JCVI: About / Bios / Brett Pickett
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Brett Pickett, Ph.D.
Assistant Professor

Research Interests and Accomplishments

Dr. Pickett received his Ph.D. training in Microbiology from the University of Alabama at Birmingham on the various mechanisms influencing the evolution of Flaviviruses. His postdoctoral work at the University of Texas Southwestern Medical Center at Dallas, provided an opportunity to continue this comparative sequence analysis on viral genomes as well as additional understanding about the host immune response while contributing to the development of NIAID-sponsored viral databases as part of the Bioinformatics Resource Centers program. Positions at both the J. Craig Venter Institute and Thomson Reuters Life Sciences enabled him to develop statistical algorithms and bioinformatics workflows to interpret transcriptomic and systems biology data through pathway analysis and protein interaction networks. This work has been the product of successful collaborations with many prestigious domestic and international labs, with the data and results being reported at scientific conferences and in multiple peer-reviewed publications. Dr. Pickett currently focuses his effort on large-scale pathogen sequencing, host transcriptional RNA-seq during infection, and downstream bioinformatics analysis to better understand the underlying mechanism(s) of the host response during and after infections with viral pathogens.

Research Priorities

Predict, generate, and test serodiagnostic peptides having potential application to differentiate prior infection with multiple mosquito-borne viruses.

  • Useful against: Dengue 1-4, Japanese Encephalitis, St Louis encephalitis, West Nile, Yellow fever, and Zika viruses
  • Identify immunodominant epitopes from peptide array experiments using data mining techniques

Apply statistical workflows to mine existing viral genome data for evolutionary trends and host transcriptomic data for druggable signaling pathways.

  • Comparative genomics for:
    • Dengue viruses
    • Influenza virus
    • Hepatitis C virus
    • Zika virus

Contribute to the development of the NIH-funded Virus Pathogen Resource (ViPR) bioinformatics resource center (www.viprbrc.org) and the Influenza Research Database (IRD; www.fludb.org).

  • Store and analyze “-omics” data using pathway enrichment algorithms
  • Develop and integrate bioinformatics tools, statistical processes, and analytical workflows
  • Design an API-based method to run intensive analyses on a high-performance computing platform

Select Publications

Miller MA, Schwartz T, et al.
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

Evolutionary Bioinformatics Online. 2015 Nov 01; 11: 43-8.[more]

Lee AJ, Das SR, et al.
Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.

Journal of Virology. 2015 May 01; 89: 5427-40.[more]

Squires RB, Pickett BE, et al.
Toward a Method for Tracking Virus Evolutionary Trajectory Applied to the Pandemic H1N1 2009 Influenza Virus.

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in infectious Diseases. 2014 Dec 01; 28: 351-7.[more]

Dugan VG, Emrich SJ, et al.
Standardized Metadata for Human Pathogen/vector Genomic Sequences.

PloS One. 2014 Dec 01; 9: e99979.[more]

Aevermann BD, Pickett BE, et al.
A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection.

Scientific Data. 2014 Nov 01; 1: 140033.[more]

Pickett BE, Liu M, et al.
Metadata-driven Comparative Analysis Tool for Sequences (meta-CATS): an Automated Process for Identifying Significant Sequence Variations That Correlate With Virus Attributes.

Virology. 2013 Dec 01; 447: 45-51.[more]

Noronha JM, Liu M, et al.
Influenza Virus Sequence Feature Variant Type Analysis: Evidence of a Role for NS1 in Influenza Virus Host Range Restriction.

Journal of Virology. 2012 May 01; 86: 5857-66.[more]

Pickett BE, Sadat EL, et al.
ViPR: an Open Bioinformatics Database and Analysis Resource for Virology Research.

Nucleic Acids Research. 2012 Jan 01; 40: D593-8.[more]

Schmidt DJ, Pickett BE, et al.
A Phylogenetic Analysis Using Full-length Viral Genomes of South American Dengue Serotype 3 in Consecutive Venezuelan Outbreaks Reveals a Novel NS5 Mutation.

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in infectious Diseases. 2011 Dec 01; 11: 2011-9.[more]