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James Thomson

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Ning Leng; Anna I Rissman; Victor Ruotti; Bart M G Smits; Ron M Stewart; James A Thomson; John A Dawson; Michael N Gould; Jill D Haag; Christina Kendziorski
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
Jianhua Zhang; Matthew R Barron; Amanda M Herman; Todd J Herron; Luqia Hou; Jose Jalife; Matthew Klos; Xiaojun Lian; Gary E Lyons; Sean P Palecek; Kunil K Raval; Andrew G Soerens; James A Thomson; Gisela F Wilson; Junying Yu; Timothy J Kamp
Extracellular matrix promotes highly efficient cardiac differentiation of human pluripotent stem cells: the matrix sandwich method.
Kyung-Dal Choi; Akhilesh Kumar; Mitchell D Probasco; Fnu Samarjeet; Ron Stewart; Kran Suknuntha; James A Thomson; Shulan Tian; Padma Priya Togarrati; Maxim A Vodyanik; Igor I Slukvin
Identification of the hemogenic endothelial progenitor and its direct precursor in human pluripotent stem cell differentiation cultures.

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All Publications

2013: Ning Leng; Anna I Rissman; Victor Ruotti; Bart M G Smits; Ron M Stewart; James A Thomson; John A Dawson; Michael N Gould; Jill D Haag; Christina Kendziorski
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
Bioinformatics (Oxford, England) 2013;29(8):1035-43.
2012: Jianhua Zhang; Matthew R Barron; Amanda M Herman; Todd J Herron; Luqia Hou; Jose Jalife; Matthew Klos; Xiaojun Lian; Gary E Lyons; Sean P Palecek; Kunil K Raval; Andrew G Soerens; James A Thomson; Gisela F Wilson; Junying Yu; Timothy J Kamp
Extracellular matrix promotes highly efficient cardiac differentiation of human pluripotent stem cells: the matrix sandwich method.
Circulation research 2012;111(9):1125-36.
2012: Kyung-Dal Choi; Akhilesh Kumar; Mitchell D Probasco; Fnu Samarjeet; Ron Stewart; Kran Suknuntha; James A Thomson; Shulan Tian; Padma Priya Togarrati; Maxim A Vodyanik; Igor I Slukvin
Identification of the hemogenic endothelial progenitor and its direct precursor in human pluripotent stem cell differentiation cultures.
Cell reports 2012;2(3):553-67.
2012: Derek J Bailey; Justin Brumbaugh; Graeme C McAlister; Christopher M Rose; James A Thomson; Craig D Wenger; Michael S Westphall; Pengzhi Yu; Joshua J Coon
Instant spectral assignment for advanced decision tree-driven mass spectrometry.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(22):8411-6.
2012: Justin Brumbaugh; Joshua J Coon; Zhonggang Hou; Sara E Howden; Aaron R Ledvina; Jason D Russell; Pengzhi Yu; James A Thomson
Phosphorylation regulates human OCT4.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(19):7162-8.
2012: Guokai Chen; Daniel R Gulbranson; Zhonggang Hou; Pengzhi Yu; James A Thomson
Thermal stability of fibroblast growth factor protein is a determinant factor in regulating self-renewal, differentiation, and reprogramming in human pluripotent stem cells.
Stem cells (Dayton, Ohio) 2012;30(4):623-30.
2012: Xuezhu Feng; Kimberly Smuga-Otto; Ron Stewart; Shulan Tian; Junying Yu; Jiuchun Zhang; James A Thomson
Protein kinase C mediated extraembryonic endoderm differentiation of human embryonic stem cells.
Stem cells (Dayton, Ohio) 2012;30(3):461-70.
2011: Junyi Ma; BJ Swanson; James A Thomson; Timothy J Kamp; Kyle L Kolaja; Blake D Anson; Steve J Fiene; Liang Guo; Craig T January
High purity human-induced pluripotent stem cell-derived cardiomyocytes: electrophysiological properties of action potentials and ionic currents.
American journal of physiology. Heart and circulatory physiology 2011;301(5):H2006-17.
2011: Jessica Dias; Marina Gumenyuk; HyunJun Kang; James A Thomson; Maxim A Vodyanik; Junying Yu; Igor I Slukvin
Generation of red blood cells from human induced pluripotent stem cells.
Stem cells and development 2011;20(9):1639-47.
2011: Jason S Meyer; Bikash Pattnaik; Isabel Pinilla; Ron Stewart; James A Thomson; Shulan Tian; Amelia D Verhoeven; Kyle A Wallace; Lynda S Wright; Elizabeth E Capowski; Sara E Howden; Jessica M Martin; David M Gamm
Optic vesicle-like structures derived from human pluripotent stem cells facilitate a customized approach to retinal disease treatment.
Stem cells (Dayton, Ohio) 2011;29(8):1206-18.
2011: Guokai Chen; Daniel R Gulbranson; Zhonggang Hou; Jennifer M Bolin; Victor Ruotti; Mitchell D Probasco; Kimberly Smuga-Otto; Sara E Howden; Nicole R Diol; Nicholas E Propson; Ryan Wagner; Garrett O Lee; Jessica Antosiewicz-Bourget; Joyce M C Teng; James A Thomson
Chemically defined conditions for human iPSC derivation and culture.
Nature methods 2011;8(5):424-9.
2011: Kejin Hu; Junying Yu; Kran Suknuntha; Shulan Tian; Karen Montgomery; Kyung-Dal Choi; Ron Stewart; James A Thomson; Igor I Slukvin
Efficient generation of transgene-free induced pluripotent stem cells from normal and neoplastic bone marrow and cord blood mononuclear cells.
Blood 2011;117(14):e109-19.
2011: Ryan Lister; Mattia Pelizzola; Yasuyuki S Kida; R David Hawkins; Joseph R Nery; Gary Hon; Jessica Antosiewicz-Bourget; Ronan O'Malley; Rosa Castanon; Sarit Klugman; Michael Downes; Ruth Yu; Ron Stewart; Bing Ren; James A Thomson; Ronald M Evans; Joseph R Ecker
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.
Nature 2011;471(7336):68-73.
2011: Douglas H Phanstiel; Mitchell D Probasco; Victor Ruotti; Ron Stewart; Danielle L Swaney; Mark A Tervo; James A Thomson; Shulan Tian; Craig D Wenger; Derek J Bailey; Jennifer M Bolin; Justin Brumbaugh; Joshua J Coon
Proteomic and phosphoproteomic comparison of human ES and iPS cells.
Nature methods 2011;8(10):821-7.
2010: Maxim A Vodyanik; Junying Yu; Xin Zhang; Shulan Tian; Ron Stewart; James A Thomson; Igor I Slukvin
A mesoderm-derived precursor for mesenchymal stem and endothelial cells.
Cell stem cell 2010;7(6):718-29.
2010: R David Hawkins; Gary C Hon; Leonard K Lee; Queminh Ngo; Ryan Lister; Mattia Pelizzola; Lee E Edsall; Samantha Kuan; Ying Luu; Sarit Klugman; Jessica Antosiewicz-Bourget; Zhen Ye; Celso Espinoza; Saurabh Agarwahl; Li Shen; Victor Ruotti; Wei Wang; Ron Stewart; James A Thomson; Joseph R Ecker; Bing Ren
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
Cell stem cell 2010;6(5):479-91.
2010: Bao-Yang Hu; Jason Porter Weick; Junying Yu; Li-Xiang Ma; Xiao-Qing Zhang; James A Thomson; Su-Chun Zhang
Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(9):4335-40.
2010: Jeffrey C Mohr; Jianhua Zhang; Samira M Azarin; Andrew G Soerens; Juan J de Pablo; James A Thomson; Gary E Lyons; Sean P Palecek; Timothy J Kamp
The microwell control of embryoid body size in order to regulate cardiac differentiation of human embryonic stem cells.
Biomaterials 2010;31(7):1885-93.
2010: Bo Li; Victor Ruotti; Ron M Stewart; James A Thomson; Colin N Dewey
RNA-Seq gene expression estimation with read mapping uncertainty.
Bioinformatics (Oxford, England) 2010;26(4):493-500.
2009: Ryan Lister; Mattia Pelizzola; Robert H Dowen; R David Hawkins; Gary Hon; Julian Tonti-Filippini; Joseph R Nery; Leonard Lee; Zhen Ye; Que-Minh Ngo; Lee Edsall; Jessica Antosiewicz-Bourget; Ron Stewart; Victor Ruotti; A Harvey Millar; James A Thomson; Bing Ren; Joseph R Ecker
Human DNA methylomes at base resolution show widespread epigenomic differences.
Nature 2009;462(7271):315-22.
2009: You Jung Kim; Nikhil Teletia; Victor Ruotti; Christopher A. Maher; Arul M Chinnaiyan; Ron Stewart; James A Thomson; Jignesh M Patel
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
Bioinformatics (Oxford, England) 2009;25(11):1424-5.
2009: Jianhua Zhang; Gisela F Wilson; Andrew G Soerens; Chad H Koonce; Junying Yu; Sean P Palecek; James A Thomson; Timothy J Kamp
Functional cardiomyocytes derived from human induced pluripotent stem cells.
Circulation research 2009;104(4):e30-41.
2009: Danielle L Swaney; Craig D Wenger; James A Thomson; Joshua J Coon
Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(4):995-1000.
2009: Allison D Ebert; Junying Yu; Ferrill F Rose; Virginia B Mattis; Christian L Lorson; James A Thomson; Clive Svendsen
Induced pluripotent stem cells from a spinal muscular atrophy patient.
Nature 2009;457(7227):277-80.
2008: Junying Yu; James A Thomson
Pluripotent stem cell lines.
Genes & development 2008;22(15):1987-97.
2008: Marion Dejosez; Joshua S Krumenacker; Laura Jo Zitur; Marco Passeri; Li-Fang Chu; Zhou Songyang; James A Thomson; Thomas P Zwaka
Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells.
Cell 2008;133(7):1162-74.
2008: Jun Fujita; Ana Crane; Marlon K Souza; Marion Dejosez; Michael Kyba; Richard A Flavell; James A Thomson; Thomas P Zwaka
Caspase activity mediates the differentiation of embryonic stem cells.
Cell stem cell 2008;2(6):595-601.
2008: Hairong Wei; Pei-Fen Kuan; Shulan Tian; Chuhu Yang; Jeff Nie; Srikumar Sengupta; Victor Ruotti; Gudrun A Jonsdottir; Sündüz Keles; James A Thomson; Ron Stewart
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.
Nucleic acids research 2008;36(9):2926-38.
2008: Doug Phanstiel; Justin Brumbaugh; W Travis Berggren; Kevin Conard; Xuezhu Feng; Mark E Levenstein; Graeme C McAlister; James A Thomson; Joshua J Coon
Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(11):4093-8.
2008: Gene E Ananiev; Steve Goldstein; Rod Runnheim; Dan K Forrest; Shiguo Zhou; Konstantinos Potamousis; Chris P Churas; Veit Bergendahl; James A Thomson; David C Schwartz
Optical mapping discerns genome wide DNA methylation profiles.
BMC molecular biology 2008;9():68.
2007: Myon-Hee Lee; Brad Hook; Guangjin Pan; Aaron M Kershner; Christopher Merritt; Geraldine Seydoux; James A Thomson; Marvin Wickens; Judith Kimble
Conserved regulation of MAP kinase expression by PUF RNA-binding proteins.
PLoS genetics 2007;3(12):e233.
2007: Junying Yu; Maxim A Vodyanik; Kim Smuga-Otto; Jessica Antosiewicz-Bourget; Jennifer L Frane; Shulan Tian; Jeff Nie; Gudrun A Jonsdottir; Victor Ruotti; Ron Stewart; Igor I Slukvin; James A Thomson
Induced pluripotent stem cell lines derived from human somatic cells.
Science (New York, N.Y.) 2007;318(5858):1917-20.
2007: Guangjin Pan; Shulan Tian; Jeff Nie; Chuhu Yang; Victor Ruotti; Hairong Wei; Gudrun A Jonsdottir; Ron Stewart; James A Thomson
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.
2007: Dong Chen; Ping Wang; Rachel L Lewis; Christine A Daigh; Coral Ho; Xin Chen; James A Thomson; Christina Kendziorski
A microarray analysis of the emergence of embryonic definitive hematopoiesis.
Experimental hematology 2007;35(9):1344-57.
2007: Ratmir Derda; Lingyin Li; Brendan P Orner; Rachel L Lewis; James A Thomson; Laura L Kiessling
Defined substrates for human embryonic stem cell growth identified from surface arrays.
ACS chemical biology 2007;2(5):347-55.
2007: Deepika Rajesh; Nachimuthu Chinnasamy; Shoukhrat Mitalipov; Don P Wolf; Igor I Slukvin; James A Thomson; Aimen F Shaaban
Differential requirements for hematopoietic commitment between human and rhesus embryonic stem cells.
Stem cells (Dayton, Ohio) 2007;25(2):490-9.
2007: Guangjin Pan; James A Thomson
Nanog and transcriptional networks in embryonic stem cell pluripotency.
Cell research 2007;17(1):42-9.
2006: Takashi Kameda; Kim Smuga-Otto; James A Thomson
A severe de novo methylation of episomal vectors by human ES cells.
Biochemical and biophysical research communications 2006;349(4):1269-77.
2006: Maxim A Vodyanik; James A Thomson; Igor I Slukvin
Leukosialin (CD43) defines hematopoietic progenitors in human embryonic stem cell differentiation cultures.
Blood 2006;108(6):2095-105.
2006: Tenneille E Ludwig; Veit Bergendahl; Mark E Levenstein; Junying Yu; Mitchell D Probasco; James A Thomson
Feeder-independent culture of human embryonic stem cells.
Nature methods 2006;3(8):637-46.
2006: Igor I Slukvin; Maxim A Vodyanik; James A Thomson; Maryna E Gumenyuk; Kyung-Dal Choi
Directed differentiation of human embryonic stem cells into functional dendritic cells through the myeloid pathway.
Journal of immunology (Baltimore, Md. : 1950) 2006;176(5):2924-32.
2006: Mark E Levenstein; Tenneille E Ludwig; Ren-He Xu; Rachel A Llanas; Kaitlyn VanDenHeuvel-Kramer; Daisy Manning; James A Thomson
Basic fibroblast growth factor support of human embryonic stem cell self-renewal.
Stem cells (Dayton, Ohio) 2006;24(3):568-74.
2006: Tenneille E Ludwig; Mark E Levenstein; Jeffrey M Jones; W Travis Berggren; Erika R Mitchen; Jennifer L Frane; Leann J Crandall; Christine A Daigh; Kevin R Conard; Marian S Piekarczyk; Rachel A Llanas; James A Thomson
Derivation of human embryonic stem cells in defined conditions.
Nature biotechnology 2006;24(2):185-7.
2006: Junying Yu; Maxim A Vodyanik; Ping He; Igor I Slukvin; James A Thomson
Human embryonic stem cells reprogram myeloid precursors following cell-cell fusion.
Stem cells (Dayton, Ohio) 2006;24(1):168-76.
2005: Takashi Kameda; James A Thomson
Human ERas gene has an upstream premature polyadenylation signal that results in a truncated, noncoding transcript.
Stem cells (Dayton, Ohio) 2005;23(10):1535-40.
2005: Yiping Yan; Dali Yang; Ewa Zarnowska; Zhongwei Du; Brian Werbel; Chuck Valliere; Robert A Pearce; James A Thomson; Su-Chun Zhang
Directed differentiation of dopaminergic neuronal subtypes from human embryonic stem cells.
Stem cells (Dayton, Ohio) 2005;23(6):781-90.
2005: Ren-He Xu; Ruthann M Peck; Dong S Li; Xuezhu Feng; Tenneille E Ludwig; James A Thomson
Basic FGF and suppression of BMP signaling sustain undifferentiated proliferation of human ES cells.
Nature methods 2005;2(3):185-90.
2005: Thomas P Zwaka; James A Thomson
Differentiation of human embryonic stem cells occurs through symmetric cell division.
Stem cells (Dayton, Ohio) 2005;23(2):146-9.
2005: Maxim A Vodyanik; Jack A Bork; James A Thomson; Igor I Slukvin
Human embryonic stem cell-derived CD34+ cells: efficient production in the coculture with OP9 stromal cells and analysis of lymphohematopoietic potential.
Blood 2005;105(2):617-26.
2005: Thomas P Zwaka; James A Thomson
A germ cell origin of embryonic stem cells?
Development (Cambridge, England) 2005;132(2):227-33.
2004: Brendan P Orner; Ratmir Derda; Rachel L Lewis; James A Thomson; Laura L Kiessling
Arrays for the combinatorial exploration of cell adhesion.
Journal of the American Chemical Society 2004;126(35):10808-9.
2004: Behzad Gerami-Naini; Oksana V Dovzhenko; Maureen Durning; Frederick H Wegner; James A Thomson; Thaddeus G Golos
Trophoblast differentiation in embryoid bodies derived from human embryonic stem cells.
Endocrinology 2004;145(4):1517-24.
2004: Jonathan S Draper; Kath Smith; paul Gokhale; Harry D Moore; Edna Maltby; Julie Johnson; Lorraine Meisner; Thomas P Zwaka; James A Thomson; Peter W Andrews
Recurrent gain of chromosomes 17q and 12 in cultured human embryonic stem cells.
Nature biotechnology 2004;22(1):53-4.
2003: Jamie M Sperger; Xin Chen; Jonathan S Draper; Jessica E Antosiewicz; Chris H Chon; Sunita B Jones; James D Brooks; Peter W Andrews; Patrick O Brown; James A Thomson
Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(23):13350-5.
2003: Jia-Qiang He; Yue Ma; Youngsook Lee; James A Thomson; Timothy J Kamp
Human embryonic stem cells develop into multiple types of cardiac myocytes: action potential characterization.
Circulation research 2003;93(1):32-9.
2003: Thomas P Zwaka; James A Thomson
Homologous recombination in human embryonic stem cells.
Nature biotechnology 2003;21(3):319-21.
2003: Vivienne Marshall; MA Browne; L Knowles; Thaddeus G Golos; James A Thomson
Ovarian stimulation of marmoset monkeys (Callithrix jacchus) using recombinant human follicle stimulating hormone.
Journal of medical primatology 2003;32(1):57-66.
2002: Ren-He Xu; Xin Chen; Dong S Li; Rui Li; Gregory C Addicks; Clay Glennon; Thomas P Zwaka; James A Thomson
BMP4 initiates human embryonic stem cell differentiation to trophoblast.
Nature biotechnology 2002;20(12):1261-4.
2002: Michael J Wolfgang; Vivienne Marshall; Stephen G Eisele; Michele L Schotzko; James A Thomson; Thaddeus G Golos
Efficient method for expressing transgenes in nonhuman primate embryos using a stable episomal vector.
Molecular reproduction and development 2002;62(1):69-73.
2002: Jonathan S Draper; Christine Pigott; James A Thomson; Peter W Andrews
Surface antigens of human embryonic stem cells: changes upon differentiation in culture.
Journal of anatomy 2002;200(Pt 3):249-58.
2002: D S Kaufman; James A Thomson
Human ES cells--haematopoiesis and transplantation strategies.
Journal of anatomy 2002;200(Pt 3):243-8.
2002: J K Henderson; Jonathan S Draper; H S Baillie; S Fishel; James A Thomson; Harry Moore; Peter W Andrews
Preimplantation human embryos and embryonic stem cells show comparable expression of stage-specific embryonic antigens.
Stem cells (Dayton, Ohio) 2002;20(4):329-37.
2001: Su-Chun Zhang; Marius Wernig; I D Duncan; Oliver Brüstle; James A Thomson
In vitro differentiation of transplantable neural precursors from human embryonic stem cells.
Nature biotechnology 2001;19(12):1129-33.
2001: Michael J Wolfgang; Stephen G Eisele; MA Browne; Michele L Schotzko; Mark A Garthwaite; Maureen Durning; A Ramezani; R G Hawley; James A Thomson; Thaddeus G Golos
Rhesus monkey placental transgene expression after lentiviral gene transfer into preimplantation embryos.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10728-32.
2001: Vivienne Marshall; MA Waknitz; James A Thomson
Isolation and maintenance of primate embryonic stem cells.
Methods in molecular biology (Clifton, N.J.) 2001;158():11-8.
2000: Michal Amit; Melissa K Carpenter; MS Inokuma; Choy-Pik Chiu; C P Harris; MA Waknitz; Joseph Itskovitz-Eldor; James A Thomson
Clonally derived human embryonic stem cell lines maintain pluripotency and proliferative potential for prolonged periods of culture.
Developmental biology 2000;227(2):271-8.
1998: James A Thomson; Joseph Itskovitz-Eldor; S S Shapiro; MA Waknitz; J J Swiergiel; Vivienne Marshall; J M Jones
Embryonic stem cell lines derived from human blastocysts.
Science (New York, N.Y.) 1998;282(5391):1145-7.
1998: James A Thomson; Vivienne Marshall; John Q Trojanowski
Neural differentiation of rhesus embryonic stem cells.
APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 1998;106(1):149-56; discussion 156-7.
1998: James A Thomson; Vivienne Marshall
Primate embryonic stem cells.
Current topics in developmental biology 1998;38():133-65.
1997: Vivienne Marshall; J Kalishman; James A Thomson
Nonsurgical embryo transfer in the common marmoset monkey.
Journal of medical primatology 1997;26(5):241-7.
1996: James A Thomson; J Kalishman; Thaddeus G Golos; Maureen Durning; C P Harris; J P Hearn
Pluripotent cell lines derived from common marmoset (Callithrix jacchus) blastocysts.
Biology of reproduction 1996;55(2):254-9.
1996: James A Thomson; J J Scheffler
Hemorrhagic typhlocolitis associated with attaching and effacing Escherichia coli in common marmosets.
Laboratory animal science 1996;46(3):275-9.
1995: James A Thomson; J Kalishman; Thaddeus G Golos; Maureen Durning; C P Harris; R A Becker; J P Hearn
Isolation of a primate embryonic stem cell line.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(17):7844-8.
1994: James A Thomson; J Kalishman; J P Hearn
Nonsurgical uterine stage preimplantation embryo collection from the common marmoset.
Journal of medical primatology 1994;23(6):333-6.