James A. Thomson Lab - Select Publications

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A stem cell scientist

Brumbaugh J, Hou Z, Russell JD, Howden SE, Yu P, Ledvina AR, Coon JJ, Thomson JA. “Phosphorylation regulates human OCT4.” Proc Natl Acad Sci, USA (2012): 109(19): 7162-8. PMCID: PMC3358887. [PubMed]

Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Westphall MS, Thomson JA, Coon JJ. “Instant spectral assignment for advanced decision tree-driven mass spectrometry.” Proc Natl Acad Sci, USA (2012): 109(22): 8411-6. PMCID: PMC3365209. [PubMed]

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. “Chemically defined conditions for human iPS cell derivation and culture.” Nature Methods (2011). 8(5): 424-9. [Epub April 10, 2011]. [PubMed]

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, Thomson JA. “Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy.” Proc Natl Acad Sci USA (2011). 108(16): 6537-42. [Epub April 4, 2011]. [PubMed]

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, Ecker JR. “Hotspots of aberrant epigenomic reprogramming in human iPS cells.” Nature (2011). 471(7336): 68-73. [PubMed]

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, Zhang K. “Somatic coding mutations in human induced pluripotent stem cells.” Nature (2011). 471: 63-71. [PubMed]

Yu P, Pan G, Yu J, Thomson JA. “FGF2 sustains NANOG and switches BMP4 induced human ES cell differentiation from trophoblast to mesendoderm.” Cell Stem Cell (2011). 8: 326-34 [PubMed]

Hu BY, Weick JP, Yu J, Ma LX, Zhang XQ, Thomson JA, Zhang SC. “Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency.” Proc Natl Acad Sci USA (2010). 107(9):4335-40. [Epub Feb 16, 2010]. [PubMed]

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 J, Ecker J, Ren B. “Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.” Cell Stem Cell (2010). 6: 1-13. [Epub May 7, 2010]. [Epub]

Chen C, Hou Z, Gulbranson D, Thomson JA. "Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells." Cell Stem Cell (2010). 7(2): 240-8. [Epub]

Cho M, Xiao Y, Nie J, Stewart R, Csordas A, Oh S, Thomson JA, Soh H. "Quantitative selection of DNA aptamers through microfluidic selection and high throughput sequencing.” Proc Natl Acad Sci USA (2010). 107(35): 15373-8. [Epub Aug 12, 2010]. [PubMed]

Yu J, Hu K, Smuga-Otto K, Tian S, Stewart R, Slukvin II, Thomson JA. "Human induced pluripotent stem cells free of vector and transgene sequences." Science (2009). 324(5928): 797-801. [Epub Mar 26, 2009]. [PubMed]

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo LQ, Edsall LE, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. "Human DNA methylomes at base resolution show widespread epigenomic differences." Nature (2009). 462(7271): 315-22. [Epub Oct 14, 2009]. [PubMed]

Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik K. "MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells." Cell (2009). 137(4): 647-58. [PubMed]

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B. "Histone modifications at human enhancers reflect global cell-type-specific gene expression." Nature (2009). 459: 108-12. [PubMed]

Swaney DL, Wenger CD, Thomson JA, Coon JJ. "Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry." Proc Natl Acad Sci USA (2009). 106(4): 995-1000. [PubMed]

Ebert AD, Yu J, Rose FF Jr, Mattis VB, Lorson CL, Thomson JA, Svendsen CN. "Induced pluripotent stem cells from a spinal muscular atrophy patient." Nature (2009). 457(7227): 277-80. [PubMed]

Xu RH, Sampsell-Barron TL, Gu F, Root S, Peck RM, Pan G, Yu J, Antosiewicz-Bourget J, Tian S, Stewart R, Thomson JA. "NANOG is a direct target of TGFbeta/activin-mediated SMAD signaling in human ESCs." Cell Stem Cell (2008). 3(2): 196-206. [PubMed]

Yu J, Thomson JA. "Pluripotent stem cell lines." Genes Dev (2008). 22(15): 1987-97. Review. [PubMed]

Dejosez M, Krumenacker JS, Zitur LJ, Passeri M, Chu LF, Songyang Z, Thomson JA, Zwaka TP. "Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells." Cell (2008). 133(7): 1162-74. [Erratum in: Cell (2008). 134(4): 692.] [PubMed]

Fujita J, Crane AM, Souza MK, Dejosez M, Kyba M, Flavell RA, Thomson JA, Zwaka TP. "Caspase activity mediates the differentiation of embryonic stem cells." Cell Stem Cell (2008). 2(6): 595-601. [PubMed]

Phanstiel D, Brumbaugh J, Berggren WT, Conard K, Feng X, Levenstein ME, McAlister GC, Thomson JA, Coon JJ. "Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells." Proc Natl Acad Sci USA (2008). 105(11): 4093-8. [PubMed]

Yu J, Vodyanik M, Smuga-Otto K, Frane J, Antosiewicz-Bourget J, Frane J, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA."Induced pluripotent stem cell lines derived from human somatic cells." Science (2007). 318:1917-20. [Science Abstract] [Science Complete Article] [PubMed]

Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA. "Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells." Cell Stem Cell (2007). 1(3): 299-312. [PubMed]

Yu J, Vodyanik MA, He P, Slukvin II, Thomson JA. "Human embryonic stem cells reprogram myeloid precursors following cell-cell fusion." Stem Cells (2006). 24(1): 168-76. [PubMed]

Ludwig TE, Bergendahl V, Levenstein ME, Yu J, Probasco MD, Thomson JA. "Feeder-independent culture of human embryonic stem cells." Nat Methods (2006). 3(8): 637-46. [PubMed]

Ludwig TE, Levenstein ME, Jones J, Berggren W, Mitchen E, Frane J, Crandall L, Daigh CA, Conard K, Piekarczyk M, Llanas R, Thomson JA. "Derivation of human embryonic stem cells in defined conditions." Nat Biotechnol (2006). 24(2): 185-7. [PubMed]

Xu RH, Peck RM, Li DS, Feng X, Ludwig T, Thomson JA. "Basic FGF and suppression of BMP signaling sustain undifferentiated proliferation of human ES cells." Nat Methods (2005). 2(3): 185-90. [PubMed]

Zwaka TP, Thomson JA. "A germ cell origin of embryonic stem cells?" Development (2005). 132(2): 227-33. [PubMed]

Draper JS, Smith K, Gokhale P, Moore HD, Maltby E, Johnson J, Meisner L, Zwaka TP, Thomson JA, Andrews PW. “Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells.” Nat Biotechnol (2004). 22: 53-4. [PubMed]

Sperger JM, Chen X, Draper JS, Antosiewicz JE, Chon C, Jones S, Brooks JD, Andrews PW, Brown PO, Thomson JA. “Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors.” Proc Natl Acad Sci USA (2003). 10013350-5. [PubMed]

Zwaka TP, Thomson JA. “Homologous recombination in human embryonic stem cells.” Nat Biotechnol (2003). 21: 319-21. [PubMed]

Xu R, Chen X, Li DS, Li R, Addicks GC, Glennon C, Zwaka TP, Thomson JA. “BMP4 initiates human embryonic stem cell differentiation to trophoblast.” Nat Biotechnol (2002). 20: 1261-4. [PubMed]

Zhang S-C, Wernig M, Duncan ID, Brustle O, Thomson JA. "In vitro differentiation and transplantation of human ES cell-derived neural precursors." Nat Biotechnol (2001). 19: 1129-33. [PubMed]

Kaufman DS, Hanson ET, Lewis RL, Auerbach R, Thomson JA. “Hematopoietic colony forming cells derived from human embryonic stem cells.” Proc Natl Acad Sci USA (2001). 98: 10716-21. [PubMed]

Amit M, Carpenter M, Inokuma M, Chiu C, Harris CP, Waknitz MA, Itskovitz-Eldor J, Thomson JA. “Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture.” Dev Biol (2000). 227(2): 271-8. [PubMed]

Thomson JA, Itskovitz-Eldor J, Shapiro S, Waknitz MA, Swiergiel JJ, Marshall VS, Jones JM. “Embryonic stem cell lines derived from human blastocysts.” Science (1998). 282: 1145-7. [PubMed]

Thomson JA, Marshall VS. “Primate embryonic stem cells.” Curr Top in Dev Biol (1998). 38: 133-60. [PubMed]

Thomson JA, Becker R, Durning M, Golos TG, Harris C, Kalishman J, Hearn JP. “Isolation of a primate embryonic stem cell line.” Proc Natl Acad Sci USA (1995). 92: 7844-8. [PubMed]