PAST PROJECT

Virus Pathogen Resource (ViPR)

In order to support research focused on newly emerging pathogens, the Division of Microbiology and Infectious Diseases (DMID) of the National Institute of Allergy and Infectious Diseases (NIAID), at the US National Institutes of Health (NIH), is supporting a variety of resources for researchers including: the Genomic Sequencing Centers for Infectious Diseases, Structural Genomics Centers for Infectious Diseases, Systems Biology for Infectious Diseases Research, and BEI Resources Repository programs to increase public availability of genome sequence data, 3D protein structures, systems biology models, isolated organisms and experiment reagents. The Bioinformatics Resource Centers (BRC) for Infectious Diseases were created to serve as database resources for the integration of research and surveillance data being generated by these DMID-sponsored resources and by other primary investigators working on infectious diseases caused by different groups of human pathogens and their insect vectors. The objective of the BRC program is to provide a one-stop-shop for data and analytical tools to support data mining and analysis workflows for both basic and applied research.

The Virus Pathogen Resource (ViPR) is a US NIH/NIAID-funded, freely-available online bioinformatics resource for search, analysis and visualization of data about 14 different families of human pathogenic viruses, including Coronaviridae (SARS, MERS), Flaviviridae (Dengue, Zika, West Nile, Yellow fever, Hepatitis C), Picornaviridae (Polio, Enterovirus D68), Togaviridae (Chikungunya, EEEV, VEEV, Rubella), Arenaviridae (Lassa), Filoviridae (Ebola, Marburg), Herpesviridae (HSV, EBV, CMV), and Poxviridae (Smallpox). Cross-referencing data and integrating computational tools into the online ViPR resource allows complex analyses to be easily performed by researchers regardless of their bioinformatics training or expertise.

ViPR is accessed ~1638 sessions per week (Google Analytics - 2016 average) and has been cited in more that 255 scientific publications.

Publications

Methods in molecular biology (Clifton, N.J.). 2019-01-01; 1911.47-69.

Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR)

Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH

PMID: 30593617

PloS one. 2017-05-31; 12.5: e0178199.

Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses

Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE

PMID: 28562637

PloS one. 2017-01-26; 12.1: e0170462.

Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus

Sun G, Larsen CN, Baumgarth N, Klem EB, Scheuermann RH

PMID: 28125631

Virus evolution. 2016-06-15; 2.1: vew015.

Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak

Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH

PMID: 28512577

Nature. 2016-03-10; 531.7593: 173.

Zika virus: designate standardized names

Scheuermann RH

PMID: 26961650

Evolutionary bioinformatics online. 2015-03-16; 11.43-8.

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway

Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA

PMID: 25861210

Scientific data. 2014-10-14; 1.140033.

A comprehensive collection of systems biology data characterizing the host response to viral infection

Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH

PMID: 25977790

PloS one. 2014-06-17; 9.6: e99979.

Standardized metadata for human pathogen/vector genomic sequences

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH

PMID: 24936976

Virology. 2013-12-01; 447.1-2: 45-51.

Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes

Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH

PMID: 24210098

Viruses. 2012-11-19; 4.11: 3209-26.

Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community

Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH

PMID: 23202522

Nucleic acids research. 2012-01-01; 40.Database issue: D593-8.

ViPR: an open bioinformatics database and analysis resource for virology research

Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, Klem EB, Scheuermann RH

PMID: 22006842

Viruses. 2010-10-13; 2.10: 2258-2268.

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Mercier PL, Le Mercier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D, Shrivastava S, Sterk P, Zeng Q, Klimke W, Tatusova T

PMID: 21994619

Funding

This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under contract no. HHSN272201400028C.