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Brett Pickett

Brett Pickett

Assistant Professor
Microbiology & Molecular Biology

3141 LSB
Provo, UT 84602

Biography

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.

Research Interests

The research in our group can be divided into two distinct but complementary categories: comparative genomics of pathogens, and the human transcriptional response to a stimulus (i.e. infection, cancer, etc).

To perform comparative genomics, we begin by either assembling consensus genomes or retrieving them from public databases. We then generate multiple sequence alignments, reconstruct phylogenetic trees, identify significant changes between groups of sequences, and apply other relevant methods. Our goal is to better understand how the pathogens evolve over time, what advantages certain mutations may confer, and whether we can predict future changes before they occur.

To analyze the human transcriptional during acute infection (e.g. influenza, Streptococcus) or chronic disease (e.g. cancer, autoimmunity), we begin by retrieving raw sequencing data from the National Center for Biotechnology Information. These sequences are then subjected to an analytical pipeline that quantifies how many times each mRNA in the sample is present. We can then run statistics to identify significant 1) differentially-expressed genes, 2) functional enrichment of terms, and 3) signaling pathways that are represented. The signaling pathway results can then be cross-referenced to other data sources to find drugs that target host processes that the infection or chronic condition generally affects. By targeting such "key pathways", we can potentially reduce the severity, symptoms, and/or progression of these acute or chronic diseases.

The results from either research category can then be combined and subjected to machine learning algorithms. These types of analyses can identify prominent and/or subtle trends that can then be tested for biological relevance and function in the laboratory.

Teaching Interests

Molecular Biology
Genomics


Education

  • Ph.D., Microbiology , University of Alabama at Birmingham (2010)
  • B.S., Microbiology , Brigham Young University (2005)

Honors and Awards

  • Hiramoto Travel Award, University of Alabama at Birmingham, Department of Microbiology (2009 - 2009)
  • T32 Training Grant, National Institutes of Health (2007 - 2008)
  • Student Travel Award, Cold Spring Harbor Laboratory (2007 - 2007)
  • Eagle Scout, Boy Scouts of America (1995)

Memberships

  • American Society for Microbiology (2017 - Present)
  • European Virus Bioinformatics Center (2017 - Present)
  • American Society for Virology (2009 - Present)
  • Sigma Delta Pi (2004 - Present)
  • Scientists and Engineers for America (2009 - 2010)

Professional Citizenship

  • Board Member, Viruses Editorial Office (2021 - Present)
  • Committee/Council Chair, Operation Outbreak (2020 - Present)
  • Editorial Review Board Member, PeerJ (2019 - Present)

Courses Taught

Publications

Kara L Phipps Ketaki Ganti Nathan T Jacobs CY Lee Silvia Carnaccini MC White Miglena Manandhar Brett Earl Pickett Gene S Tan Lucas M Ferreri Daniel R Perez Anice C Lowen D Kaul R Rathnasinghe M Ferres Gene S Tan A Barrera Brett Earl Pickett BA Methe Suman R Das I Budnik Rebecca A Halpin David Wentworth M Schmolke I Mena RA Albrecht Indresh Singh Karen E Nelson Adolfo García-Sastre Christopher L Dupont Rafael A Medina Maria Del Pilar Martinez Viedma Nirgun Kose Leda Parham Angel Balmaseda Guillermina Kuan Ivette Lorenzana Eva Harris James E. Crowe Brett Earl Pickett Sean M Bialosuknia Yi Tan Steven D Zink Cheri A Koetzner Joseph G Maffei Rebecca A Halpin Emmi A Mueller Mark Novotny Meghan Shilts Nadia B Fedorova Paolo Amedeo Suman R Das Brett Earl Pickett Laura D Kramer Alexander T Ciota Maria Del Pilar Martinez Viedma Vinita Puri Lauren M. Oldfield Reed S Shabman Gene S Tan Brett Earl Pickett Bashar Ibrahim Ksenia Arkhipova Arno C Andeweg Susana Posada-Cespedes Francois Enault Arthur Gruber Eugene V Koonin Anne Kupczok Philippe Lemey Alice C McHardy Dino P McMahon Brett Earl Pickett David L Robertson Richard H Scheuermann Alexandra Zhernakova Mark P Zwart Alexander Schonhuth Bas E Dutilh Manja Marz Maria del Pilar Martinez Viedma Brett Earl Pickett Yi Tan Brett Earl Pickett Susmita Shrivastava Lionel Gresh Angel Balmaseda Paolo Amedeo Lihui Hu Vinita Puri Nadia B. Fedorova Rebecca A. Halpin Matthew P LaPointe MR Cone L Heberlein-Larson Laura D Kramer Alexander T Ciota A Gordon Reed S Shabman Suman R Das Eva Harris Lindsey A Moser Brendan T Boylan Fernando R Moreira Laurel J Myers Emma L Svenson Nadia B Fedorova Brett Earl Pickett Kristen A Bernard Susmita Shrivastava Vinita Puri Karrie A Dilley Erika Ngouajio Jessica Shifflett Lauren M Oldfield Nadia B Fedorova Lihui Hu Torrey Williams Alan Durbin Paolo Amedeo S Rashid Reed S Shabman Brett Earl Pickett Martin M Nyaga Yi Tan Mapaseka L Seheri Rebecca A Halpin Asmik Akopov Karla M Stucker Nadia B Fedorova Susmita Shrivastava A Duncan Steele Jason M Mwenda Brett Earl Pickett SR Das JM Mphahlele Alex J Lee Roshni Bhattacharya Richard H Scheuermann Brett Earl Pickett Yun Zhang Brian D Aevermann Tavis K Anderson David F Burke Gwenaelle Dauphin Zhiping Gu Sherry He Sanjeev Kumar Christopher N Larsen Alexandra J Lee X Li Catherine Macken C Mahaffey Brett Earl Pickett B Reardon T Smith L Stewart C Suloway G Sun L Tong AL Vincent B Walters Sam Zaremba H Zhao L Zhou Christian Zmasek Ed B Klem Richard H Scheuermann Mark A Miller Terri Schwartz Brett Earl Pickett Sherry He Edward B Klem Richard H Scheuermann Maria Passarotti Seth Kaufman Maureen A O'Leary Alexandra J Lee Suman R Das Wei Wang Theresa Fitzgerald Brett Earl Pickett Brian D Aevermann David J Topham Ann R Falsey Richard H Scheuermann Brian D Aevermann Brett Earl Pickett Sanjeev Kumar Edward B Klem Sudhakar Agnihothram Peter S Askovich Armand Bankhead, III Meagen Bolles Victoria Carter Jean Chang TR Clauss P Dash AH Diercks AJ Eisfeld A Ellis S Fan MT Ferris LE Gralinski RR Green MA Gritsenko M Hatta RA Heegel JM Jacobs S Jeng L Josset SM Kaiser S Kelly GL Law C Li J Li C Long ML Luna M Matzke J McDermott V Menachery TO Metz H Mitchell ME Monroe G Navarro Gabi Neumann RL Podyminogin SO Purvine CM Rosenberger CJ Sanders AA Schepmoes AK Shukla A Sims P Sova VC Tam N Tchitchek PG Thomas SC Tilton A Totura J Wang BJ Webb-Robertson J Wen JM Weiss F Yang B Yount Q Zhang S McWeeney RD Smith Katrina M Waters Yoshihiro Kawaoka Ralph Baric Alan Aderem MG Katze Richard H Scheuermann VG Dugan SJ Emrich GI Giraldo-Calderón OS Harb RM Newman Brett Earl Pickett LM Schriml TB Stockwell CJ Stoeckert Jr DE Sullivan Indresh Singh DV Ward Alison Yao J Zheng Tanya Barrett Bruce Birren Lauren Brinkac VM Bruno E Caler S Chapman FH Collins CA Cuomo Valentina Di Francesco S Durkin M Eppinger M Feldgarden C Fraser WF Fricke Maria Giovanni Matthew R Henn E Hine JD Hotopp Ilene Karsch-Mizrachi JC Kissinger EM Lee P Mathur EF Mongodin CI Murphy G Myers DE Neafsey Karen E Nelson William C Nierman Julia Puzak D Rasko David S Roos L Sadzewicz JC Silva Bruno Sobral R Burke Squires RL Stevens L Tallon H Tettelin D Wentworth Owen White R Will Jennifer Wortman Yun Zhang Richard H Scheuermann R Burke Squires Brett Earl Pickett Sajal Das Richard H Scheuermann Brett Earl Pickett M Liu EL Sadat RB Squires JM Noronha S He W Jen S Zaremba Z Gu L Zhou Chris N Larsen Irene Bosch L Gehrke Monnie McGee Ed B Klem Richard H Scheuermann R Burke Squires Jyothi Noronha Victoria Hunt Adolfo Garcia-Sastre Catherine Macken Nicole Baumgarth David Suarez Brett Earl Pickett Yun Zhang Chris N Larsen A Ramsey L Zhou Sam Zaremba S Kumar J Deitrich Ed Klem Richard H Scheuermann Jyothi M Noronha Mengya Liu R Burke Squires Brett Earl Pickett Benjamin G Hale Gillian M Air Summer E Galloway Toru Takimoto Mirco Schmolke Victoria Hunt Edward Klem Adolfo García-Sastre Monnie McGee Richard H Scheuermann Brett Earl Pickett Douglas Greer Yun Zhang Lucy Stewart Liwei Zhou Guangyu Sun Zhiping Gu Sanjeev Kumar Sam Zaremba Christopher N Larsen W Jen Ed B Klem Richard H Scheuermann DJ Schmidt Brett Earl Pickett D Camacho G Comach K Xhaja NJ Lennon K Rizzolo N De Bosch A Becerra ML Nogueira A Mondini E V da Silva P F Vasconcelos J L Muñoz-Jordán G A Santiago R Ocazionez Lee Gehrke Elliot L Lefkowitz Bruce W Birren Matthew R Henn Irene Bosch Brett Earl Pickett Rob Striker Elliot J Lefkowitz Gregory S White Brett Earl Pickett Elliot J Lefkowitz Amelia G Johnson Christy Ottendorfer Lillian M Stark Thomas R Unnasch Brett Earl Pickett Eva L Sadat Yun Zhang Jyothi M Noronha R Burke Squires Victoria Hunt Mengya Liu Sanjeev Kumar Sam Zaremba Zhiping Gu L Zhou Chris N Larsen John Dietrich Ed B Klem Richard H Scheuermann Brett Earl Pickett Elliot J Lefkowitz

Presentations

Brett Earl Pickett
Jacquelyne Howell Caroline Jackson Tiana M Scott Anice C Lowen Gene S Tan Brett Earl Pickett
Kennedy Gifford Brett Earl Pickett
Tiana M Scott Sam Jensen Brett Earl Pickett
Madison Gray Brett Earl Pickett
Avantika Lal MG Ferrarini R Rebollo A Gruber A Guarracino IM Gonzalez T Floyd D Siqueira de Oliveira T Pusa Brett Earl Pickett Vanessa Aguiar-Pulido
Avantika Lal MG Ferrarini R Rebollo A Gruber A Guarracino IM Gonzalez T Floyd D Siqueira de Oliveira T Pusa Brett Earl Pickett Vanessa Aguiar-Pulido
Brett Earl Pickett
Brett Pickett