (OUP), 2020usegalaxy.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. - Springer Science and Business Media LLC, 2020

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
M. Chiara - A. D’Erchia, C. Gissi, C. Manzari et al. - Oxford University Press (OUP), 2020usegalaxy.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, 2020usegalaxy.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, 2020usegalaxy.eu

Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
F. Stiehler - M. Steinborn, S. Scholz, D. Dey et al. - Oxford University Press (OUP), 2020

MOSGA: Modular Open-Source Genome Annotator
R. Martin - T. Hackl, G. Hattab, M. Fischer et al. - Oxford University Press (OUP), 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. - Springer Science and Business Media LLC, 2020usegalaxy.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. - Elsevier BV, 2020usegalaxy.eu

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

Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
I. Meyer-Cifuentes - J. Werner, N. Jehmlich, S. Will et al. - Springer Science and Business Media LLC, 2020

Survey of metaproteomics software tools for functional microbiome analysis
R. Sajulga - C. Easterly, M. Riffle, B. Mesuere et al. - Public Library of Science (PLoS), 2020usegalaxy.eu

Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells
V. Čermák - D. Tyč, A. Přibylová, L. Fischer - Elsevier BV, 2020usegalaxy.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. - Wiley, 2020usegalaxy.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. - Springer Science and Business Media LLC, 2020usegalaxy.eu

The environment drives microbial trait variability in aquatic habitats
S. Beier - A. Andersson, P. Galand, C. Hochart et al. - Wiley, 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 - Oxford University Press (OUP), 2020usegalaxy.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. - Springer Science and Business Media LLC, 2020usegalaxy.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 - Springer Science and Business Media LLC, 2020usegalaxy.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. - Public Library of Science (PLoS), 2020usegalaxy.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. - MDPI AG, 2020usegalaxy.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 - Elsevier BV, 2020usegalaxy.eu

Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
L. Estrada Mallarino - C. Engel, . Ilık, D. Maticzka et al. - Springer Science and Business Media LLC, 2020usegalaxy.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. - American Society for Microbiology, 2020usegalaxy.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 Media SA, 2020usegalaxy.eu

tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
S. Bose - A. Suescún, J. Song, C. Castillo-González et al. - Springer Science and Business Media LLC, 2020usegalaxy.eu

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

Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
S. Boneva - J. Wolf, D. Rosmus, A. Schlecht et al. - Frontiers Media SA, 2020usegalaxy.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. - F1000 Research Ltd, 2020usegalaxy.eu

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
S. Bray - T. Senapathi, C. Barnett, B. Grüning - Springer Science and Business Media LLC, 2020usegalaxy.eu

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

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

Deep learning-based diatom taxonomy on virtual slides
M. Kloster - D. Langenkämper, M. Zurowietz, B. Beszteri et al. - Springer Science and Business Media LLC, 2020

Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
T. Wilke - T. Hauffe, E. Jovanovska, A. Cvetkoska et al. - American Association for the Advancement of Science (AAAS), 2020

Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
J. Ma - J. Chen, B. Louro, R. Martins et al. - Elsevier BV, 2020usegalaxy.eu

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
H. Schiebenhoefer - K. Schallert, B. Renard, K. Trappe et al. - Springer Science and Business Media LLC, 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 Endocrine Society, 2020usegalaxy.eu

Training Infrastructure as a Service
H. Rasche - B. Grüning - Cold Spring Harbor Laboratory, 2020usegalaxy.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. - Public Library of Science (PLoS), 2020usegalaxy.eu

Draft Genome Sequences of Three Clostridia Isolates Involved in Lactate-Based Chain Elongation
B. Liu - D. Popp, H. Sträuber, H. Harms et al. - American Society for Microbiology, 2020

pyGenomeTracks: reproducible plots for multivariate genomic datasets 
L. Lopez-Delisle - L. Rabbani, J. Wolff, V. Bhardwaj et al. - Oxford University Press (OUP), 2020usegalaxy.eu

Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
M. Buhl - M. Marschal - Microbiology Society, 2020usegalaxy.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. - Elsevier BV, 2020usegalaxy.eu

A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
S. Dhamija - C. Yang, J. Seiler, K. Myacheva et al. - Springer Science and Business Media LLC, 2020usegalaxy.eu

An Interactive Visualization for Feature Localization in Deep Neural Networks
M. Zurowietz - T. Nattkemper - Frontiers Media SA, 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 Media SA, 2020usegalaxy.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. - EMBO, 2020usegalaxy.eu

The landscape of SARS-CoV-2 RNA modifications
M. Miladi - J. Fuchs, W. Maier, S. Weigang et al. - 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. - Wiley, 2020usegalaxy.eu

Lake expansion elevates equilibrium diversity via increasing colonization
T. Hauffe - D. Delicado, R. Etienne, L. Valente - Wiley, 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. - Ovid Technologies (Wolters Kluwer Health), 2020

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
T. Villa - M. Barucco, M. Martin-Niclos, A. Jacquier et al. - Elsevier BV, 2020usegalaxy.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. - MDPI AG, 2020usegalaxy.eu

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

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. - Oxford University Press (OUP), 2020usegalaxy.eu

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
S. Bray - X. Lucas, A. Kumar, B. Grüning - Springer Science and Business Media LLC, 2020usegalaxy.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 - Oxford University Press (OUP), 2020usegalaxy.eu

Galactic Circos: User-friendly Circos plots within the Galaxy platform
H. Rasche, S. Hiltemann - Oxford University Press (OUP), 2020usegalaxy.eu

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
A. Busch - M. Brüggemann, S. Ebersberger, K. Zarnack - Elsevier BV, 2020usegalaxy.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. - Springer Science and Business Media LLC, 2020usegalaxy.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. - Springer Science and Business Media LLC, 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. - Oxford University Press (OUP), 2020usegalaxy.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 - Oxford University Press (OUP), 2020

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 - Oxford University Press (OUP), 2020

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

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 - Oxford University Press (OUP), 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. - Elsevier BV, 2020usegalaxy.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, 2020usegalaxy.eu

Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
T. Hepp - M. Fischer, M. Winkelmann, S. Baldenhofer et al. - Ovid Technologies (Wolters Kluwer Health), 2020

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

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

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
G. Lodewijk - D. Fernandes, I. Vretzakis, J. Savage et al. - Oxford University Press (OUP), 2020usegalaxy.eu

An epigenetic map of malaria parasite development from host to vector
K. Witmer - S. Fraschka, D. Vlachou, R. Bártfai et al. - Springer Science and Business Media LLC, 2020usegalaxy.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 - Oxford University Press (OUP), 2020usegalaxy.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 - Oxford University Press (OUP), 2020usegalaxy.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. - Springer Science and Business Media LLC, 2020usegalaxy.eu

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
S. Kumaran - A. Ngo, F. Schultes, D. Tischler - Springer Science and Business Media LLC, 2020usegalaxy.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. - Cold Spring Harbor Laboratory, 2020usegalaxy.eu

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 Media SA, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
J. Garrido - M. Aguilar, P. Prieto - Springer Science and Business Media LLC, 2020usegalaxy.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, 2020usegalaxy.eu

Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann et al. - Springer Science and Business Media LLC, 2020usegalaxy.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. - The Royal Society, 2020usegalaxy.eu

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
D. Hofacker - J. Broche, L. Laistner, S. Adam et al. - MDPI AG, 2020usegalaxy.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. - American Society for Microbiology, 2020usegalaxy.eu

MedGAN: Medical image translation using GANs
K. Armanious - C. Jiang, M. Fischer, T. Küstner et al. - Elsevier BV, 2020

BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
M. Hanussek - F. Bartusch, J. Krüger - Elsevier BV, 2020

Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
M. Zurowietz - T. Nattkemper - Institute of Electrical and Electronics Engineers (IEEE), 2020

Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye - 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. - Elsevier BV, 2020usegalaxy.eu

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

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
G. Sevillya, D. Doerr, Y. Lerner, J. Stoye, M. Steel, S. Snir - Oxford University Press (OUP), 2019

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

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger et al. - Oxford University Press (OUP), 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. - Oxford University Press (OUP), 2019usegalaxy.eu

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata - Cold Spring Harbor Laboratory, 2019usegalaxy.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 - Springer Science and Business Media LLC, 2019

Highly efficient library preparation for Ion Torrent sequencing using Y-adapters
L. Forth - D. Höper - Future Science Ltd, 2019usegalaxy.eu

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
J. Torres-Paz - J. Leclercq, S. Rétaux - eLife Sciences Publications, Ltd, 2019usegalaxy.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 Media SA, 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. - Oxford University Press (OUP), 2019usegalaxy.eu

An intrinsically disordered proteins community for ELIXIR
N. Davey - M. Babu, M. Blackledge, A. Bridge et al. - F1000 Research Ltd, 2019usegalaxy.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. - Springer Science and Business Media LLC, 2019usegalaxy.eu

Development of novel microsatellite markers for Alkanna tinctoria  by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer et al. - Wiley, 2019usegalaxy.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. - Elsevier BV, 2019usegalaxy.eu

Candida auris in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen et al. - Centers for Disease Control and Prevention (CDC), 2019usegalaxy.eu

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

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

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

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

Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion et al. - American Chemical Society (ACS), 2019

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

A pan-cancer analysis of synonymous mutations
Y. Sharma - M. Miladi, S. Dukare, K. Boulay et al. - Springer Science and Business Media LLC, 2019usegalaxy.eu

de.NBI Cloud federation through ELIXIR AAI
P. Belmann - B. Fischer, J. Krüger, M. Procházka et al. - F1000 Research Ltd, 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. - Springer Science and Business Media LLC, 2019

Versatile interactions and bioinformatics analysis of noncoding RNAs
Q. Chen - X. Meng, Q. Liao, M. Chen - Oxford University Press (OUP), 2019usegalaxy.eu

RNApolis: Computational Platform for RNA Structure Analysis
M. Szachniuk - Walter de Gruyter GmbH, 2019usegalaxy.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. - Public Library of Science (PLoS), 2019

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

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

BOOTABLE: Bioinformatics Benchmark Tool Suite
M. Hanussek - F. Bartusch, J. Kruger, O. Kohlbacher - 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 Media SA, 2019usegalaxy.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. - Public Library of Science (PLoS), 2019usegalaxy.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. - Springer Science and Business Media LLC, 2019usegalaxy.eu

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

CAMISIM: simulating metagenomes and microbial communities
A. Fritz - P. Hofmann, S. Majda, E. Dahms et al. - Springer Science and Business Media LLC, 2019

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

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

Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
I. Prislan - S. Sajko, N. Ulrih, L. Fürst - Royal Society of Chemistry (RSC), 2019usegalaxy.eu

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

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
P. Kumar - P. Panigrahi, J. Johnson, W. Weber et al. - American Chemical Society (ACS), 2018usegalaxy.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 Media SA, 2018

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

MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
M. Zurowietz - D. Langenkämper, B. Hosking, H. Ruhl et al. - Public Library of Science (PLoS), 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. - Oxford University Press (OUP), 2018

Aequatus: an open-source homology browser
A. Thanki - N. Soranzo, J. Herrero, W. Haerty et al. - Oxford University Press (OUP), 2018usegalaxy.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. - Springer Science and Business Media LLC, 2018usegalaxy.eu

ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
V. Piro - T. Dadi, E. Seiler, K. Reinert et al. - Cold Spring Harbor Laboratory, 2018

Common ELIXIR Service for Researcher Authentication and Authorisation
M. Linden - M. Prochazka, I. Lappalainen, D. Bucik et al. - F1000 Research Ltd, 2018

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

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
I. Maus - M. Rumming, I. Bergmann, K. Heeg et al. - Springer Science and Business Media LLC, 2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J. Wolff - V. Bhardwaj, S. Nothjunge, G. Richard et al. - Oxford University Press (OUP), 2018usegalaxy.eu

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

ASaiM: a Galaxy-based framework to analyze microbiota data
B. Batut - K. Gravouil, C. Defois, S. Hiltemann et al. - Oxford University Press (OUP), 2018usegalaxy.eu

Biology Needs Evolutionary Software Tools: Let’s Build Them Right
A. Nekrutenko - G. Team, J. Goecks, J. Taylor et al. - Oxford University Press (OUP), 2018usegalaxy.eu

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

CMV: visualization for RNA and protein family models and their comparisons
F. Eggenhofer - I. Hofacker, R. Backofen, C. Höner zu Siederdissen - Oxford University Press (OUP), 2018usegalaxy.eu

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
I. Maus - A. Bremges, Y. Stolze, S. Hahnke et al. - Springer Science and Business Media LLC, 2017

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

Bioinformatics for NGS-based metagenomics and the application to biogas research
S. Jünemann - N. Kleinbölting, S. Jaenicke, C. Henke et al. - Elsevier BV, 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. - Oxford University Press (OUP), 2017usegalaxy.eu

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper - Frontiers Media SA, 2017