Sean Thomas, PhD
Assistant Professor
Epidemiology & Biostatistics
School of Medicine

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.

• Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma.
  Oral oncology 2017 Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J
• The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes.
  Molecular cell 2017 Conrad RJ, Fozouni P, Thomas S, Sy H, Zhang Q, Zhou MM, Ott M
• Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-Seq) Protocol for Zebrafish Embryos.
  Methods in molecular biology (Clifton, N.J.) 2017 Doganli C, Sandoval M, Thomas S, Hart D
• SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells.
  eLife 2016 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
• Somatostatin receptor 2a is a more sensitive diagnostic marker of meningioma than epithelial membrane antigen.
  Acta neuropathologica 2015 Menke JR, Raleigh DR, Gown AM, Thomas S, Perry A, Tihan T
• Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature.
  Development (Cambridge, England) 2014 Delgado-Olguín P, Dang LT, He D, Thomas S, Chi L, Sukonnik T, Khyzha N, Dobenecker MW, Fish JE, Bruneau BG
• RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.
  Current protocols in human genetics 2014 Williams AG, Thomas S, Wyman SK, Holloway AK
• Long-read sequencing of chicken transcripts and identification of new transcript isoforms.
  PloS one 2014 Thomas S, Underwood JG, Tseng E, Holloway AK, Bench To Basinet CvDC Informatics Subcommittee
• Temporal regulation of Dpp signaling output in the Drosophila wing.
  Developmental dynamics : an official publication of the American Association of Anatomists 2014 O'Keefe DD, Thomas S, Edgar BA, Buttitta L
• Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.
  Molecular cell 2013 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
• DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.
  Proceedings of the National Academy of Sciences of the United States of America 2012 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
• Combinatorial control of temporal gene expression in the Drosophila wing by enhancers and core promoters.
  BMC genomics 2012 O'Keefe DD, Thomas SR, Bolin K, Griggs E, Edgar BA, Buttitta LA
• A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development.
  Cell 2012 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
• An integrated encyclopedia of DNA elements in the human genome.
  Nature 2012 ENCODE Project Consortium
• BEDOPS: high-performance genomic feature operations.
  Bioinformatics (Oxford, England) 2012 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
• Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.
  Genome biology 2011 Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA
• The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.
  Genome biology 2011 Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD
• Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.
  PLoS genetics 2011 Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB
• Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA
• Histone acetylations mark origins of polycistronic transcription in Leishmania major.
  BMC genomics 2009 Thomas S, Green A, Sturm NR, Campbell DA, Myler PJ
• Kinetoplastid genomics: the thin end of the wedge.
  Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2008 Sturm NR, Martinez LL, Thomas S
• A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing.
  BMC genomics 2007 Thomas S, Martinez LL, Westenberger SJ, Sturm NR
• The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes.
  BMC microbiology 2007 Hitchcock RA, Thomas S, Campbell DA, Sturm NR
• A non-universal transcription factor? The Leishmania tarentolae TATA box-binding protein LtTBP associates with a subset of promoters.
  International journal for parasitology 2006 Thomas S, Yu MC, Sturm NR, Campbell DA
• Intragenomic spliced leader RNA array analysis of kinetoplastids reveals unexpected transcribed region diversity in Trypanosoma cruzi.
  Gene 2005 Thomas S, Westenberger SJ, Campbell DA, Sturm NR
• Transcription in kinetoplastid protozoa: why be normal?
  Microbes and infection 2003 Campbell DA, Thomas S, Sturm NR