VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023

Jorge Álvarez-Jarreta(European Bioinformatics Institute), B Kirtley Amos(University of Liverpool), Cristina Aurrecoechea(University of Georgia), Saikou Y. Bah(University of Glasgow), Matthieu Barba(European Bioinformatics Institute), Ana Barreto(University of Pennsylvania), Evelina Y. Basenko(University of Liverpool), Robert Belnap(University of Georgia), Ann S. Blevins(University of Pennsylvania), Ulrike Böhme(University of Georgia), John Brestelli(University of Pennsylvania), Stuart M. Brown(University of Pennsylvania), Danielle Callan(University of Pennsylvania), Lahcen Campbell(European Bioinformatics Institute), George K. Christophides(Imperial College London), Kathryn Crouch(University of Glasgow), Helen Davison(University of Liverpool), Jeremy D. DeBarry(University of Georgia), Richard Demko(University of Pennsylvania), Ryan Doherty(University of Pennsylvania), Yikun Duan(University of Pennsylvania), Walter Dundore(University of Georgia), Sarah Dyer(European Bioinformatics Institute), Dave Falke(University of Georgia), Steve Fischer(University of Pennsylvania), Bindu Gajria(University of Pennsylvania), Daniel Galdi(University of Pennsylvania), Gloria I. Giraldo-Calderón(University of Notre Dame), Omar S. Harb(University of Pennsylvania), Elizabeth I. Harper(University of Pennsylvania), Danica Helb(University of Pennsylvania), Connor Howington(University of Notre Dame), Sufen Hu(University of Pennsylvania), Jay C. Humphrey(University of Georgia), John Iodice(University of Pennsylvania), Andrew R. Jones(University of Liverpool), J. Judkins(University of Pennsylvania), Sarah Kelly(Imperial College London), Jessica C. Kissinger(University of Georgia), Nupur Kittur(University of Georgia), Dae Kun Kwon(University of Notre Dame), Kristopher Lamoureux(University of Georgia), Wei Li(University of Pennsylvania), Disha Lodha(European Bioinformatics Institute), Robert M. MacCallum(Imperial College London), G. Maslen(Imperial College London), Mary Ann McDowell(University of Notre Dame), Jeremy S. Myers(University of Pennsylvania), Mustafa V. Nural(University of Georgia), David S. Roos(University of Pennsylvania), Samuel S. C. Rund(University of Notre Dame), Achchuthan Shanmugasundram(University of Liverpool), Vasily Sitnik(European Bioinformatics Institute), Drew Spruill(University of Georgia), David Starns(University of Liverpool), Sheena Shah Tomko(University of Pennsylvania), Haiming Wang(University of Georgia), Susanne Warrenfeltz(University of Georgia), Robert Wieck(University of Notre Dame), Paul A. Wilkinson(University of Liverpool), Jie Zheng(University of Pennsylvania)
Nucleic Acids Research
November 11, 2023
10.1093/nar/gkad1003
Cited by 242Open Access
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Abstract

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.

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