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Amos B, Aurrecoechea C, Barba M, et al. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022;50:D898-D911doi: 10.1093/nar/gkab929.
Amos, B., Aurrecoechea, C., Barba, M., Barreto, A., Basenko, E. Y., Bażant, W., Belnap, R., Blevins, A. S., Böhme, U., Brestelli, J., Brunk, B. P., Caddick, M., Callan, D., Campbell, L., Christensen, M. B., Christophides, G. K., Crouch, K., Davis, K., DeBarry, J., Doherty, R., Duan, Y., Dunn, M., Falke, D., Fisher, S., Flicek, P., Fox, B., Gajria, B., Giraldo-Calderón, G. I., Harb, O. S., Harper, E., Hertz-Fowler, C., Hickman, M. J., Howington, C., Hu, S., Humphrey, J., Iodice, J., Jones, A., Judkins, J., Kelly, S. A., Kissinger, J. C., Kwon, D. K., Lamoureux, K., Lawson, D., Li, W., Lies, K., Lodha, D., Long, J., MacCallum, R. M., Maslen, G., McDowell, M. A., Nabrzyski, J., Roos, D. S., Rund, S. S. C., Schulman, S. W., Shanmugasundram, A., Sitnik, V., Spruill, D., Starns, D., Stoeckert, C. J., Tomko, S. S., Wang, H., Warrenfeltz, S., Wieck, R., Wilkinson, P. A., Xu, L., & Zheng, J. (2022). VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic acids research, 50D898-D911. https://doi.org/10.1093/nar/gkab929
Amos, Beatrice, et al. "VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center." Nucleic acids research vol. 50 (2022): D898-D911. doi: https://doi.org/10.1093/nar/gkab929
Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Bażant W, Belnap R, Blevins AS, Böhme U, Brestelli J, Brunk BP, Caddick M, Callan D, Campbell L, Christensen MB, Christophides GK, Crouch K, Davis K, DeBarry J, Doherty R, Duan Y, Dunn M, Falke D, Fisher S, Flicek P, Fox B, Gajria B, Giraldo-Calderón GI, Harb OS, Harper E, Hertz-Fowler C, Hickman MJ, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kwon DK, Lamoureux K, Lawson D, Li W, Lies K, Lodha D, Long J, MacCallum RM, Maslen G, McDowell MA, Nabrzyski J, Roos DS, Rund SSC, Schulman SW, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Stoeckert CJ, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Xu L, Zheng J. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022 Jan 07;50:D898-D911. doi: 10.1093/nar/gkab929. PMID: 34718728; PMCID: PMC8728164.
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Nucleic Acids Res. 2022 Jan 07;50:D898-D911. doi: 10.1093/nar/gkab929.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

Nucleic acids research

Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y Basenko, Wojciech Bażant, Robert Belnap, Ann S Blevins, Ulrike Böhme, John Brestelli, Brian P Brunk, Mark Caddick, Danielle Callan, Lahcen Campbell, Mikkel B Christensen, George K Christophides, Kathryn Crouch, Kristina Davis, Jeremy DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I Giraldo-Calderón, Omar S Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J Hickman, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A Kelly, Jessica C Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S Roos, Samuel S C Rund, Stephanie Wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J Stoeckert, Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A Wilkinson, Lin Xu, Jie Zheng

Affiliations

  1. Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
  2. Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
  3. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  4. Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
  5. Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
  6. Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK.
  7. Department of Pathology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
  8. Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
  9. Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
  10. Center for Research Computing, University of Notre Dame, Notre Dame, IN 46556, USA.
  11. Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
  12. Departamento de Ciencias Biológicas y Departamento de Ciencias Básicas Médicas, Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia.
  13. Department of Genetics, University of Georgia, Athens, GA 30602, USA.
  14. Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
  15. Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.

PMID: 34718728 PMCID: PMC8728164 DOI: 10.1093/nar/gkab929

Abstract

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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