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    Sean Thomas, PhD

    TitleAssistant Professor
    SchoolUCSF School of Medicine
    DepartmentEpidemiology & Biostatistics
    Address550 16th Street
    San Francisco CA 94158
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      Collapse Biography 
      Collapse Education and Training
      University of California, Los AngelesPh.D.Molecular Biology2006
      University of North Carolina, CharlotteBAArchitecture2000
      Unviersity of North Carolina, CharlotteBSBiology2000
      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 Interests
      regulation of gene expression, bioinformatics, genomics, computational biology, epigenetics, chromatin structure, stem cell differentiation, organismal development

      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.
      List All   |   Timeline
      1. Doganli C, Sandoval M, Thomas S, Hart D. Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-Seq) Protocol for Zebrafish Embryos. Methods Mol Biol. 2017; 1507:59-66. PMID: 27832532.
        View in: PubMed
      2. 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. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife. 2016; 5. PMID: 26949256.
        View in: PubMed
      3. Menke JR, Raleigh DR, Gown AM, Thomas S, Perry A, Tihan T. Somatostatin receptor 2a is a more sensitive diagnostic marker of meningioma than epithelial membrane antigen. Acta Neuropathol. 2015 Sep; 130(3):441-3. PMID: 26195322.
        View in: PubMed
      4. Delgado-Olguín P, Dang LT, He D, Thomas S, Chi L, Sukonnik T, Khyzha N, Dobenecker MW, Fish JE, Bruneau BG. Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature. Development. 2014 Dec; 141(23):4610-7. PMID: 25359725; PMCID: PMC4302930.
      5. Williams AG, Thomas S, Wyman SK, Holloway AK. RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis. Curr Protoc Hum Genet. 2014; 83:11.13.1-11.13.20. PMID: 25271838; PMCID: PMC4230301.
      6. Thomas S, Underwood JG, Tseng E, Holloway AK. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS One. 2014; 9(4):e94650. PMID: 24736250; PMCID: PMC3988055.
      7. O'Keefe DD, Thomas S, Edgar BA, Buttitta L. Temporal regulation of Dpp signaling output in the Drosophila wing. Dev Dyn. 2014 Jun; 243(6):818-32. PMID: 24591046; PMCID: PMC4034111.
      8. 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. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 7; 52(3):314-24. PMID: 24207025; PMCID: PMC3936344.
      9. 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. 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. PMID: 23236164; PMCID: PMC3535648.
      10. O'Keefe DD, Thomas SR, Bolin K, Griggs E, Edgar BA, Buttitta LA. Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters. BMC Genomics. 2012; 13:498. PMID: 22992320; PMCID: PMC3641971.
      11. 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. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell. 2012 Sep 28; 151(1):221-32. PMID: 22981225; PMCID: PMC3462257.
      12. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414):57-74. PMID: 22955616; PMCID: PMC3439153.
      13. 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. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012 Jul 15; 28(14):1919-20. PMID: 22576172; PMCID: PMC3389768.
      14. Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011; 12(5):R43. PMID: 21569360; PMCID: PMC3219966.
      15. Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011; 12(4):R34. PMID: 21473766; PMCID: PMC3218860.
      16. Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 2011; 7(2):e1001290. PMID: 21304941; PMCID: PMC3033374.
      17. Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5; 107(1):139-44. PMID: 19966280; PMCID: PMC2806781.
      18. Thomas S, Green A, Sturm NR, Campbell DA, Myler PJ. Histone acetylations mark origins of polycistronic transcription in Leishmania major. BMC Genomics. 2009; 10:152. PMID: 19356248; PMCID: PMC2679053.
      19. Lewis SL, Lopez-Gonzalez G, Sonké B, Affum-Baffoe K, Baker TR, Ojo LO, Phillips OL, Reitsma JM, White L, Comiskey JA, Djuikouo K MN, Ewango CE, Feldpausch TR, Hamilton AC, Gloor M, Hart T, Hladik A, Lloyd J, Lovett JC, Makana JR, Malhi Y, Mbago FM, Ndangalasi HJ, Peacock J, Peh KS, Sheil D, Sunderland T, Swaine MD, Taplin J, Taylor D, Thomas SC, Votere R, Wöll H. Increasing carbon storage in intact African tropical forests. Nature. 2009 Feb 19; 457(7232):1003-6. PMID: 19225523.
        View in: PubMed
      20. Sturm NR, Martinez LL, Thomas S. Kinetoplastid genomics: the thin end of the wedge. Infect Genet Evol. 2008 Dec; 8(6):901-6. PMID: 18675383; PMCID: PMC2676795.
      21. Thomas S, Martinez LL, Westenberger SJ, Sturm NR. A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. BMC Genomics. 2007; 8:133. PMID: 17524149; PMCID: PMC1892023.
      22. Hitchcock RA, Thomas S, Campbell DA, Sturm NR. The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes. BMC Microbiol. 2007; 7:44. PMID: 17517143; PMCID: PMC1888695.
      23. Thomas S, Yu MC, Sturm NR, Campbell DA. 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. PMID: 16753168.
        View in: PubMed
      24. Thomas S, Westenberger SJ, Campbell DA, Sturm NR. Intragenomic spliced leader RNA array analysis of kinetoplastids reveals unexpected transcribed region diversity in Trypanosoma cruzi. Gene. 2005 Jun 6; 352:100-8. PMID: 15925459.
        View in: PubMed
      25. Wright IJ, Reich PB, Westoby M, Ackerly DD, Baruch Z, Bongers F, Cavender-Bares J, Chapin T, Cornelissen JH, Diemer M, Flexas J, Garnier E, Groom PK, Gulias J, Hikosaka K, Lamont BB, Lee T, Lee W, Lusk C, Midgley JJ, Navas ML, Niinemets U, Oleksyn J, Osada N, Poorter H, Poot P, Prior L, Pyankov VI, Roumet C, Thomas SC, Tjoelker MG, Veneklaas EJ, Villar R. The worldwide leaf economics spectrum. Nature. 2004 Apr 22; 428(6985):821-7. PMID: 15103368.
        View in: PubMed
      26. Campbell DA, Thomas S, Sturm NR. Transcription in kinetoplastid protozoa: why be normal? Microbes Infect. 2003 Nov; 5(13):1231-40. PMID: 14623019.
        View in: PubMed
      27. Henry HA, Thomas SC. Interactive effects of lateral shade and wind on stem allometry, biomass allocation, and mechanical stability in Abutilon theophrasti (Malvaceae). Am J Bot. 2002 Oct; 89(10):1609-15. PMID: 21665588.
        View in: PubMed
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