Sean Thomas, PhD

Title(s)Assistant Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
AddressLocation Required, #001
Varies CA 00000
Phone--
ORCID ORCID Icon0000-0002-9740-4161 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of California, Los AngelesPh.D.2006Molecular Biology
    University of North Carolina, CharlotteBA2000Architecture
    Unviersity of North Carolina, CharlotteBS2000Biology
    Collapse Awards and Honors
    UCSF2014CTSI Consultant of the Year

    Collapse Overview 
    Collapse Overview
    The regulation of gene expression in eukaryotes is my major interest. Chromatin structure, epigenetic marks, context-dependent signaling, and the scrum of transcription factor binding throughout the genome all contribute to the expression of a gene. I collaborate with other researchers to study the regulation of gene expression in a number of contexts from embryonic development, to stem cell differentiation, to cross-species comparisons of regulatory architecture.

    I also specialize generally in computational biology approaches to understanding and analyzing enormous biological datasets.

    As a professional consultant with Gladstone Institutes and UCSF's CTSI, I have a number of ongoing research projects across a range of subjects and am available for consultations with new researchers.

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Macrophage Infection Models for Mycobacterium tuberculosis. Methods Mol Biol. 2021; 2314:167-182. Johnson BK, Thomas SM, Olive AJ, Abramovitch RB. PMID: 34235652.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    2. WYZ: a pilot study protocol for designing and developing a mobile health application for engagement in HIV care and medication adherence in youth and young adults living with HIV. BMJ Open. 2019 05 05; 9(5):e030473. Erguera XA, Johnson MO, Neilands TB, Ruel T, Berrean B, Thomas S, Saberi P. PMID: 31061063; PMCID: PMC6501960.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    3. Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction. BMC Med Genomics. 2018 05 25; 11(1):50. Marco EJ, Aitken AB, Nair VP, da Gente G, Gerdes MR, Bologlu L, Thomas S, Sherr EH. PMID: 29801487; PMCID: PMC5970458.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    4. The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. J Virol. 2018 02 01; 92(3). Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JL. PMID: 29142137; PMCID: PMC5774889.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    5. A Simple Pre-Exposure Prophylaxis (PrEP) Optimization Intervention for Health Care Providers Prescribing PrEP: Pilot Study. JMIR Form Res. 2018 Jan-Jun; 2(1). Saberi P, Berrean B, Thomas S, Gandhi M, Scott H. PMID: 30637375; PMCID: PMC6325636.
      View in: PubMed   Mentions: 13  
    6. Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma. Oral Oncol. 2017 11; 74:8-14. Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J. PMID: 29103756.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    7. The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes. Mol Cell. 2017 Sep 21; 67(6):1001-1012.e6. Conrad RJ, Fozouni P, Thomas S, Sy H, Zhang Q, Zhou MM, Ott M. PMID: 28844864; PMCID: PMC5610089.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    8. Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-Seq) Protocol for Zebrafish Embryos. Methods Mol Biol. 2017; 1507:59-66. Doganli C, Sandoval M, Thomas S, Hart D. PMID: 27832532.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    9. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife. 2016 Mar 07; 5:e10647. Myers SA, Peddada S, Chatterjee N, Friedrich T, Tomoda K, Krings G, Thomas S, Maynard J, Broeker M, Thomson M, Pollard K, Yamanaka S, Burlingame AL, Panning B. PMID: 26949256; PMCID: PMC4841768.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    10. Somatostatin receptor 2a is a more sensitive diagnostic marker of meningioma than epithelial membrane antigen. Acta Neuropathol. 2015 Sep; 130(3):441-3. Menke JR, Raleigh DR, Gown AM, Thomas S, Perry A, Tihan T. PMID: 26195322.
      View in: PubMed   Mentions: 48     Fields:    Translation:Humans
    11. Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature. Development. 2014 Dec; 141(23):4610-7. Delgado-Olguín P, Dang LT, He D, Thomas S, Chi L, Sukonnik T, Khyzha N, Dobenecker MW, Fish JE, Bruneau BG. PMID: 25359725; PMCID: PMC4302930.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    12. RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Curr Protoc Hum Genet. 2014 Oct 01; 83:11.13.1-20. Williams AG, Thomas S, Wyman SK, Holloway AK. PMID: 25271838; PMCID: PMC4230301.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    13. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One. 2014; 9(4):e94650. Thomas S, Underwood JG, Tseng E, Holloway AK, Bench To Basinet CvDC Informatics Subcommittee. PMID: 24736250; PMCID: PMC3988055.
      View in: PubMed   Mentions: 36     Fields:    Translation:Animals
    14. Temporal regulation of Dpp signaling output in the Drosophila wing. Dev Dyn. 2014 Jun; 243(6):818-32. O'Keefe DD, Thomas S, Edgar BA, Buttitta L. PMID: 24591046; PMCID: PMC4034111.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    15. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 07; 52(3):314-24. Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. PMID: 24207025; PMCID: PMC3936344.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    16. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21330-5. Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. PMID: 23236164; PMCID: PMC3535648.
      View in: PubMed   Mentions: 83     Fields:    Translation:AnimalsCells
    17. Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters. BMC Genomics. 2012 Sep 20; 13:498. O'Keefe DD, Thomas SR, Bolin K, Griggs E, Edgar BA, Buttitta LA. PMID: 22992320; PMCID: PMC3641971.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    18. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell. 2012 Sep 28; 151(1):221-32. Paige SL, Thomas S, Stoick-Cooper CL, Wang H, Maves L, Sandstrom R, Pabon L, Reinecke H, Pratt G, Keller G, Moon RT, Stamatoyannopoulos J, Murry CE. PMID: 22981225; PMCID: PMC3462257.
      View in: PubMed   Mentions: 199     Fields:    Translation:HumansAnimalsCells
    19. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. ENCODE Project Consortium. PMID: 22955616; PMCID: PMC3439153.
      View in: PubMed   Mentions: 8536     Fields:    Translation:HumansAnimalsCells
    20. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012 Jul 15; 28(14):1919-20. Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. PMID: 22576172; PMCID: PMC3389768.
      View in: PubMed   Mentions: 426     Fields:    
    21. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011; 12(5):R43. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. PMID: 21569360; PMCID: PMC3219966.
      View in: PubMed   Mentions: 101     Fields:    Translation:AnimalsCells
    22. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011; 12(4):R34. Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. PMID: 21473766; PMCID: PMC3218860.
      View in: PubMed   Mentions: 123     Fields:    Translation:AnimalsCells
    23. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 2011 Feb 03; 7(2):e1001290. Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. PMID: 21304941; PMCID: PMC3033374.
      View in: PubMed   Mentions: 92     Fields:    Translation:AnimalsCells
    24. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 05; 107(1):139-44. Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. PMID: 19966280; PMCID: PMC2806781.
      View in: PubMed   Mentions: 318     Fields:    Translation:HumansAnimalsCells
    25. Histone acetylations mark origins of polycistronic transcription in Leishmania major. BMC Genomics. 2009 Apr 08; 10:152. Thomas S, Green A, Sturm NR, Campbell DA, Myler PJ. PMID: 19356248; PMCID: PMC2679053.
      View in: PubMed   Mentions: 75     Fields:    Translation:AnimalsCells
    26. Kinetoplastid genomics: the thin end of the wedge. Infect Genet Evol. 2008 Dec; 8(6):901-6. Sturm NR, Martinez LL, Thomas S. PMID: 18675383; PMCID: PMC2676795.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    27. A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. BMC Genomics. 2007 May 24; 8:133. Thomas S, Martinez LL, Westenberger SJ, Sturm NR. PMID: 17524149; PMCID: PMC1892023.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    28. The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes. BMC Microbiol. 2007 May 22; 7:44. Hitchcock RA, Thomas S, Campbell DA, Sturm NR. PMID: 17517143; PMCID: PMC1888695.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    29. A non-universal transcription factor? The Leishmania tarentolae TATA box-binding protein LtTBP associates with a subset of promoters. Int J Parasitol. 2006 Sep; 36(10-11):1217-26. Thomas S, Yu MC, Sturm NR, Campbell DA. PMID: 16753168.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    30. Intragenomic spliced leader RNA array analysis of kinetoplastids reveals unexpected transcribed region diversity in Trypanosoma cruzi. Gene. 2005 Jun 06; 352:100-8. Thomas S, Westenberger SJ, Campbell DA, Sturm NR. PMID: 15925459.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    31. Transcription in kinetoplastid protozoa: why be normal? Microbes Infect. 2003 Nov; 5(13):1231-40. Campbell DA, Thomas S, Sturm NR. PMID: 14623019.
      View in: PubMed   Mentions: 75     Fields:    Translation:AnimalsCells
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