Brian P Brunk
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Explore the profile of Brian P Brunk including associated specialties, affiliations and a list of published articles.
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26
Citations
3349
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Recent Articles
1.
Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko E, Bazant W, et al.
Nucleic Acids Res
. 2021 Oct;
50(D1):D898-D911.
PMID: 34718728
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...
2.
Ruhamyankaka E, Brunk B, Dorsey G, Harb O, Helb D, Judkins J, et al.
Gates Open Res
. 2020 Jun;
3:1661.
PMID: 32047873
The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets...
3.
Oliveira F, Brestelli J, Cade S, Zheng J, Iodice J, Fischer S, et al.
Nucleic Acids Res
. 2017 Nov;
46(D1):D684-D691.
PMID: 29106667
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens...
4.
Aurrecoechea C, Barreto A, Basenko E, Brestelli J, Brunk B, Cade S, et al.
Nucleic Acids Res
. 2016 Dec;
45(D1):D581-D591.
PMID: 27903906
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen...
5.
Lorenzi H, Khan A, Behnke M, Namasivayam S, Swapna L, Hadjithomas M, et al.
Nat Commun
. 2016 Jan;
7:10147.
PMID: 26738725
Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from...
6.
Krishna R, Xia D, Sanderson S, Shanmugasundram A, Vermont S, Bernal A, et al.
Proteomics
. 2015 Apr;
15(15):2618-28.
PMID: 25867681
Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important...
7.
Aurrecoechea C, Barreto A, Brestelli J, Brunk B, Cade S, Doherty R, et al.
Nucleic Acids Res
. 2012 Nov;
41(Database issue):D684-91.
PMID: 23175615
EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated...
8.
Logan-Klumpler F, De Silva N, Boehme U, Rogers M, Velarde G, McQuillan J, et al.
Nucleic Acids Res
. 2011 Nov;
40(Database issue):D98-108.
PMID: 22116062
GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated...
9.
Stajich J, Harris T, Brunk B, Brestelli J, Fischer S, Harb O, et al.
Nucleic Acids Res
. 2011 Nov;
40(Database issue):D675-81.
PMID: 22064857
FungiDB (http://FungiDB.org) is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user...
10.
Fischer S, Brunk B, Chen F, Gao X, Harb O, Iodice J, et al.
Curr Protoc Bioinformatics
. 2011 Sep;
Chapter 6:6.12.1-6.12.19.
PMID: 21901743
OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL-DB is a public database that allows users to browse and view ortholog groups that...