Scientific research using & citing the European Galaxy server

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. Alcaraz,A.J.G. et al. (2021) Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (Pimephales promelas). Environmental Science & Technology, 55, 5024–5036.
  2. Batut,B. et al. (2021) RNA-Seq Data Analysis in Galaxy. In, Picardi,E. (ed), RNA Bioinformatics, Methods in Molecular Biology. Springer US, New York, NY, pp. 367–392.
  3. Bossche,T.V.D. et al. (2021) Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. bioRxiv, 2021.03.05.433915.
  4. Bray,S. et al. (2021) Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. ChemRxiv.
  5. Broche,J. et al. (2021) Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing. Nucleic Acids Research, 49, 158–176.
  6. Chiara,M. et al. (2021) Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings in Bioinformatics, 22, 616–630.
  7. Dorone,Y. et al. (2021) A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell, 184, 4284–4298.e27.
  8. Fahrner,M. et al. (2021) A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines. Proteomes, 9, 26.
  9. Föll,M.C. et al. (2021) Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework. bioRxiv, 2021.08.09.455649.
  10. Friedrich,M. et al. (2021) Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas. Nature Cancer, 1–18.
  11. Greve,G. et al. (2021) Decitabine Induces Gene Derepression on Monosomic Chromosomes: In Vitro and In Vivo Effects in Adverse-Risk Cytogenetics AML. Cancer Research, 81, 834–846.
  12. Gu,Q. et al. (2021) Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLOS Computational Biology, 17, e1009014.
  13. Hesse,M. et al. (2021) Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes. Journal of Molecular and Cellular Cardiology, 152, 95–104.
  14. Hildebrandt,S. et al. (2021) ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib. Stem Cell Reviews and Reports, 17, 1039–1052.
  15. Kumar,A. et al. (2021) The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato. Journal of Experimental Botany, 72, 426–444.
  16. Kumar,A. et al. (2021) Tool recommender system in Galaxy using deep learning. GigaScience, 10.
  17. Liu,Z. et al. (2021) DenovoProfiling: a webserver for de novo generated molecule library profiling. Research Square.
  18. Luo,X. et al. (2021) 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Cell, 184, 723–740.e21.
  19. Maier,W. et al. (2021) Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring. bioRxiv, 2021.03.25.437046.
  20. Maier,W. et al. (2021) Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nature Biotechnology, 1–2.
  21. Marisaldi,L. et al. (2021) De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage. Marine Genomics, 58, 100834.
  22. Mehta,S. et al. (2021) ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research, 10, 103.
  23. Mehta,S. et al. (2021) Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of Proteome Research.
  24. Mootapally,C. et al. (2021) Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data. Microbial Ecology, 81, 540–548.
  25. Morsli,M. et al. (2021) Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing. Pathogens, 10, 610.
  26. Nagy,N.A. et al. (2021) Draft genome of a biparental beetle species, Lethrus apterus. BMC Genomics, 22, 301.
  27. Naimi,S. et al. (2021) Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome, 9, 66.
  28. Niemöller,C. et al. (2021) Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction. Communications Biology, 4, 1–10.
  29. Ostrovsky,A. et al. (2021) Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update. Current Protocols, 1, e31.
  30. Pinter,S. et al. (2021) A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation. Nucleic Acids Research, 49, 4350–4370.
  31. Rajczewski,A.T. et al. (2021) A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clinical Proteomics, 18, 15.
  32. Rauschmeier,R. et al. (2021) Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis. bioRxiv, 2021.03.12.435122.
  33. Simon-Chica,A. et al. (2021) Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels. Cardiovascular Research.
  34. Stachurová,T. et al. (2021) Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants. Chemosphere, 280, 130749.
  35. Videm,P. et al. (2021) ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data. GigaScience, 10.
  36. Villa,T. et al. (2021) Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy. Data in Brief, 35, 106951.
  37. Weterings,V. et al. (2021) Duration of Colonisation With Extended-spectrum Beta-lactamase-producing Escherichia Coli: Results of an Open Cohort Study With Dutch Nursing Home Residents (2013 – 2019). Research Square.
  38. Wolf,J. et al. (2021) Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration. bioRxiv, 2021.05.10.443381.
  39. Yanta,C.A. et al. (2021) CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification. Food and Waterborne Parasitology, 23, e00115.
  40. Yu,Y. et al. (2021) Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis. Molecular Plant, 14, 888–904.
  41. Gilbertson,S.E. and Weinmann,A.S. (2021) Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis. Trends in Immunology, 42, 1077–1087.
  42. Glaros,V. et al. (2021) Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response. 54, 2005–2023.e10.
  43. Phan,I.Q. et al. (2021) The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design. Scientific Reports, 11.
  44. Macnee,M. et al. (2021) SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities. Bioinformatics.
  45. Page-Karjian,A. et al. (2021) Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii). Animals, 11, 3076.
  46. Barbosa,D.A. et al. (2021) New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei.
  47. Ranchou-Peyruse,M. et al. (2021) Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. 12.
  48. Camargo Romera,P. (2021) Isoform 2 of DLG2 gene as a possible candidate tumour suppressor of neuroblastoma. 32.
  49. Tu,Z. et al. (2021) Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate. 9, 667.
  50. Stein,C.M. et al. (2021) Single-cell omics: Overview, analysis, and application in biomedical science.
  51. Deng,S. et al. (2021) LAMP assay for distinguishing Fusarium oxysporum and Fusarium commune in lotus (Nelumbo nucifera) rhizomes.
  52. Pérez-Schindler Joaquı́n et al. (2021) Discovery of lipotoxicity-sensitive transcription factors in non-alcoholic steatohepatitis.
  53. Hölper,J.E. et al. (2021) A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass. 13, 1574.
  54. Baron,S.A. et al. (2021) Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal. 65.
  55. Li,X.-Y. et al. (2021) The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm, Antheraea pernyi (Lepidoptera: Saturniidae). 7, 233–243.
  56. Weigang,S. et al. (2021) Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants.
  57. Klein,A. et al. (2021) Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates. 10.
  58. Hering,S. et al. (2021) Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species. 71.
  59. Nagy,N.A. et al. (2021) Draft genome of a biparental beetle species, Lethrus apterus. 22.
  60. Volkova,P.Y. et al. (2021) Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone. 777, 146206.
  61. Rogg,M. et al. (2021) SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance. 32, 563–579.
  62. Pérez-Schindler Joaquı́n et al. (2021) RNA-bound PGC-1\upalpha controls gene expression in liquid-like nuclear condensates. 118, e2105951118.
  63. Fiedler,G. et al. (2021) Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences. 9, 246.
  64. Bayona-Feliu,A. et al. (2021) The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts. 53, 1050–1063.
  65. Peters,K. et al. (2021) Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid. 11.
  66. Apostolakos,I. et al. (2021) Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics. 8.
  67. Voelker,J. et al. (2021) A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species. 2021, 1–15.
  68. Tosar,J. et al. (2021) RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities. 11.
  69. Barragán-Rosillo,A.C. et al. (2021) Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis. 118, e2107558118.
  70. Dvir,S. et al. (2021) Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. 35, 109198.
  71. Friedrich,S. et al. (2021) Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. 11.
  72. Wolfien,M. et al. (2021) Single-Cell RNA Sequencing Procedures and Data Analysis. Exon Publications, pp. 19–35.
  73. Estell,C. et al. (2021) ZC3H4 restricts non-coding transcription in human cells. 10.
  74. Ali,R. et al. (2021) Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies.
  75. Genolet,O. et al. (2021) Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach. 22.
  76. Gessara,I. et al. (2021) Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds. 16, 784–796.
  77. Pelletier,D. et al. (2021) A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas. 8.
  78. Feng,S. et al. (2021) Scarless engineering of the Drosophila genome near any site-specific integration site. 217.
  79. Bamford,C.G.G. et al. (2021) Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution.
  80. Mauer,K.M. et al. (2021) Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host. 22.
  81. Katsanos,D. et al. (2021) Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID. 148.
  82. Cova,G. et al. (2021) Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells. 218.
  83. Pallares-Vega,R. et al. (2021) Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. 12.
  84. Soares,M.A.F. et al. (2021) Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells. 35, 1020–1034.
  85. Fell,C.W. et al. (2021) FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder.
  86. Bandyopadhyay,S. et al. (2021) Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein. 1–17.
  87. Delroisse,J. et al. (2021) Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae). 8.
  88. Darkow,E. et al. (2021) Small Conductance Ca2 \mathplus-Activated K\mathplus (SK) Channel mRNA Expression in Human Atrial and Ventricular Tissue: Comparison Between Donor, Atrial Fibrillation and Heart Failure Tissue. 12.
  89. Wichers,J.S. et al. (2021) Common virulence gene expression in adult first-time infected malaria patients and severe cases. 10.
  90. Yol,E. et al. (2021) A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame. 12.
  91. Poulose,N. et al. (2021) VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer.
  92. Kaiser,V.B. et al. (2021) Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome.
  93. Bartas,M. et al. (2021) The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity. 22, 8512.
  94. Gjaltema,R.A.F. et al. (2021) Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at theXistlocus.
  95. Migur,A. et al. (2021) The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts.
  96. Oselusi,S.O. et al. (2021) Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds. 26, 3970.
  97. Hetz,S.A. and Horn,M.A. (2021) Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra. 12.
  98. Roquis,D. et al. (2021) Genomic impact of stress-induced transposable element mobility in Arabidopsis. 49, 10431–10447.
  99. Martins Rodrigues,C. et al. (2021) DataPLANT – Ein NFDI-Konsortium der Pflanzen-Grundlagenforschung.
  100. Zhuang,X. et al. (2021) Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue. 1–14.
  101. Kavas,M. et al. (2021) Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. 27, 1885–1902.
  102. King,T.L. et al. (2021) Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa. 24, 321–324.
  103. Chen,D.-B. et al. (2021) First complete mitochondrial genome of Rhodinia species (Lepidoptera: Saturniidae): genome description and phylogenetic implication. 1–10.
  104. Bauer,T.L. et al. (2021) Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development. 13, 3801.
  105. Musmeci,E. et al. (2021) Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709. 10.
  106. Faddetta,T. et al. (2021) The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures. 11.
  107. Sun,S.-W. et al. (2021) The complete mitochondrial genome of the wild silkmoth Antheraea yamamai from Heilongjiang, China (Lepidoptera: Saturniidae). 6, 2209–2211.
  108. Spradling,T.A. et al. (2021) Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse. 16, e0254138.
  109. Winkler,M.A. and Pan,A.A. (2021) Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis.
  110. Carattoli,A. et al. (2021) Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates. 65.
  111. Aggarwal,D. et al. (2021) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe.
  112. Roncoroni,M. et al. (2021) A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinformatics.
  113. Moreno,P. et al. (2021) User-friendly, scalable tools and workflows for single-cell RNA-seq analysis. Nature Methods.
  114. Cordellier,M. et al. (2021) Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment. Zoology, 125895.


  1. Afouda,P. et al. (2020) Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates. Microorganisms, 8, 1522.
  2. Ahmed,S. et al. (2020) High prevalence of mcr-1 -encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh. Scientific Reports, 10, 18637.
  3. 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.
  4. Bazzucchi,M. et al. (2020) Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy. Archives of Virology, 165, 3007–3009.
  5. 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.
  6. Bohlender,L.L. et al. (2020) Stable Protein Sialylation in Physcomitrella. Frontiers in Plant Science, 11.
  7. 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.
  8. Boneva,S. et al. (2020) MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue. Scientific Reports, 10, 21292.
  9. Boneva,S.K. et al. (2020) Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population. Frontiers in Immunology, 11.
  10. Bose,S. et al. (2020) tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. Plant Cell Reports, 39, 1669–1685.
  11. Bray,S.A. et al. (2020) The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. Journal of Cheminformatics, 12, 40.
  12. Bray,S.A. et al. (2020) Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. Journal of Cheminformatics, 12, 54.
  13. 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.
  14. Buttimer,C. et al. (2020) Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics, 9, 352.
  15. 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.
  16. Cantarella,S. (2020) Insights into Alu retrotransposons: mechanism of Alu transcriptome alteration in response to virus infection and novel effects on gene expression.
  17. Čermák,V. et al. (2020) Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1863, 194647.
  18. Dad,A. et al. (2020) Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 858-860, 503256.
  19. Deng,L. et al. (2020) Gene expression in immortalized versus primary isolated cardiac endothelial cells. Scientific Reports, 10, 1–9.
  20. Dhamija,S. et al. (2020) A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation. Nature Cell Biology, 22, 999–1010.
  21. Di Dalmazi,G. et al. (2020) DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas. The Journal of Clinical Endocrinology & Metabolism, 105, e4605–e4615.
  22. Dorn,A. et al. (2020) LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity. Cancers, 12, 1227.
  23. Espíndola-Hernández,P. et al. (2020) Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls. Genome Biology and Evolution, 12, 1895–1908.
  24. Estrada Mallarino,L. et al. (2020) Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules. Scientific Reports, 10, 15954.
  25. 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.
  26. 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.
  27. Fernandes,M. (2020) GuavaDB: O BANCO DE DADOS DA GENÔMICA DE Psidium guajava L.
  28. Foschini,M.P. et al. (2020) Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer. Frontiers in Oncology, 10.
  29. Gaafar,Y.Z.A. and Ziebell,H. (2020) Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets. PeerJ, 8, e10096.
  30. 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.
  31. Gao,M. et al. (2020) Pluripotency factors select gene expression repertoire at Zygotic Genome Activation. bioRxiv, 2020.02.16.949362.
  32. Garrido,J. et al. (2020) Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis. Scientific Reports, 10, 1–12.
  33. Genolet,O. et al. (2020) Identification of X-chromosomal genes that drive global X-dosage effects in mammals. bioRxiv, 2020.03.09.983544.
  34. Greenfield,G. et al. (2020) Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms. Cancers, 12, 2669.
  35. Guendel,F. et al. (2020) Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues. Immunity, 53, 1015–1032.e8.
  36. Hahn,A. et al. (2020) DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons. Frontiers in Cell and Developmental Biology, 8.
  37. 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.
  38. 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.
  39. 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.
  40. Jalili,V. et al. (2020) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48, W395–W402.
  41. Kumar,A. et al. (2020) Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server. Preprints.
  42. Kumaran,S. et al. (2020) Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium. 3 Biotech, 10, 175.
  43. Lahm,H. et al. (2020) Congenital heart disease risk loci identified by genome-wide association study in European patients. The Journal of Clinical Investigation.
  44. 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.
  45. Lange,C. et al. (2020) Expression of the COVID-19 receptor ACE2 in the human conjunctiva. Journal of Medical Virology, n/a.
  46. Lastic, et al. (2020) Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation. Preprints.
  47. Lezameta,L. et al. (2020) Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru. Microbiology Resource Announcements, 9.
  49. Lodewijk,G.A. et al. (2020) Evolution of human brain size-associated NOTCH2NL genes proceeds towards reduced protein levels. Molecular Biology and Evolution.
  50. Lopez-Delisle,L. et al. (2020) pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics.
  51. Lother,A. et al. (2020) Diabetes changes gene expression but not DNA methylation in cardiac cells. Journal of Molecular and Cellular Cardiology, 0.
  52. Ma,J. et al. (2020) Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation. Aquaculture and Fisheries.
  53. Martinez-Fabregas,J. et al. (2020) CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci. Cell Reports, 33, 108545.
  54. Marzoli,F. et al. (2020) Next generation sequencing study on RNA viruses of Vespa velutina and Apis mellifera sharing the same foraging area. Transboundary and Emerging Diseases, n/a.
  55. McErlean,P. et al. (2020) Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis. bioRxiv, 2020.12.04.410191.
  56. 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.
  57. McGowan,T. et al. (2020) Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. GigaScience, 9.
  58. Mehta,S. et al. (2020) Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform. Proteomes, 8, 15.
  59. Miao,Z. et al. (2020) Putative cell type discovery from single-cell gene expression data. arXiv.
  60. 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.
  61. Müller-Ruch,U. et al. (2020) GLP: A requirement in cell therapies - perspectives for the cardiovascular field. Advanced Drug Delivery Reviews.
  62. 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.
  63. Núñez-Sánchez,M.A. et al. (2020) Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model. Microorganisms, 8, 1374.
  64. 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.
  65. 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.
  66. Qi,W. et al. (2020) A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans. bioRxiv, 2020.12.04.408260.
  67. Rasche,H. and Hiltemann,S. (2020) Galactic Circos: User-friendly Circos plots within the Galaxy platform. GigaScience, 9.
  68. Rasche,H. and Gruening,B.A. (2020) Training Infrastructure as a Service. bioRxiv, 2020.08.23.263509.
  69. Roland Wirth (2020) Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health. Research Square.
  70. Sabrina,K. (2020) Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data.
  71. Sajulga,R. et al. (2020) Survey of metaproteomics software tools for functional microbiome analysis. PLOS ONE, 15, e0241503.
  72. Sauriol,A. et al. (2020) Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease. Cancers, 12, 2222.
  73. Schäfer,R.A. et al. (2020) GLASSGo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs. Bioinformatics.
  74. 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.
  75. Senapathi,T. et al. (2020) BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations. Bio-protocol, 10, e3731–e3731.
  76. Tangaro,M.A. et al. (2020) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. GigaScience, 9.
  77. Tekman,M. et al. (2020) A single-cell RNA-sequencing training and analysis suite using the Galaxy framework. GigaScience, 9.
  78. 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.
  79. Villa,T. et al. (2020) Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Reports, 32, 107942.
  80. 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.
  81. Winkler,R. and Rosas-Román,I. (2020) Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ). ChemRxiv.
  82. Wirth,R. et al. (2020) Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. Frontiers in Bioengineering and Biotechnology, 8.
  83. Witmer,K. et al. (2020) An epigenetic map of malaria parasite development from host to vector. Scientific Reports, 10, 6354.
  84. Wolf,J. et al. (2020) Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages. Molecular Immunology, 128, 188–194.
  85. Wolf,J. et al. (2020) Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures. Scientific Reports, 10, 17022.
  86. Yoshida,N. and Kaito,C. (2020) Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus. Data in Brief, 30, 105388.
  87. Zavala-Alvarado,C. et al. (2020) The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress. PLOS Pathogens, 16, e1008904.
  88. Kumar,A. et al. (2020) The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato. 72, 426–444.
  89. Riediger,M. et al. (2020) Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). 33, 248–269.
  90. Buttimer,C. et al. (2020) Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. 9, 352.
  91. Teixeira Pereira,B.F. (2020) A comprehensive analysis of Med12 controlled (l)ncRNAs and characterization of a novel Sall1 antisense transcript.
  92. Gao,M. et al. (2020) Pluripotency factors determine gene expression repertoire at zygotic genome activation.
  93. Chiara,M. et al. (2020) Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings in Bioinformatics.
  94. Valsecchi,C.I.K. et al. (2020) RNA nucleation by MSL2 induces selective X chromosome compartmentalization. Nature.
  95. Hesse,M. et al. (2020) Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes. Journal of Molecular and Cellular Cardiology.


  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. Fallmann,J. et al. (2019) The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Research.
  12. Föll,M.C. et al. (2019) Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. GigaScience, 8.
  13. Forth,L.F. and Höper,D. (2019) Highly efficient library preparation for Ion Torrent sequencing using Y-adapters. BioTechniques.
  14. Gener,A.R. and Kimata,J.T. (2019) Full-coverage native RNA sequencing of HIV-1 viruses. bioRxiv, 845610.
  15. 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.
  16. 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.
  17. Hamprecht,A. et al. (2019) Candida auris in Germany and Previous Exposure to Foreign Healthcare. Emerging Infectious Diseases, 25, 1763–1765.
  18. Holthausen Bermejo,R. (2019) A workflow-based algorithm for tracing Computational Synteny Blocks along different species.
  19. 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.
  20. 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.
  21. 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.
  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. Owen,N. and Moosajee,M. (2019) RNA-sequencing in ophthalmology research: considerations for experimental design and analysis. Therapeutic Advances in Ophthalmology, 11, 251584141983546.
  27. Perez‐Riverol,Y. and Moreno,P. (2019) Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines. PROTEOMICS, n/a, 1900147.
  28. Prislan,I. et al. (2019) Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding. RSC Advances, 9, 41453–41461.
  29. Rasche,H. and Europe,G.P. (2019) Community, Training, Infrastructure, and Users. F1000Research, 8.
  30. Rauschmeier,R. et al. (2019) Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity. The EMBO Journal, 0, e101233.
  31. Sánchez,L.F.H. et al. (2019) PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. GigaScience, 8.
  32. Senapathi,T. et al. (2019) Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE). Bioinformatics.
  33. Sharma,Y. et al. (2019) A pan-cancer analysis of synonymous mutations. Nature Communications, 10.
  34. Szachniuk,M. (2019) RNApolis: Computational Platform for RNA Structure Analysis. Foundations of Computing and Decision Sciences, 44, 241–257.
  35. Tari,M. et al. (2019) U2AF65 assemblies drive sequence-specific splice site recognition. EMBO reports, 20, e47604.
  36. 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.
  37. Torres-Paz,J. et al. (2019) Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution. eLife, 8, e50160.
  38. Wibberg,D. et al. (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research, 8, 1877.
  39. 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.
  40. Wolfien,M. et al. (2019) Workflow Development for the Functional Characterization of ncRNAs. 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. 111–132.
  41. 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.
  42. Youssar,L. et al. (2019) Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLOS Genetics, 15, e1008029.
  43. Papatheodorou,I. et al. (2019) Expression Atlas update: from tissues to single cells. Nucleic Acids Research.


  1. Batut,B. et al. (2018) ASaiM: a Galaxy-based framework to analyze microbiota data. GigaScience, 7.
  2. Batut,B. et al. (2018) Community-Driven Data Analysis Training for Biology. Cell Systems, 6, 752–758.e1.
  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. Bovio,P.P. et al. (2018) Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo. Molecular Neurobiology.
  5. Chen,Q. et al. (2018) Versatile interactions and bioinformatics analysis of noncoding RNAs. Briefings in Bioinformatics.
  6. Eggenhofer,F. et al. (2018) CMV - Visualization for RNA and Protein family models and their comparisons. Bioinformatics.
  7. Konovalovas,A. (2018) Molecular determinants of Totiviridae family viruses of Saccharomyces sensu stricto clade.
  8. Kumar,P. et al. (2018) QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. Journal of Proteome Research.
  9. Nekrutenko,A. et al. (2018) Biology needs evolutionary software tools: Let’s build them right. Molecular Biology and Evolution.
  10. Retamal-Morales,G. et al. (2018) Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium. Journal of Biotechnology, 280, 38–41.
  11. Thanki,A.S. et al. (2018) Aequatus: An open-source homology browser. GigaScience.
  12. Weise,S.C. et al. (2018) FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus. Molecular Neurobiology.
  13. 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.
  14. Wright*,P.R. et al. (2018) Structure and Interaction Prediction in Prokaryotic RNA Biology. Microbiology Spectrum, 6.
  15. Batut,B. et al. (2018) ASaiM: a Galaxy-based framework to analyze microbiota data. GigaScience, 7, giy057.


  1. Grüning,B.A. et al. (2017) The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Research, 45, W560–W566.