Galaxy EU citations

This is the list of scientific publications that cited the European Galaxy instance sorted by year.


  1. Gao,M. et al. (2020) Pluripotency factors select gene expression repertoire at Zygotic Genome Activation. bioRxiv, 2020.02.16.949362.
  2. Kumar,A. et al. (2020) Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server. Preprints.
  3. Schlecht,A. et al. (2020) Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-related Macular Degeneration. The American Journal of Pathology.
  4. Müller,S. et al. (2020) SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss. Gene, 753, 144787.
  5. Miao,Z. et al. (2020) Putative cell type discovery from single-cell gene expression data. arXiv:2004.09847 [q-bio].
  6. Dorn,A. et al. (2020) LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity. Cancers, 12, 1227.
  7. Von Suchodoletz,D. et al. (2020) Lessons learned from Virtualized Research Environments in today’s scientific compute infrastructures. In, E-Science-Tage 2019.
  8. Cantarella,S. (2020) Insights into Alu retrotransposons: mechanism of Alu transcriptome alteration in response to virus infection and novel effects on gene expression.
  9. Lange,C. et al. (2020) Expression of the COVID-19 receptor ACE2 in the human conjunctiva. Journal of Medical Virology, n/a.
  10. Lodewijk,G.A. et al. (2020) Evolution of human brain-size associated NOTCH2NL genes proceeds towards reduced protein levels. Molecular Biology and Evolution.
  11. Blomberg,N. and Lauer,K.B. (2020) Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic. European Journal of Human Genetics, 1–5.
  12. Gao,L. et al. (2020) Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. bioRxiv, 2020.04.27.064386.
  13. Witmer,K. et al. (2020) An epigenetic map of malaria parasite development from host to vector. Scientific Reports, 10, 6354.
  14. Kumaran,S. et al. (2020) Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium. 3 Biotech, 10, 175.
  15. Uellendahl-Werth,F. et al. (2020) A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples. Scientific Reports, 10, 1–10.
  16. McGill,M.M. et al. (2020) The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha. Journal of Neuroimmunology, 342, 577209.
  17. Teams,G.and H.P.developments et al. (2020) No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics. bioRxiv, 2020.02.21.959973.
  18. Genolet,O. et al. (2020) Identification of X-chromosomal genes that drive global X-dosage effects in mammals. bioRxiv, 2020.03.09.983544.
  19. Garrido,J. et al. (2020) Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis. Scientific Reports, 10, 1–12.
  20. Hernández,I. et al. (2020) Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains. Frontiers in Microbiology, 11.
  21. Farmiloe,G. et al. (2020) Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. Philosophical Transactions of the Royal Society B: Biological Sciences, 375, 20190333.
  22. Deng,L. et al. (2020) Gene expression in immortalized versus primary isolated cardiac endothelial cells. Scientific Reports, 10, 1–9.
  23. Sabrina,K. (2020) Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data.
  24. Hofacker,D. et al. (2020) Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects. International Journal of Molecular Sciences, 21, 502.
  25. Candeliere,F. et al. (2020) Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages. Microbiology Resource Announcements, 9.


  2. Holthausen Bermejo,R. (2019) A workflow-based algorithm for tracing Computational Synteny Blocks along different species.
  3. Föll,M.C. et al. (2019) Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. GigaScience, 8.
  4. Torres-Paz,J. et al. (2019) Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution. eLife, 8, e50160.
  5. Kolosov,D. and O’Donnell,M.J. (2019) Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms. Journal of Experimental Biology, 222.
  6. Etherington,G.J. et al. (2019) A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses. GigaScience, 8.
  7. Gissi,D.B. et al. (2019) 13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients. Journal of Clinical Medicine, 8, 2107.
  8. Kumar,A. et al. (2019) Tool recommender system in Galaxy using deep learning. bioRxiv, 838599.
  9. Wibberg,D. et al. (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research, 8, 1877.
  10. Perez‐Riverol,Y. and Moreno,P. (2019) Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines. PROTEOMICS, n/a, 1900147.
  11. Busch,A. et al. (2019) iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods.
  12. Kalmbach,A. et al. (2019) Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenetic and Genome Research, 159, 1–11.
  13. Gener,A.R. and Kimata,J.T. (2019) Full-coverage native RNA sequencing of HIV-1 viruses. bioRxiv, 845610.
  15. Ahmad,M. et al. (2019) Development of novel microsatellite markers for Alkanna tinctoria by comparative transcriptomics. Applications in Plant Sciences, 7, e11296.
  16. Wirth,R. et al. (2019) Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage. Frontiers in Energy Research, 7.
  17. Haas,M. et al. (2019) ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia. Cell Reports, 28, 3338–3352.e6.
  18. Emperle,M. et al. (2019) Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns. Nucleic Acids Research.
  19. Lambrecht,S.J. et al. (2019) Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4. Scientific Reports, 9, 1–15.
  20. Forth,L.F. and Höper,D. (2019) Highly efficient library preparation for Ion Torrent sequencing using Y-adapters. BioTechniques.
  21. Davey,N.E. et al. (2019) An intrinsically disordered proteins community for ELIXIR. F1000Research, 8, 1753.
  22. Tari,M. et al. (2019) U2AF65 assemblies drive sequence-specific splice site recognition. EMBO reports, 20, e47604.
  23. Jude,B.A. (2019) Draft Genome Sequence of a Chitinimonas Species from Hudson Valley Waterways That Expresses Violacein Pigment. Microbiology Resource Announcements, 8, e00683–19, /mra/8/35/MRA.00683–19.atom.
  24. Hamprecht,A. et al. (2019) Candida auris in Germany and Previous Exposure to Foreign Healthcare. Emerging Infectious Diseases, 25, 1763–1765.
  25. Rauschmeier,R. et al. (2019) Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity. The EMBO Journal, 0, e101233.
  26. Larsen,F.T. et al. (2019) Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies. Molecular Immunology, 114, 216–225.
  27. Lengfelder,I. et al. (2019) Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Frontiers in Immunology, 10.
  28. Sharma,Y. et al. (2019) A pan-cancer analysis of synonymous mutations. Nature Communications, 10.
  29. Brunet,M.A. and Roucou,X. (2019) Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames. JoVE (Journal of Visualized Experiments), e59589.
  30. Espenshade,J. et al. (2019) Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study. Frontiers in Microbiology, 10.
  31. Senapathi,T. et al. (2019) Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE). Bioinformatics.
  32. Youssar,L. et al. (2019) Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLOS Genetics, 15, e1008029.
  33. Teikari,J.E. et al. (2019) Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315. Scientific Reports, 9, 4888.
  34. Wylie,K.M. et al. (2019) Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection. Frontiers in Cellular and Infection Microbiology, 9.
  35. Bagnacani,A. et al. (2019) Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis. In, Lai,X. et al. (eds), Computational Biology of Non-Coding RNA: Methods and Protocols, Methods in Molecular Biology. Springer New York, New York, NY, pp. 199–214.
  36. Lother,A. et al. (2019) Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis. Journal of Endocrinology, 240, 15–26.


  1. Thanki,A.S. et al. (2018) Aequatus: An open-source homology browser. GigaScience.
  2. Konovalovas,A. (2018) Molecular determinants of Totiviridae family viruses of Saccharomyces sensu stricto clade.
  3. Blagitko-Dorfs,N. et al. (2018) Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation. Leukemia, 1.
  4. Batut,B. et al. (2018) Community-Driven Data Analysis Training for Biology. Cell Systems, 6, 752–758.e1.
  5. Kumar,P. et al. (2018) QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. Journal of Proteome Research.
  6. Wolff,J. et al. (2018) Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Research, 46, W11–W16.
  7. Weise,S.C. et al. (2018) FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus. Molecular Neurobiology.
  8. Bovio,P.P. et al. (2018) Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo. Molecular Neurobiology.
  9. Retamal-Morales,G. et al. (2018) Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium. Journal of Biotechnology, 280, 38–41.
  10. Nekrutenko,A. et al. (2018) Biology needs evolutionary software tools: Let’s build them right. Molecular Biology and Evolution.