Galaxy Europe citations

This is the list of scientific publications that cited the European Galaxy instance sorted by year. Please help us to support this project with your acknowledgement.


  1. Afouda,P. et al. (2020) Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates. Microorganisms, 8, 1522.
  2. Baker,D. et al. (2020) No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLOS Pathogens, 16, e1008643.
  3. 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.
  4. Boneva,S. et al. (2020) 3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage. Laboratory Investigation, 1–11.
  5. Buhl,M. and Marschal,M. (2020) Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient. International Journal of Systematic and Evolutionary Microbiology.
  6. Buttimer,C. et al. (2020) Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics, 9, 352.
  7. 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.
  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. Deng,L. et al. (2020) Gene expression in immortalized versus primary isolated cardiac endothelial cells. Scientific Reports, 10, 1–9.
  10. Dhamija,S. et al. (2020) A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation. Nature Cell Biology, 22, 999–1010.
  11. Dorn,A. et al. (2020) LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity. Cancers, 12, 1227.
  12. 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.
  13. Feldker,N. et al. (2020) Genome-wide cooperation of EMT transcription factor ZEB1 with YAP and AP-1 in breast cancer. The EMBO Journal, n/a, e103209.
  14. Fernandes,M. (2020) GuavaDB: O BANCO DE DADOS DA GENÔMICA DE Psidium guajava L.
  15. Foschini,M.P. et al. (2020) Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer. Frontiers in Oncology, 10.
  16. 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.
  17. Gao,M. et al. (2020) Pluripotency factors select gene expression repertoire at Zygotic Genome Activation. bioRxiv, 2020.02.16.949362.
  18. Garrido,J. et al. (2020) Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis. Scientific Reports, 10, 1–12.
  19. Genolet,O. et al. (2020) Identification of X-chromosomal genes that drive global X-dosage effects in mammals. bioRxiv, 2020.03.09.983544.
  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. Hille,L. et al. (2020) Ultrastructural, transcriptional, and functional differences between human reticulated and non-reticulated platelets. Journal of Thrombosis and Haemostasis, 18, 2034–2046.
  22. 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.
  23. Jalili,V. et al. (2020) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48, W395–W402.
  24. Kumar,A. et al. (2020) Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server. Preprints.
  25. Kumaran,S. et al. (2020) Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium. 3 Biotech, 10, 175.
  26. Lahm,H. et al. (2020) Congenital heart disease risk loci identified by genome-wide association study in European patients. The Journal of Clinical Investigation.
  27. Lahm,H. et al. (2020) Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart. bioRxiv, 2020.06.19.161067.
  28. Lange,C. et al. (2020) Expression of the COVID-19 receptor ACE2 in the human conjunctiva. Journal of Medical Virology, n/a.
  30. Lodewijk,G.A. et al. (2020) Evolution of human brain-size associated NOTCH2NL genes proceeds towards reduced protein levels. Molecular Biology and Evolution.
  31. Lopez-Delisle,L. et al. (2020) pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics.
  32. Lother,A. et al. (2020) Diabetes changes gene expression but not DNA methylation in cardiac cells. Journal of Molecular and Cellular Cardiology, 0.
  33. 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.
  34. McGowan,T. et al. (2020) Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. GigaScience, 9.
  35. Miao,Z. et al. (2020) Putative cell type discovery from single-cell gene expression data. arXiv.
  36. Morandi,L. et al. (2020) An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species. Cells, 9, 2092.
  37. 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.
  38. Núñez-Sánchez,M.A. et al. (2020) Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model. Microorganisms, 8, 1374.
  39. Oeyen,J.P. et al. (2020) Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biology and Evolution, 12, 1099–1188.
  40. Parenti,I. et al. (2020) MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome. Cell Reports, 31, 107647.
  41. Qi,W. et al. (2020) A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans. bioRxiv, 2020.12.04.408260.
  42. Rasche,H. and Hiltemann,S. (2020) Galactic Circos: User-friendly Circos plots within the Galaxy platform. GigaScience, 9.
  43. Rasche,H. and Gruening,B.A. (2020) Training Infrastructure as a Service. bioRxiv, 2020.08.23.263509.
  44. Roland Wirth (2020) Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health. Research Square.
  45. Sabrina,K. (2020) Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data.
  46. Sajulga,R. et al. (2020) Survey of metaproteomics software tools for functional microbiome analysis. PLOS ONE, 15, e0241503.
  47. 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.
  48. Tangaro,M.A. et al. (2020) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. GigaScience, 9.
  49. 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.
  50. Villa,T. et al. (2020) Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Reports, 32, 107942.
  51. Von Suchodoletz,D. et al. (2020) Lessons learned from Virtualized Research Environments in today’s scientific compute infrastructures. In, E-Science-Tage 2019. University Library Heidelberg.
  52. Winkler,R. and Rosas-Román,I. (2020) Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ). ChemRxiv.
  53. Wirth,R. et al. (2020) Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. Frontiers in Bioengineering and Biotechnology, 8.
  54. Witmer,K. et al. (2020) An epigenetic map of malaria parasite development from host to vector. Scientific Reports, 10, 6354.
  55. Wolf,J. et al. (2020) Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages. Molecular Immunology, 128, 188–194.


  2. Ahmad,M. et al. (2019) Development of novel microsatellite markers for Alkanna tinctoria by comparative transcriptomics. Applications in Plant Sciences, 7, e11296.
  3. 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.
  5. 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.
  6. Busch,A. et al. (2019) iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods.
  7. Davey,N.E. et al. (2019) An intrinsically disordered proteins community for ELIXIR. F1000Research, 8, 1753.
  8. Emperle,M. et al. (2019) Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns. Nucleic Acids Research.
  9. 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.
  10. Etherington,G.J. et al. (2019) A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses. GigaScience, 8.
  11. Föll,M.C. et al. (2019) Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. GigaScience, 8.
  12. Forth,L.F. and Höper,D. (2019) Highly efficient library preparation for Ion Torrent sequencing using Y-adapters. BioTechniques.
  13. Gener,A.R. and Kimata,J.T. (2019) Full-coverage native RNA sequencing of HIV-1 viruses. bioRxiv, 845610.
  14. 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.
  15. 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.
  16. Hamprecht,A. et al. (2019) Candida auris in Germany and Previous Exposure to Foreign Healthcare. Emerging Infectious Diseases, 25, 1763–1765.
  17. Holthausen Bermejo,R. (2019) A workflow-based algorithm for tracing Computational Synteny Blocks along different species.
  18. 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.
  19. 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.
  20. 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.
  21. Kumar,A. et al. (2019) Tool recommender system in Galaxy using deep learning. bioRxiv, 838599.
  22. 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.
  23. 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.
  24. 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.
  25. Lother,A. et al. (2019) Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis. Journal of Endocrinology, 240, 15–26.
  26. Perez‐Riverol,Y. and Moreno,P. (2019) Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines. PROTEOMICS, n/a, 1900147.
  27. Rasche,H. and Europe,G.P. (2019) Community, Training, Infrastructure, and Users. F1000Research, 8.
  28. Rauschmeier,R. et al. (2019) Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity. The EMBO Journal, 0, e101233.
  29. Sánchez,L.F.H. et al. (2019) PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. GigaScience, 8.
  30. Senapathi,T. et al. (2019) Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE). Bioinformatics.
  31. Sharma,Y. et al. (2019) A pan-cancer analysis of synonymous mutations. Nature Communications, 10.
  32. Tari,M. et al. (2019) U2AF65 assemblies drive sequence-specific splice site recognition. EMBO reports, 20, e47604.
  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. Torres-Paz,J. et al. (2019) Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution. eLife, 8, e50160.
  35. Wibberg,D. et al. (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research, 8, 1877.
  36. 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.
  37. 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.
  38. Youssar,L. et al. (2019) Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLOS Genetics, 15, e1008029.


  1. Batut,B. et al. (2018) Community-Driven Data Analysis Training for Biology. Cell Systems, 6, 752–758.e1.
  2. 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.
  3. Konovalovas,A. (2018) Molecular determinants of Totiviridae family viruses of Saccharomyces sensu stricto clade.
  4. Kumar,P. et al. (2018) QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. Journal of Proteome Research.
  5. Thanki,A.S. et al. (2018) Aequatus: An open-source homology browser. GigaScience.
  6. Weise,S.C. et al. (2018) FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus. Molecular Neurobiology.
  7. 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.