Dr. Brett Pickett is an Assistant Professor in the Microbiology and Molecular Biology Department. Before joining the faculty, he completed his B.S degree in Microbiology from BYU in 2005, his Ph.D. training in Microbiology at the University of Alabama at Birmingham, and his postdoctoral training in Pathology at the University of Texas Southwestern Medical Center at Dallas. He then obtained additional experience in industry, and at the J. Craig Venter Institute. He applies his past training to perform genome sequencing and comparative genomics analyses of human pathogens and cancers. He works to develop data mining workflows, apply machine learning techniques, and use advanced statistical workflows on the Fulton high-performance computing environment at BYU to better understand how human cells respond during infection acute infection or chronic disease (e.g. flu, Streptococcus, cancer, etc). The results from these analyses will then be used to generate hypotheses that can be tested in the wet lab. Dr. Pickett enjoys waterskiing, playing the piano, archery, and spending time with his wonderful wife Laura and their six children.
Molecular Biology, Quantitative Genomics
We are interested in learning more about how human pathogens cause infectious diseases. We do this through two separate but complementary approaches.
- We apply “big data” techniques on the high-performance computing environment at BYU to mine existing sequence information from public databases. Specifically, we look at how a human cell responds to disease by calculating how the messenger RNA (mRNA) changes when comparing disease and non-disease samples. We can then use this information to determine the functions and signals that are changed during and after infection or disease.
- We perform comparative genomics analyses of viruses and bacteria to better understand how, why, and where they accumulate mutations in their genomes. We also apply statistical methods to determine how these mutations affect the phenotype of the pathogen.
Honors and Awards
University of Alabama at Birmingham, Department of Microbiology: Hiramoto Travel Award
National Institutes of Health: T32 Training Grant
Cold Spring Harbor Laboratory: Student Travel Award
Boy Scouts of America: Eagle Scout
Selected Peer-Reviewed Journal Articles (see complete list here: https://www.ncbi.nlm.nih.gov/myncbi/brett.pickett.1/bibliography/public/ )
Viedma MPM, Kose N, Parham L, Balmaseda A, Kuan G, Lorenzana I, Harris E, Crowe JE, Pickett BE. Peptide Arrays Incubated with Three Collections of Human Sera from Patients Infected with Mosquito-Borne Viruses. F1000Res. 2019 Nov 7;8:1875. doi: 10.12688/f1000research.20981.1. PMID: 32201571
Viedma Martinez MP, Puri V, Oldfield LM, Shabman RS, Tan GS, Pickett BE. Optimization of qRT-PCR assay for Zika virus detection in human serum and urine. Virus Research 2019 Feb 10; 263:173-178. doi: 10.1016/j.virusres.2019.01.013. PMID: 30742853.
Viedma Martinez MP, Pickett BE. Characterizing the Different Effects of Zika Virus Infection in Placenta and Microglia Cells. Viruses 2018, 10(11), 649. https://doi.org/10.3390/v10110649 . PMID: 30453684.
Moser LA, Boylan BT, Moreira FR, Myers LJ, Svenson EL, Fedorova NB, Pickett BE, Bernard KA. Growth and adaptation of Zika virus in mammalian and mosquito cells. PLoS Negl Trop Dis. 2018 Nov 12;12(11):e0006880. doi: 10.1371/journal.pntd.0006880. PMID: 30418969.
Shrivastava S, Puri V, Dilley KA, Ngouajio E, Shifflett J, Oldfield L, Fedorova N, Hu L, Williams T, Durbin A, Amedeo P, Rashid S, Shabman RS, Pickett BE. Whole genome sequencing, variant analysis, phylogenetics, deep sequencing, and development of diagnostic assays for Zika virus strains. Nature Sci Rep. 2018 Oct 26;8(1):15843. doi: 10.1038/s41598-018-34147-7. PMID: 30367096.
Tan Y*, Pickett BE*, Shrivastava S, Gresh L, Balmaseda A, Amedeo P, Hu L, Puri V, Fedorova NB, Halpin RA, LaPointe MP, Cone MR, Larson LH, Kramer LD, Ciota AT, Gordon A, Shabman RS, Das SR, Harris E. Differing epidemiological dynamics of Chikungunya virus in the Americas during 2014- 2015 epidemic. PLoS Neglected Tropical Diseases. 2018 Jul 30; 12(7):e0006670. PMID: 30059496
Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA. A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol Bioinform Online. 2015 Mar 16;11:43-8. PMID: 25861210.
Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH. Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans. J Virol. 2015 May;89(10):5427-40. PMID: 25741011.
Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A 3rd, 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. A comprehensive collection of systems biology data characterizing the host response to viral infection. Nature Scientific Data. 2014 Oct 14;1. PMID: 25977790.
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. Metadata-driven Comparative Analysis Tool for Sequences (meta-CATS): an Automated Process for Identifying Significant Sequence Variations that Correlate with Virus Attributes. Virology. 2013 41(1), 45-51. PMID: 24210098.
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. ViPR: An Open Bioinformatics Database and Analysis Resource for Virology Research. Nucleic Acids Res. 2012 Jan;40(Database issue):D593-8. PMID: 22006842.
Schmidt D*, Pickett BE*, Camacho D, Comach G, Xhaja K, Henn M, Lennon N, Ritzzolo K, Vasconcelos P, Nogueira M, Mondini A, Muñoz-Jordán J, de Bosch N, Becerra AA, Harris E, Lefkowitz EJ, Gehrke L, Bosch I. A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation. Infect Genet Evol. 2011 Dec;11(8):2011-9. PMID: 21964598.
Pickett BE, Striker RT, Lefkowitz EJ. Evidence for separation of HCV Subtype 1A into Two Distinct Clades. J. Viral Hepat. 2011 Sep;18(9):608-18. PMID: 20565573.
Pickett BE, Lefkowitz EJ. Recombination in West Nile Virus: minimal contribution to genomic diversity. Virol J. 2009 Oct 12;6(1):165. PMID: 19821990.
Pickett BE. Identification and Validation of Diagnostic Peptides to Differentiate Serum Antibody Patterns Between Zika and Other Mosquito-Borne Viruses. 37th Annual American Society for Virology meeting. College Park, Maryland. July 14-18, 2018.
Pickett BE. Deep-sequencing Analysis of coding-complete Zika virus genomes. 36th Annual American Society for Virology meeting. Madison, Wisconsin. June 24-28, 2017
Pickett BE. Peptide array technology: an opportunity for standardization. 19th Genomic Standards Consortium meeting. Brisbane, Queensland, Australia. May 15-17, 2017
Pickett BE, Zhang Y, Scheuermann R. ViPR Resource Workshop. 37th Annual International Herpesvirus Workshop. Calgary, Alberta, Canada. August 4-9, 2012.
Pickett BE, Schmidt D, Camacho D, Comach G, Bosch I, Lefkowitz EJ. Analysis of Dengue Type 3 Sequences from Two Venezuelan Outbreaks. 29th American Society for Virology Annual Meeting. Bozeman, Montana. July 17-21, 2010.
Pickett BE, Lefkowitz EJ. Separating HCV genotype 1a into 2 clades and implications for drug resistance. University of Alabama at Birmingham Virology Discussion Group. Birmingham, Alabama. November 7, 2008.
Pickett BE, Lefkowitz EJ. CovarView—A program for visual display of genome-wide covariance analyses. 7th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics. Cold Spring Harbor, New York. November 1-5, 2007.
Pickett BE, Breakwell DP. Antibiotic Resistance Gene Cassettes Associated With Integrons in Escherichia coli. 53rd Annual meeting of the American Society for Microbiology regional meeting. Weber State University, Ogden, Utah. March 12th, 2005.