Publications by authors named "Brian Brunk"

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VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.
Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y Basenko, Brian P Brunk

Nucleic Acids Res· January 2022

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ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies.
Emmanuel Ruhamyankaka, Brian P Brunk, Grant Dorsey, Omar S Harb, Danica A Helb

Gates Open Res· April 2020

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MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments.
Francislon S Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Brian P Brunk

Nucleic Acids Res· January 2018

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EuPathDB: the eukaryotic pathogen genomics database resource.
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk

Nucleic Acids Res· January 2017

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Companion: a web server for annotation and analysis of parasite genomes.
Sascha Steinbiss, Fatima Silva-Franco, Brian Brunk, Bernardo Foth, Christiane Hertz-Fowler

Nucleic Acids Res· July 2016

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Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes.
Hernan Lorenzi, Asis Khan, Michael S Behnke, Sivaranjani Namasivayam, Lakshmipuram S Swapna, Brian P Brunk

Nat Commun· January 2016

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A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum.
Ritesh Krishna, Dong Xia, Sanya Sanderson, Achchuthan Shanmugasundram, Sarah Vermont, Brian P Brunk

Proteomics· August 2015

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RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.
Andrew S Warren, Cristina Aurrecoechea, Brian Brunk, Prerak Desai, Scott Emrich

Bioinformatics· May 2015

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EuPathDB: the eukaryotic pathogen database.
Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P Brunk, Shon Cade

Nucleic Acids Res· January 2013

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Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.
Adam James Reid, Sarah J Vermont, James A Cotton, David Harris, Grant A Hill-Cawthorne, Brian Brunk

PLoS Pathog· July 2012

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FungiDB: an integrated functional genomics database for fungi.
Jason E Stajich, Todd Harris, Brian P Brunk, John Brestelli, Steve Fischer

Nucleic Acids Res· January 2012

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GeneDB--an annotation database for pathogens.
Flora J Logan-Klumpler, Nishadi De Silva, Ulrike Boehme, Matthew B Rogers, Giles Velarde, Brian P Brunk

Nucleic Acids Res· January 2012

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The Strategies WDK: a graphical search interface and web development kit for functional genomics databases.
Steve Fischer, Cristina Aurrecoechea, Brian P Brunk, Xin Gao, Omar S Harb

Database (Oxford)· October 2011

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Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
Gregory R Grant, Michael H Farkas, Angel D Pizarro, Nicholas F Lahens, Jonathan Schug, Brian P Brunk

Bioinformatics· September 2011

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Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.
Steve Fischer, Brian P Brunk, Feng Chen, Xin Gao, Omar S Harb

Curr Protoc Bioinformatics· September 2011

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AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.
Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P Brunk, Elisabet V Caler

Nucleic Acids Res· January 2011

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TriTrypDB: a functional genomic resource for the Trypanosomatidae.
Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P Brunk

Nucleic Acids Res· January 2010

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EuPathDB: a portal to eukaryotic pathogen databases.
Cristina Aurrecoechea, John Brestelli, Brian P Brunk, Steve Fischer, Bindu Gajria

Nucleic Acids Res· January 2010

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HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana.
Xiao-Ning Zhang, Yingjie Wu, John W Tobias, Brian P Brunk, Gerald F Deitzer

PLoS One· February 2009

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GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.
Cristina Aurrecoechea, John Brestelli, Brian P Brunk, Jane M Carlton, Jennifer Dommer

Nucleic Acids Res· January 2009

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PlasmoDB: a functional genomic database for malaria parasites.
Cristina Aurrecoechea, John Brestelli, Brian P Brunk, Jennifer Dommer, Steve Fischer

Nucleic Acids Res· January 2009

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The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation.
Dong Xia, Sanya J Sanderson, Andrew R Jones, Judith H Prieto, John R Yates, Brian P Brunk

Genome Biol· October 2008

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ToxoDB: an integrated Toxoplasma gondii database resource.
Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Brian P Brunk

Nucleic Acids Res· January 2008

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Identification of candidate maternal-effect genes through comparison of multiple microarray data sets.
Jesse Mager, Richard M Schultz, Brian P Brunk, Marisa S Bartolomei

Mamm Genome· September 2006

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Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.
Yunxia Zhu, Benjamin L King, Babak Parvizi, Brian P Brunk, Christian J Stoeckert

Genome Biol· March 2003

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