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.

2022

  1. Amaral,M.do et al. (2022) TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens. Scientific Reports, 12.
  2. Arcari,G. et al. (2022) Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report. European Journal of Clinical Microbiology & Infectious Diseases, 41, 495–500.
  3. Bamford,C.G.G. et al. (2022) Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Viruses, 14, 325.
  4. Blacklock,E. (2022) Examination of crustacean immune responses through dsRNA-nanoparticle injection and phylogenetic analysis.
  5. Bray,S. et al. (2022) Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. Journal of Cheminformatics, 14, 22.
  6. Colin,L. et al. (2022) What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach. Conservation Genetics Resources.
  7. Deng,S. et al. (2022) LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus (Nelumbo nucifera) Rhizomes. Plant Disease, 106, 231–246.
  8. Dias,D. et al. (2022) Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care? Science of The Total Environment, 812, 152324.
  9. Dugar,G. et al. (2022) A chromosomal loop anchor mediates bacterial genome organization. Nature Genetics, 1–8.
  10. Fahrner,M. et al. (2022) Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. GigaScience, 11.
  11. Gao,M. et al. (2022) Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nature Communications, 13.
  12. Guindo,C.O. et al. (2022) A Tetragenococcus halophilus human gut isolate. Current Research in Microbial Sciences, 3, 100112.
  13. Katsanos,D. and Barkoulas,M. (2022) Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. Science Advances, 8.
  14. Koeppel,K.N. et al. (2022) SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa. Viruses, 14, 120.
  15. Kumaran,S. et al. (2022) In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp. Genomics, 114, 110266.
  16. Lucaci,A.G. et al. (2022) RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis. bioRxiv.
  17. Mack,H.I.D. et al. (2022) Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans. BMC Genomics, 23.
  18. Martin,D.P. et al. (2022) Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA. 1 that likely impact Spike function. bioRxiv.
  19. McDonald,M.S. et al. (2022) Ultraviolet vision in larval Neogonodactylus oerstedii. Journal of Experimental Biology.
  20. Mossad,O. et al. (2022) Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine. Nature Neuroscience, 1–11.
  21. Nührenberg,T.G. et al. (2022) Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis. PLOS ONE, 17, e0260222.
  22. Ragot,R. and Villemur,R. (2022) eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters. Environmental monitoring and assessment, 194, 1–13.
  23. Shi,S. et al. (2022) Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids. Cellular and Molecular Gastroenterology and Hepatology, 13, 541–564.
  24. Stephen Jr,D.B. et al. (2022) Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PeerJ, 9, e12632.
  25. Sun,Q. et al. (2022) STENCIL: A web templating engine for visualizing and sharing life science datasets. PLOS Computational Biology, 18, e1009859.
  26. Verma,D. et al. (2022) Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage.
  27. Werner,E. et al. (2022) The Mitochondrial RNA Granule is Necessary for Parkinsonism-Associated Metal Toxicity. bioRxiv.
  28. Wolf,J. et al. (2022) 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. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1868, 166340.
  29. Wolf,J. et al. (2022) The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue. Genomics, 110286.

2021

  1. Aggarwal,D. et al. (2021) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe.
  2. 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.
  3. Ali,R. et al. (2021) Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies.
  4. 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.
  5. Bamford,C.G.G. et al. (2021) Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution.
  6. 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.
  7. 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.
  8. Baron,S.A. et al. (2021) Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal. 65.
  9. 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.
  10. Bartas,M. et al. (2021) The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity. 22, 8512.
  11. 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.
  12. 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.
  13. Bayona-Feliu,A. et al. (2021) The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts. 53, 1050–1063.
  14. 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.
  15. 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.
  16. Camargo Romera,P. (2021) Isoform 2 of DLG2 gene as a possible candidate tumour suppressor of neuroblastoma.
  17. Carattoli,A. et al. (2021) Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates. 65.
  18. Chen,D.-B. et al. (2021) First complete mitochondrial genome of Rhodinia species (Lepidoptera: Saturniidae): genome description and phylogenetic implication. 1–10.
  19. Chiara,M. et al. (2021) Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings in Bioinformatics, 22, 616–630.
  20. Cordellier,M. et al. (2021) Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment. Zoology, 125895.
  21. Cova,G. et al. (2021) Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells. 218.
  22. Darkow,E. et al. (2021) Small Conductance Ca2 +-Activated K+ (SK) Channel mRNA Expression in Human Atrial and Ventricular Tissue: Comparison Between Donor, Atrial Fibrillation and Heart Failure Tissue. Frontiers in Physiology, 12.
  23. Delroisse,J. et al. (2021) Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae). 8.
  24. Dorone,Y. et al. (2021) A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell, 184, 4284–4298.e27.
  25. Dvir,S. et al. (2021) Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. 35, 109198.
  26. Estell,C. et al. (2021) ZC3H4 restricts non-coding transcription in human cells. 10.
  27. 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.
  28. 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.
  29. 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.
  30. Feng,S. et al. (2021) Scarless engineering of the Drosophila genome near any site-specific integration site. 217.
  31. 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.
  32. 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.
  33. Friedrich,S. et al. (2021) Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. 11.
  34. Friedrich,M. et al. (2021) Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas. Nature Cancer, 1–18.
  35. 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.
  36. Gessara,I. et al. (2021) Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds. 16, 784–796.
  37. 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.
  38. Gjaltema,R.A.F. et al. (2021) Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at theXistlocus.
  39. 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.
  40. 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.
  41. Gu,Q. et al. (2021) Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLOS Computational Biology, 17, e1009014.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. Kaiser,V.B. et al. (2021) Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome.
  48. Katsanos,D. et al. (2021) Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID. 148.
  49. Kavas,M. et al. (2021) Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. 27, 1885–1902.
  50. 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.
  51. Klein,A. et al. (2021) Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates. 10.
  52. 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.
  53. Kumar,A. et al. (2021) Tool recommender system in Galaxy using deep learning. GigaScience, 10.
  54. 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.
  55. Liu,Z. et al. (2021) DenovoProfiling: a webserver for de novo generated molecule library profiling. Research Square.
  56. Luo,X. et al. (2021) 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Cell, 184, 723–740.e21.
  57. Macnee,M. et al. (2021) SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities. Bioinformatics.
  58. Maier,W. et al. (2021) Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring. bioRxiv, 2021.03.25.437046.
  59. Maier,W. et al. (2021) Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nature Biotechnology, 1–2.
  60. 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.
  61. Martins Rodrigues,C. et al. (2021) DataPLANT – Ein NFDI-Konsortium der Pflanzen-Grundlagenforschung.
  62. 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.
  63. Mehta,S. et al. (2021) ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research, 10, 103.
  64. Mehta,S. et al. (2021) Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of Proteome Research.
  65. Migur,A. et al. (2021) The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts. Journal of Experimental Botany.
  66. 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.
  67. Moreno,P. et al. (2021) Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Research, 50, D129–D140.
  68. Moreno,P. et al. (2021) User-friendly, scalable tools and workflows for single-cell RNA-seq analysis. Nature Methods.
  69. Morsli,M. et al. (2021) Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing. Pathogens, 10, 610.
  70. Musmeci,E. et al. (2021) Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709. 10.
  71. Nagy,N.A. et al. (2021) Draft genome of a biparental beetle species, Lethrus apterus. BMC Genomics, 22, 301.
  72. Naimi,S. et al. (2021) Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome, 9, 66.
  73. Niemöller,C. et al. (2021) Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction. Communications Biology, 4, 1–10.
  74. Oselusi,S.O. et al. (2021) Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds. 26, 3970.
  75. Ostrovsky,A. et al. (2021) Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update. Current Protocols, 1, e31.
  76. Page-Karjian,A. et al. (2021) Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii). Animals, 11, 3076.
  77. Pallares-Vega,R. et al. (2021) Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. 12.
  78. 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.
  79. Pérez-Schindler,J. et al. (2021) Discovery of lipotoxicity-sensitive transcription factors in non-alcoholic steatohepatitis.
  80. Pérez-Schindler,J. et al. (2021) RNA-bound PGC-1{}upalpha controls gene expression in liquid-like nuclear condensates. 118, e2105951118.
  81. Peters,K. et al. (2021) Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid. 11.
  82. Phan,I.Q. et al. (2021) The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design. Scientific Reports, 11.
  83. 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.
  84. Poulose,N. et al. (2021) VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer.
  85. 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.
  86. Ranchou-Peyruse,M. et al. (2021) Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. 12.
  87. 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.
  88. Rogg,M. et al. (2021) SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance. 32, 563–579.
  89. Roncoroni,M. et al. (2021) A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinformatics.
  90. Roquis,D. et al. (2021) Genomic impact of stress-induced transposable element mobility in Arabidopsis. 49, 10431–10447.
  91. Saleh,O. et al. (2021) Nascent Transcript Sequencing for the Mapping of Promoters in thaliana Mitochondria. In, Methods in Molecular Biology. Springer US, pp. 279–300.
  92. Simon-Chica,A. et al. (2021) Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels. Cardiovascular Research.
  93. 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.
  94. Spradling,T.A. et al. (2021) Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse. 16, e0254138.
  95. Stachurová,T. et al. (2021) Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants. Chemosphere, 280, 130749.
  96. Stein,C.M. et al. (2021) Single-cell omics: Overview, analysis, and application in biomedical science.
  97. Sun,S.-W. et al. (2021) The complete mitochondrial genome of the wild silkmoth Antheraea yamamai from Heilongjiang, China (Lepidoptera: Saturniidae). 6, 2209–2211.
  98. Tosar,J. et al. (2021) RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities. 11.
  99. Tu,Z. et al. (2021) Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate. 9, 667.
  100. Videm,P. et al. (2021) ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data. GigaScience, 10.
  101. 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.
  102. 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.
  103. Volkova,P.Y. et al. (2021) Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone. 777, 146206.
  104. Weigang,S. et al. (2021) Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants.
  105. 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.
  106. Wichers,J.S. et al. (2021) Common virulence gene expression in adult first-time infected malaria patients and severe cases. 10.
  107. Winkler,M.A. and Pan,A.A. (2021) Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis.
  108. 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.
  109. Wolfien,M. et al. (2021) Single-Cell RNA Sequencing Procedures and Data Analysis. Exon Publications, pp. 19–35.
  110. Yanta,C.A. et al. (2021) CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification. Food and Waterborne Parasitology, 23, e00115.
  111. Yol,E. et al. (2021) A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame. 12.
  112. 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.
  113. Zhuang,X. et al. (2021) Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue. 1–14.

2020

  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. 9, 352.
  15. Buttimer,C. et al. (2020) Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics, 9, 352.
  16. 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.
  17. Cantarella,S. (2020) Insights into Alu retrotransposons: mechanism of Alu transcriptome alteration in response to virus infection and novel effects on gene expression.
  18. 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.
  19. Chiara,M. et al. (2020) Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings in Bioinformatics.
  20. 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.
  21. Deng,L. et al. (2020) Gene expression in immortalized versus primary isolated cardiac endothelial cells. Scientific Reports, 10, 1–9.
  22. Dhamija,S. et al. (2020) A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation. Nature Cell Biology, 22, 999–1010.
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2019

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2018

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2017

  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.