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Faculty: James A. Thomson, VMD, PhD

Dept: Professor, Cell & Regenerative Biology (UW)
Director of Regenerative Biology
Contact: Morgridge Institute for Research
330 N. Orchard
Training Areas:
  • Molecular and Cellular Pharmacology Program
  • Endocrine & Reproductive Physiology Program
Lab Website: Regenerative Biology

Research Interests

In the early 1990s, my lab derived ES cells from an Old World monkey (the rhesus macaque) and a New World monkey (the common marmoset), work that led to derivation of human ES cells in 1998.  Much of my lab’s research after that derivation was dedicated to establishing human ES cells as an accepted, practical model system. To that end, we developed defined culture conditions, methods for genetic manipulation, and approaches for the in vitro differentiation of human ES cells to key lineages of clinical importance including hematopoietic, neural, cardiac, and placental tissues.  More recently, in 2007, my laboratory described the isolation of human induced pluripotent (iPS cells) cells with the basic properties of human ES cells but derived from somatic cells. 

My research now focuses on understanding how a cell can maintain or change identity, how a cell chooses between self-renewal and the initial decision to differentiate, and how a differentiated cell with limited developmental potential can be reprogrammed to a pluripotent cell.

My current research interests include:

Honors & Awards

Other Positions & Affiliations


Recent Publications (Find recent publications on PubMed)

  • Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, and Dewey CN (2013). Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. PLoS Comput Biol. 9:e1002936. Epub 2013 Mar 7. PMID: 23505351
  • Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, and Kendziorski C (2013). EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 29:1035-1043 [Epub ahead of print] PMID: 23428641
  • Choi KD, Vodyanik MA, Togarrati PP, Suknuntha K, Kumar A, Samarjeet F, Probasco MD, Tian S, Stewart R, Thomson JA, and Slukvin II (2012). Identification of the hemogenic endothelial progenitor and its direct precursor in human pluripotent stem cell differentiation cultures. Cell Rep. 2:553-67. Epub 2012 Sep 13. PMID: 22981233
  • Zhang J, Klos M, Wilson GF, Herman AM, Lian X, Raval KK, Barron MR, Hou L, Soerens AG, Yu J, Palecek SP, Lyons GE, Thomson JA, Herron TJ, Jalife J, and Kamp TJ (2012). Extracellular matrix promotes highly efficient cardiac differentiation of human pluripotent stem cells: the matrix sandwich method. Circ Res. 111:1125-36. Epub 2012 Aug 21. PMID: 22912385
  • Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Westphall MS, Thomson JA, and Coon JJ (2012). Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci USA. 109:8411-8416. Epub ahead of print May 14.
  • Beers J, Gulbranson DR, George N, Jones J, Thomson JA, and Chen G (2012). An enzyme-free dissociation method for passaging and colony expansion of human pluripotent stem cells in chemically defined conditions. Nature Protocols. 7:2029-2040.
  • Brumbaugh J, Hou Z, Russell JD, Howden SE, Yu P, Ledvina AR, Coon JJ, and Thomson JA (2012). Phosphorylation regulates human OCT4. Proc Natl Acad Sci. USA. 109:7162-7168.
  • Feng X, Zhang J, Smuga-Otto K, Tian S, Yu J, Stewart R,and Thomson JA .(2012). Protein kinase C mediated extraembryonic endoderm differentiation of human embryonic stem cells. Stem Cells 30: 461-470.
  • Chen G, Gulbranson D, Yu, P, Hou Z, and Thomson JA (2012). Thermal stability of FGF protein is a determinant factor in regulating self-renewal, differentiation and reprogramming in human pluripotent stem cells. Stem Cells. 30:623-630.
  • Soh H, Gong Q, Rossi J, Zhou J, Ahmad K, Csordas A, Wang J, Stewart R, Thomson JA, and Nie J (2012). Selection strategy to generate multivalent aptamer sets that bind to distinct sites on protein targets. Analytical Chemistry, in press.
  • Howden SE, Gore A, Li Zhe, Fung H, Nisler BS, Nie J, Chen G, McIntosh BE, Gulbranson DR, Diol NR, Taapken SM, Vereide DT, Montgomery KD, Zhang K, Gamm D, and Thomson JA (2011). Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy. Proc Natl Acad Sci USA. Proc Natl Acad Sci USA. 108:6537-6542.
  • Hu K, Yu J, Suknuntha K, Montgomery K, Thomson JA, and Slukvin II (2011). Efficient Generation of Transgene-Free Induced Pluripotent Stem Cells from Normal and Neoplastic Bone Marrow and Cord Blood Mononuclear Cells. Blood 117:e109-119.
  • Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, and Ecker JR. (2011). Hotspots of aberrant epigenomic reprogramming in human iPS cells. Nature. 471:68-73.
  • Gore A, Li Z, Fung H, Young J, Agarwal S, Antosiewicz-Bourget J, Canto I, Israel M, Kiskinis E, Lee J, Loh Y, Manos PD, Montserrat N, Wilbert M, Yu J, Kirkness E, Izpisua Belmonte JC, Rossi DJ, Thomson JA, Eggan K, Daley GQ, Goldstein LSB, and Zhang K (2011.) Somatic coding mutations in human induced pluripotent stem cells. Nature 471:63-71.
  • Yu P, Pan G, Yu J,and Thomson JA (2011.) FGF2 sustains NANOG and switches BMP4 induced human ES cell differentiation from trophoblast to mesendoderm. Stem Cell. 8:326-334.
  • Chen G, Gulbranson D, Hou Z, Bolin J, Probasco MD, Smuga-Otto K, Howden S, Diol N, Propson NE, Wagner R, Lee GO, Antosiewicz-Bourget J, Teng JMC, Thomson JA (2011). Chemically defined conditions for human iPS cell derivation and culture. Nature Methods. 8:424-429.
  • Hu BY, Weick JP, Yu J, Ma LX, Zhang XQ, Thomson JA, and Zhang S (2010). Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci USA. 107:4335-4340.
  • Cho M, Xiao Y, Nie J, Stewart R, Csordas A, Oh S, Thomson JA, and Soh H (2010). Quantitative Selection of DNA Aptamers through Microfluidic Selection and High Throughput Sequencing. Proc Natl Acad Sci USA. 107:15373-15378.
  • Hawkins R, Hon G, Lee L, Ngo Q, Lister R, Pelizzola M, Kuan, S, Edsall L, Ye Z, Espinoza C, Antosiewicz-Bourget J, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker J, and Ren B (2010). Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6:1-13.
  • Chen C, Hou Z, Gulbranson D, and Thomson JA (2010). Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells. Cell Stem Cell. 7:240-248.
  • Sengupta S, Ruotti V, Bolin J, Elwell A, Hernandez A, Thomson JA, and Stewart R (2010). Highly consistent, fully representative mRNA-Seq libraries from 1000 cells. BioTechniques. 49:898-904.
  • Winkler T, Cantilena A, Metais JY, Xu X, Nguyen AD, Borate B, Antosiewicz-Bourget JE, Wolfsberg TG, Thomson JA, and Dunbar CE. No evidence for clonal selection due to lentiviral integration sites in human induced pluripotent stem cells. Stem Cells. 28:687-694.
  • Li B, Ruotti V, Stewart R, Thomson JA, and Dewey C (2010). RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 26:493-500.
  • Mohr JC, Zhang J, Azarin SM, Soerens AG, de Pablo JJ, Thomson JA, Lyons GE, Palecek SP, and Kamp TJ (2010). The Microwell Control of Embryoid Body Size in Order to Regulate Cardiac Differentiation of Human Embryonic Stem Cells. Biomaterials. 31:1885-1893.
  • Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MM, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, and Thomson JA (2010). The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotech. 28:1045-1048.
  • Vodyanik MA, Yu J, Zhang X, Tian S, Stewart R, Thomson JA,and Slukvin II (2010). A mesoderm-derived precursor for mesenchymal stem and endothelial cells. Cell Stem Cell. 7:718-729.