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

Alvarez-Jarreta, J. et al. (2024) VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Research, 52(D1), D808-D816. (doi: 10.1093/nar/gkad1003) (PMID:37953350) (PMCID:PMC10767879)

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.

• Item Type: Articles
• Additional Information: Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services [75N93019C00077]; Wellcome Trust [218 288/Z/19/Z, 212 929/Z/18/Z]; No NIAID contract funds were used to fund the planning, preparation, submission or publication of this manuscript. Funding for the open access charge was provided by the University of Pennsylvania. Funding for open access charge: internal university funds.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Crouch, Dr Kathryn and Bah, Dr Saikou Y
• Authors: Alvarez-Jarreta, J., Amos, B., Aurrecoechea, C., Bah, S. Y., Barba, M., Barreto, A., Basenko, E. Y., Belnap, R., Blevins, A., Böhme, U., Brestelli, J., Brown, S., Callan, D., Campbell, L. I., Christophides, G. K., Crouch, K., Davison, H. R., DeBarry, J. D., Demko, R., Doherty, R., Duan, Y., Dundore, W., Dyer, S., Falke, D., Fischer, S., Gajria, B., Galdi, D., Giraldo-Calderón, G. I., Harb, O. S., Harper, E., Helb, D., Howington, C., Hu, S., Humphrey, J., Iodice, J., Jones, A., Judkins, J., Kelly, S. A., Kissinger, J. C., Kittur, N., Kwon, D. K., Lamoureux, K., Li, W., Lodha, D., MacCallum, R. M., Maslen, G., McDowell, M. A., Myers, J., Nural, M. V., Roos, D. S., Rund, S. S. C., Shanmugasundram, A., Sitnik, V., Spruill, D., Starns, D., Tomko, S. S., Wang, H., Warrenfeltz, S., Wieck, R., Wilkinson, P. A., and Zheng, J.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: Nucleic Acids Research
• Publisher: Oxford University Press
• ISSN: 0305-1048
• ISSN (Online): 1362-4962
• Published Online: 11 November 2023
• Copyright Holders: Copyright © 2023 The Author(s)
• First Published: First published in Nucleic Acids Research 52(D1):D808-D816
• Publisher Policy: Reproduced under a Creative Commons license