James Alexander Thomson, V.M.D., Ph.D., Diplomate A.C.V.P. - Publications

Affiliations: 
University of Wisconsin, Madison, Madison, WI 
 University of California, Santa Barbara, Santa Barbara, CA, United States 
 2009- Regenerative Biology The Morgrdige Institute for Research 
Area:
Embryonic Stem Cell, Regenerative Biology, Induce Pluripotent Stem Cell,

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Year Citation  Score
2018 Bacher R, Leng N, Chu LF, Ni Z, Thomson JA, Kendziorski C, Stewart R. Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments. Bmc Bioinformatics. 19: 380. PMID 30326833 DOI: 10.1186/s12859-018-2405-x  0.36
2017 Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C. SCnorm: robust normalization of single-cell RNA-seq data. Nature Methods. PMID 28418000 DOI: 10.1038/nmeth.4263  0.36
2016 Chu LF, Leng N, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendziorski C, Stewart R, Thomson JA. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biology. 17: 173. PMID 27534536 DOI: 10.1186/s13059-016-1033-x  0.48
2016 Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R. OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data. Bioinformatics (Oxford, England). PMID 26743507 DOI: 10.1093/bioinformatics/btw004  0.36
2015 Schwartz MP, Hou Z, Propson NE, Zhang J, Engstrom CJ, Costa VS, Jiang P, Nguyen BK, Bolin JM, Daly W, Wang Y, Stewart R, Page CD, Murphy WL, Thomson JA. Human pluripotent stem cell-derived neural constructs for predicting neural toxicity. Proceedings of the National Academy of Sciences of the United States of America. PMID 26392547 DOI: 10.1073/pnas.1516645112  0.48
2015 Leng N, Chu LF, Barry C, Li Y, Choi J, Li X, Jiang P, Stewart RM, Thomson JA, Kendziorski C. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nature Methods. 12: 947-50. PMID 26301841 DOI: 10.1038/nmeth.3549  0.36
2015 Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C. EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinformatics (Oxford, England). PMID 25847007 DOI: 10.1093/bioinformatics/btv193  0.36
2015 Hou Z, Jiang P, Swanson SA, Elwell AL, Nguyen BK, Bolin JM, Stewart R, Thomson JA. A cost-effective RNA sequencing protocol for large-scale gene expression studies. Scientific Reports. 5: 9570. PMID 25831155 DOI: 10.1038/srep09570  0.48
2015 Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, ... Thomson JA, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 518: 331-6. PMID 25693564 DOI: 10.1038/nature14222  0.48
2015 McIntosh BE, Brown ME, Duffin BM, Maufort JP, Vereide DT, Slukvin II, Thomson JA. Nonirradiated NOD,B6.SCID Il2rγ-/- Kit(W41/W41) (NBSGW) mice support multilineage engraftment of human hematopoietic cells. Stem Cell Reports. 4: 171-80. PMID 25601207 DOI: 10.1016/j.stemcr.2014.12.005  0.48
2015 Hou Z, Meyer S, Propson NE, Nie J, Jiang P, Stewart R, Thomson JA. Characterization and target identification of a DNA aptamer that labels pluripotent stem cells. Cell Research. 25: 390-3. PMID 25591927 DOI: 10.1038/cr.2015.7  0.48
2015 Cho M, Oh SS, Nie J, Stewart R, Radeke MJ, Eisenstein M, Coffey PJ, Thomson JA, Soh HT. Array-based discovery of aptamer pairs. Analytical Chemistry. 87: 821-8. PMID 25495696 DOI: 10.1021/ac504076k  0.48
2015 Raval KK, Tao R, White BE, De Lange WJ, Koonce CH, Yu J, Kishnani PS, Thomson JA, Mosher DF, Ralphe JC, Kamp TJ. Pompe disease results in a Golgi-based glycosylation deficit in human induced pluripotent stem cell-derived cardiomyocytes. The Journal of Biological Chemistry. 290: 3121-36. PMID 25488666 DOI: 10.1074/jbc.M114.628628  0.32
2015 Leng N, Chu LF, Barry C, Li Y, Choi J, Li X, Jiang P, Stewart RM, Thomson JA, Kendziorski C. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments Nature Methods. DOI: 10.1038/nmeth.3549  0.36
2014 Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro. Stem Cell Reports. 2: 18-25. PMID 28039751 DOI: 10.1016/j.stemcr.2013.12.005  0.32
2014 Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology. 15: 553. PMID 25608678 DOI: 10.1186/s13059-014-0553-5  0.48
2014 Vereide DT, Vickerman V, Swanson SA, Chu LF, McIntosh BE, Thomson JA. An expandable, inducible hemangioblast state regulated by fibroblast growth factor. Stem Cell Reports. 3: 1043-57. PMID 25458896 DOI: 10.1016/j.stemcr.2014.10.003  0.48
2014 Uenishi G, Theisen D, Lee JH, Kumar A, Raymond M, Vodyanik M, Swanson S, Stewart R, Thomson J, Slukvin I. Tenascin C promotes hematoendothelial development and T lymphoid commitment from human pluripotent stem cells in chemically defined conditions. Stem Cell Reports. 3: 1073-84. PMID 25448067 DOI: 10.1016/j.stemcr.2014.09.014  0.48
2014 McAlpine JA, Lu HT, Wu KC, Knowles SK, Thomson JA. Down-regulation of argininosuccinate synthetase is associated with cisplatin resistance in hepatocellular carcinoma cell lines: implications for PEGylated arginine deiminase combination therapy. Bmc Cancer. 14: 621. PMID 25164070 DOI: 10.1186/1471-2407-14-621  0.48
2014 Elcheva I, Brok-Volchanskaya V, Kumar A, Liu P, Lee JH, Tong L, Vodyanik M, Swanson S, Stewart R, Kyba M, Yakubov E, Cooke J, Thomson JA, Slukvin I. Direct induction of haematoendothelial programs in human pluripotent stem cells by transcriptional regulators. Nature Communications. 5: 4372. PMID 25019369 DOI: 10.1038/ncomms5372  0.48
2014 Jiang P, Meyer S, Hou Z, Propson NE, Soh HT, Thomson JA, Stewart R. MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. Bioinformatics (Oxford, England). 30: 2665-7. PMID 24872422 DOI: 10.1093/bioinformatics/btu348  0.48
2014 Sengupta S, Johnson BP, Swanson SA, Stewart R, Bradfield CA, Thomson JA. Aggregate culture of human embryonic stem cell-derived hepatocytes in suspension are an improved in vitro model for drug metabolism and toxicity testing. Toxicological Sciences : An Official Journal of the Society of Toxicology. 140: 236-45. PMID 24752503 DOI: 10.1093/toxsci/kfu069  0.48
2014 Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports. 2: 18-25. PMID 24678451 DOI: 10.1016/j.stemcr.2013.12.005  0.48
2014 Magli A, Schnettler E, Swanson SA, Borges L, Hoffman K, Stewart R, Thomson JA, Keirstead SA, Perlingeiro RC. Pax3 and Tbx5 specify whether PDGFRα+ cells assume skeletal or cardiac muscle fate in differentiating embryonic stem cells. Stem Cells (Dayton, Ohio). 32: 2072-83. PMID 24677751 DOI: 10.1002/stem.1713  0.48
2014 Shi X, Richard J, Zirbes KM, Gong W, Lin G, Kyba M, Thomson JA, Koyano-Nakagawa N, Garry DJ. Cooperative interaction of Etv2 and Gata2 regulates the development of endothelial and hematopoietic lineages. Developmental Biology. 389: 208-18. PMID 24583263 DOI: 10.1016/j.ydbio.2014.02.018  0.48
2014 Howden SE, Thomson JA. Gene targeting of human pluripotent stem cells by homologous recombination. Methods in Molecular Biology (Clifton, N.J.). 1114: 37-55. PMID 24557896 DOI: 10.1007/978-1-62703-761-7_4  0.48
2014 Phillips MJ, Perez ET, Martin JM, Reshel ST, Wallace KA, Capowski EE, Singh R, Wright LS, Clark EM, Barney PM, Stewart R, Dickerson SJ, Miller MJ, Percin EF, Thomson JA, et al. Modeling human retinal development with patient-specific induced pluripotent stem cells reveals multiple roles for visual system homeobox 2. Stem Cells (Dayton, Ohio). 32: 1480-92. PMID 24532057 DOI: 10.1002/stem.1667  0.48
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/nature13843  0.48
2013 Hou Z, Zhang J, Schwartz MP, Stewart R, Page CD, Murphy WL, Thomson JA. A human pluripotent stem cell platform for assessing developmental neural toxicity screening. Stem Cell Research & Therapy. 4: S12. PMID 24565336 DOI: 10.1186/scrt373  0.48
2013 Cho M, Soo Oh S, Nie J, Stewart R, Eisenstein M, Chambers J, Marth JD, Walker F, Thomson JA, Soh HT. Quantitative selection and parallel characterization of aptamers. Proceedings of the National Academy of Sciences of the United States of America. 110: 18460-5. PMID 24167271 DOI: 10.1073/pnas.1315866110  0.48
2013 Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP. Integrated module and gene-specific regulatory inference implicates upstream signaling networks. Plos Computational Biology. 9: e1003252. PMID 24146602 DOI: 10.1371/journal.pcbi.1003252  0.48
2013 Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA. Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents. Plos One. 8: e71798. PMID 23967247 DOI: 10.1371/journal.pone.0071798  0.48
2013 Hou Z, Zhang Y, Propson NE, Howden SE, Chu LF, Sontheimer EJ, Thomson JA. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proceedings of the National Academy of Sciences of the United States of America. 110: 15644-9. PMID 23940360 DOI: 10.1073/pnas.1313587110  0.48
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, ... ... Thomson JA, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/j.cell.2013.04.022  0.48
2013 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, et al. Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. Plos Computational Biology. 9: e1002936. PMID 23505351 DOI: 10.1371/journal.pcbi.1002936  0.48
2013 Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (Oxford, England). 29: 1035-43. PMID 23428641 DOI: 10.1093/bioinformatics/btt087  0.48
2013 Yu J, Thomson JA. Embryonic Stem Cells: Derivation and Properties Essentials of Stem Cell Biology: Third Edition. 387-398. DOI: 10.1016/B978-0-12-409503-8.00027-5  0.32
2013 Chang HY, Thomson JA, Chen X. Microarray Analysis of Stem Cells and Differentiation Handbook of Stem Cells. 1: 399-407. DOI: 10.1016/B978-0-12-385942-6.00034-2  0.48
2013 Zwaka TP, Thomson JA. Homologous Recombination in Human Embryonic Stem Cells Handbook of Stem Cells. 1: 339-345. DOI: 10.1016/B978-0-12-385942-6.00027-5  0.48
2013 Yu J, Thomson JA. Embryonic Stem Cells. Derivation and Properties. Handbook of Stem Cells. 1: 275-286. DOI: 10.1016/B978-0-12-385942-6.00022-6  0.48
2012 Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R. Single-round, multiplexed antibody mimetic design through mRNA display. Angewandte Chemie (International Ed. in English). 51: 12449-53. PMID 23125174 DOI: 10.1002/anie.201207005  0.48
2012 Beers J, Gulbranson DR, George N, Siniscalchi LI, Jones J, Thomson JA, Chen G. Passaging and colony expansion of human pluripotent stem cells by enzyme-free dissociation in chemically defined culture conditions. Nature Protocols. 7: 2029-40. PMID 23099485 DOI: 10.1038/nprot.2012.130  0.48
2012 Choi KD, Vodyanik MA, Togarrati PP, Suknuntha K, Kumar A, Samarjeet F, Probasco MD, Tian S, Stewart R, Thomson JA, Slukvin II. Identification of the hemogenic endothelial progenitor and its direct precursor in human pluripotent stem cell differentiation cultures. Cell Reports. 2: 553-67. PMID 22981233 DOI: 10.1016/j.celrep.2012.08.002  0.48
2012 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, et al. Extracellular matrix promotes highly efficient cardiac differentiation of human pluripotent stem cells: the matrix sandwich method. Circulation Research. 111: 1125-36. PMID 22912385 DOI: 10.1161/CIRCRESAHA.112.273144  0.48
2012 Gong Q, Wang J, Ahmad KM, Csordas AT, Zhou J, Nie J, Stewart R, Thomson JA, Rossi JJ, Soh HT. Selection strategy to generate aptamer pairs that bind to distinct sites on protein targets. Analytical Chemistry. 84: 5365-71. PMID 22624874 DOI: 10.1021/ac300873p  0.48
2012 Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Wenger CD, Westphall MS, Thomson JA, Coon JJ. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 109: 8411-6. PMID 22586074 DOI: 10.1073/pnas.1205292109  0.48
2012 Brumbaugh J, Hou Z, Russell JD, Howden SE, Yu P, Ledvina AR, Coon JJ, Thomson JA. Phosphorylation regulates human OCT4. Proceedings of the National Academy of Sciences of the United States of America. 109: 7162-8. PMID 22474382 DOI: 10.1073/pnas.1203874109  0.48
2012 Chen G, Gulbranson DR, Yu P, Hou Z, Thomson JA. 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). 30: 623-30. PMID 22213113 DOI: 10.1002/stem.1021  0.48
2012 Feng X, Zhang J, Smuga-Otto K, Tian S, Yu J, Stewart R, Thomson JA. Protein kinase C mediated extraembryonic endoderm differentiation of human embryonic stem cells. Stem Cells (Dayton, Ohio). 30: 461-70. PMID 22213079 DOI: 10.1002/stem.1018  0.48
2011 Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, Keleş S. A Statistical Framework for the Analysis of ChIP-Seq Data. Journal of the American Statistical Association. 106: 891-903. PMID 26478641 DOI: 10.1198/jasa.2011.ap09706  0.48
2011 Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R. Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA. Journal of Visualized Experiments : Jove. e3340. PMID 22064688 DOI: 10.3791/3340  0.48
2011 Brumbaugh J, Rose CM, Phanstiel DH, Thomson JA, Coon JJ. Proteomics and pluripotency. Critical Reviews in Biochemistry and Molecular Biology. 46: 493-506. PMID 21999516 DOI: 10.3109/10409238.2011.624491  0.48
2011 Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nature Methods. 8: 821-7. PMID 21983960 DOI: 10.1038/nmeth.1699  0.48
2011 Ma J, Guo L, Fiene SJ, Anson BD, Thomson JA, Kamp TJ, Kolaja KL, Swanson BJ, January CT. 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. 301: H2006-17. PMID 21890694 DOI: 10.1152/ajpheart.00694.2011  0.48
2011 Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z, Kuan S, Yu P, Liu H, Zhang X, Green RD, ... ... Thomson JA, et al. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency. Cell Research. 21: 1393-409. PMID 21876557 DOI: 10.1038/cr.2011.146  0.48
2011 Rajesh D, Dickerson SJ, Yu J, Brown ME, Thomson JA, Seay NJ. Human lymphoblastoid B-cell lines reprogrammed to EBV-free induced pluripotent stem cells. Blood. 118: 1797-800. PMID 21708888 DOI: 10.1182/blood-2011-01-332064  0.48
2011 Meyer JS, Howden SE, Wallace KA, Verhoeven AD, Wright LS, Capowski EE, Pinilla I, Martin JM, Tian S, Stewart R, Pattnaik B, Thomson JA, Gamm DM. Optic vesicle-like structures derived from human pluripotent stem cells facilitate a customized approach to retinal disease treatment. Stem Cells (Dayton, Ohio). 29: 1206-18. PMID 21678528 DOI: 10.1002/stem.674  0.48
2011 Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, Cui X, Wei H. TF-Cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). Bmc Systems Biology. 5: 53. PMID 21496241 DOI: 10.1186/1752-0509-5-53  0.48
2011 Chen G, Gulbranson DR, Hou Z, Bolin JM, Ruotti V, Probasco MD, Smuga-Otto K, Howden SE, Diol NR, Propson NE, Wagner R, Lee GO, Antosiewicz-Bourget J, Teng JM, Thomson JA. Chemically defined conditions for human iPSC derivation and culture. Nature Methods. 8: 424-9. PMID 21478862 DOI: 10.1038/nmeth.1593  0.48
2011 Howden SE, Gore A, Li Z, Fung HL, Nisler BS, Nie J, Chen G, McIntosh BE, Gulbranson DR, Diol NR, Taapken SM, Vereide DT, Montgomery KD, Zhang K, Gamm DM, ... Thomson JA, et al. Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy. Proceedings of the National Academy of Sciences of the United States of America. 108: 6537-42. PMID 21464322 DOI: 10.1073/pnas.1103388108  0.48
2011 Dias J, Gumenyuk M, Kang H, Vodyanik M, Yu J, Thomson JA, Slukvin II. Generation of red blood cells from human induced pluripotent stem cells. Stem Cells and Development. 20: 1639-47. PMID 21434814 DOI: 10.1089/scd.2011.0078  0.48
2011 Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, Giorgetti A, Israel MA, Kiskinis E, Lee JH, Loh YH, Manos PD, Montserrat N, Panopoulos AD, ... ... Thomson JA, et al. Somatic coding mutations in human induced pluripotent stem cells. Nature. 471: 63-7. PMID 21368825 DOI: 10.1038/nature09805  0.48
2011 Yu P, Pan G, Yu J, Thomson JA. FGF2 sustains NANOG and switches the outcome of BMP4-induced human embryonic stem cell differentiation. Cell Stem Cell. 8: 326-34. PMID 21362572 DOI: 10.1016/j.stem.2011.01.001  0.48
2011 Hu K, Yu J, Suknuntha K, Tian S, Montgomery K, Choi KD, Stewart R, Thomson JA, Slukvin II. Efficient generation of transgene-free induced pluripotent stem cells from normal and neoplastic bone marrow and cord blood mononuclear cells. Blood. 117: e109-19. PMID 21296996 DOI: 10.1182/blood-2010-07-298331  0.48
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/nature09798  0.48
2011 Atala A, Lanza R, Thomson JA, Nerem RM. Principles of Regenerative Medicine Principles of Regenerative Medicine 0.48
2010 Sengupta S, Ruotti V, Bolin J, Elwell A, Hernandez A, Thomson J, Stewart R. Highly consistent, fully representative mRNA-Seq libraries from ten nanograms of total RNA. Biotechniques. 49: 898-904. PMID 21143212 DOI: 10.2144/000113556  0.48
2010 Vodyanik MA, Yu J, Zhang X, Tian S, Stewart R, Thomson JA, Slukvin II. A mesoderm-derived precursor for mesenchymal stem and endothelial cells. Cell Stem Cell. 7: 718-29. PMID 21112566 DOI: 10.1016/j.stem.2010.11.011  0.48
2010 Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/nbt1010-1045  0.48
2010 Yang TS, Lu SN, Chao Y, Sheen IS, Lin CC, Wang TE, Chen SC, Wang JH, Liao LY, Thomson JA, Wang-Peng J, Chen PJ, Chen LT. A randomised phase II study of pegylated arginine deiminase (ADI-PEG 20) in Asian advanced hepatocellular carcinoma patients. British Journal of Cancer. 103: 954-60. PMID 20808309 DOI: 10.1038/sj.bjc.6605856  0.48
2010 Cho M, Xiao Y, Nie J, Stewart R, Csordas AT, Oh SS, Thomson JA, Soh HT. Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America. 107: 15373-8. PMID 20705898 DOI: 10.1073/pnas.1009331107  0.48
2010 Chen G, Hou Z, Gulbranson DR, Thomson JA. Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells. Cell Stem Cell. 7: 240-8. PMID 20682449 DOI: 10.1016/j.stem.2010.06.017  0.48
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, ... ... Thomson JA, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/j.stem.2010.03.018  0.48
2010 Winkler T, Cantilena A, Métais JY, Xu X, Nguyen AD, Borate B, Antosiewicz-Bourget JE, Wolfsberg TG, Thomson JA, Dunbar CE. No evidence for clonal selection due to lentiviral integration sites in human induced pluripotent stem cells. Stem Cells (Dayton, Ohio). 28: 687-94. PMID 20166152 DOI: 10.1002/stem.322  0.48
2010 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. Proceedings of the National Academy of Sciences of the United States of America. 107: 4335-40. PMID 20160098 DOI: 10.1073/pnas.0910012107  0.48
2010 Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (Oxford, England). 26: 493-500. PMID 20022975 DOI: 10.1093/bioinformatics/btp692  0.48
2010 Mohr JC, Zhang J, Azarin SM, Soerens AG, de Pablo JJ, Thomson JA, Lyons GE, Palecek SP, Kamp TJ. The microwell control of embryoid body size in order to regulate cardiac differentiation of human embryonic stem cells. Biomaterials. 31: 1885-93. PMID 19945747 DOI: 10.1016/j.biomaterials.2009.11.033  0.48
2009 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, ... Thomson JA, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462: 315-22. PMID 19829295 DOI: 10.1038/nature08514  0.48
2009 Sengupta S, Nie J, Wagner RJ, Yang C, Stewart R, Thomson JA. MicroRNA 92b controls the G1/S checkpoint gene p57 in human embryonic stem cells. Stem Cells (Dayton, Ohio). 27: 1524-8. PMID 19544458 DOI: 10.1002/stem.84  0.48
2009 Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell. 137: 647-58. PMID 19409607 DOI: 10.1016/j.cell.2009.02.038  0.48
2009 Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM. ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics (Oxford, England). 25: 1424-5. PMID 19351619 DOI: 10.1093/bioinformatics/btp178  0.48
2009 Deng J, Shoemaker R, Xie B, Gore A, LeProust EM, Antosiewicz-Bourget J, Egli D, Maherali N, Park IH, Yu J, Daley GQ, Eggan K, Hochedlinger K, Thomson J, Wang W, et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology. 27: 353-60. PMID 19330000 DOI: 10.1038/nbt.1530  0.48
2009 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 (New York, N.Y.). 324: 797-801. PMID 19325077 DOI: 10.1126/science.1172482  0.48
2009 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, ... ... Thomson JA, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 459: 108-12. PMID 19295514 DOI: 10.1038/nature07829  0.48
2009 Choi KD, Yu J, Smuga-Otto K, Salvagiotto G, Rehrauer W, Vodyanik M, Thomson J, Slukvin I. Hematopoietic and endothelial differentiation of human induced pluripotent stem cells. Stem Cells (Dayton, Ohio). 27: 559-67. PMID 19259936 DOI: 10.1634/stemcells.2008-0922  0.48
2009 Zhang J, Wilson GF, Soerens AG, Koonce CH, Yu J, Palecek SP, Thomson JA, Kamp TJ. Functional cardiomyocytes derived from human induced pluripotent stem cells. Circulation Research. 104: e30-41. PMID 19213953 DOI: 10.1161/CIRCRESAHA.108.192237  0.48
2009 Swaney DL, Wenger CD, Thomson JA, Coon JJ. 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. 106: 995-1000. PMID 19144917 DOI: 10.1073/pnas.0811964106  0.48
2009 Ebert AD, Yu J, Rose FF, Mattis VB, Lorson CL, Thomson JA, Svendsen CN. Induced pluripotent stem cells from a spinal muscular atrophy patient. Nature. 457: 277-80. PMID 19098894 DOI: 10.1038/nature07677  0.48
2009 Yu J, Thomson JA. Induced Pluripotent Stem Cell Derivation Essentials of Stem Cell Biology. 329+331-337. DOI: 10.1016/B978-0-12-374729-7.00037-8  0.48
2009 Lanza R, Gearhart J, Hogan B, Melton D, Pedersen R, Thomas ED, Thomson J, Wilmut SI. Essentials of Stem Cell Biology Essentials of Stem Cell Biology 0.48
2008 Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, Stewart R, Marra M, Thomson J, Eaves C, Slukvin I. Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis Experimental Hematology. 36: 1377-1389. PMID 18922365 DOI: 10.1016/j.exphem.2008.06.015  0.48
2008 Levenstein ME, Berggren WT, Lee JE, Conard KR, Llanas RA, Wagner RJ, Smith LM, Thomson JA. Secreted proteoglycans directly mediate human embryonic stem cell-basic fibroblast growth factor 2 interactions critical for proliferation. Stem Cells (Dayton, Ohio). 26: 3099-107. PMID 18802039 DOI: 10.1634/stemcells.2007-1056  0.48
2008 Bloushtain-Qimron N, Yao J, Snyder EL, Shipitsin M, Campbell LL, Mani SA, Hu M, Chen H, Ustyansky V, Antosiewicz JE, Argani P, Halushka MK, Thomson JA, Pharoah P, Porgador A, et al. Cell type-specific DNA methylation patterns in the human breast. Proceedings of the National Academy of Sciences of the United States of America. 105: 14076-81. PMID 18780791 DOI: 10.1073/pnas.0805206105  0.48
2008 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. 3: 196-206. PMID 18682241 DOI: 10.1016/j.stem.2008.07.001  0.48
2008 Yu J, Thomson JA. Pluripotent stem cell lines. Genes & Development. 22: 1987-97. PMID 18676805 DOI: 10.1101/gad.1689808  0.48
2008 Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou S, Potamousis K, Churas CP, Bergendahl V, Thomson JA, Schwartz DC. Optical mapping discerns genome wide DNA methylation profiles. Bmc Molecular Biology. 9: 68. PMID 18667073 DOI: 10.1186/1471-2199-9-68  0.48
2008 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. 133: 1162-74. PMID 18585351 DOI: 10.1016/j.cell.2008.05.047  0.48
2008 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. 2: 595-601. PMID 18522852 DOI: 10.1016/j.stem.2008.04.001  0.48
2008 Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R. A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Research. 36: 2926-38. PMID 18385155 DOI: 10.1093/nar/gkn133  0.48
2008 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. Proceedings of the National Academy of Sciences of the United States of America. 105: 4093-8. PMID 18326628 DOI: 10.1073/pnas.0710515105  0.48
2008 Pommer MS, Zhang Y, Keerthi N, Chen D, Thomson JA, Meinhart CD, Soh HT. Dielectrophoretic separation of platelets from diluted whole blood in microfluidic channels. Electrophoresis. 29: 1213-8. PMID 18288670 DOI: 10.1002/elps.200700607  0.48
2007 He JQ, January CT, Thomson JA, Kamp TJ. Human embryonic stem cell-derived cardiomyocytes: drug discovery and safety pharmacology. Expert Opinion On Drug Discovery. 2: 739-53. PMID 23488962 DOI: 10.1517/17460441.2.5.739  0.48
2007 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. 1: 299-312. PMID 18371364 DOI: 10.1016/j.stem.2007.08.003  0.48
2007 Lee MH, Hook B, Pan G, Kershner AM, Merritt C, Seydoux G, Thomson JA, Wickens M, Kimble J. Conserved regulation of MAP kinase expression by PUF RNA-binding proteins. Plos Genetics. 3: e233. PMID 18166083 DOI: 10.1371/journal.pgen.0030233  0.48
2007 Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, 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 (New York, N.Y.). 318: 1917-20. PMID 18029452 DOI: 10.1126/science.1151526  0.48
2007 Chen D, Wang P, Lewis RL, Daigh CA, Ho C, Chen X, Thomson JA, Kendziorski C. A microarray analysis of the emergence of embryonic definitive hematopoiesis. Experimental Hematology. 35: 1344-57. PMID 17761287 DOI: 10.1016/j.exphem.2007.06.004  0.48
2007 Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O'Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, ... ... Thomson JA, et al. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biology. 8: R113. PMID 17570852 DOI: 10.1186/gb-2007-8-6-r113  0.48
2007 Derda R, Li L, Orner BP, Lewis RL, Thomson JA, Kiessling LL. Defined substrates for human embryonic stem cell growth identified from surface arrays. Acs Chemical Biology. 2: 347-55. PMID 17480050 DOI: 10.1021/cb700032u  0.36
2007 Rajesh D, Chinnasamy N, Mitalipov SM, Wolf DP, Slukvin I, Thomson JA, Shaaban AF. Differential requirements for hematopoietic commitment between human and rhesus embryonic stem cells. Stem Cells (Dayton, Ohio). 25: 490-9. PMID 17284653 DOI: 10.1634/stemcells.2006-0277  0.48
2007 Pan G, Thomson JA. Nanog and transcriptional networks in embryonic stem cell pluripotency. Cell Research. 17: 42-9. PMID 17211451 DOI: 10.1038/sj.cr.7310125  0.48
2006 Chang HY, Thomson JA, Chen X. Microarray analysis of stem cells and differentiation. Methods in Enzymology. 420: 225-54. PMID 17161699 DOI: 10.1016/S0076-6879(06)20010-7  0.64
2006 Kameda T, Smuga-Otto K, Thomson JA. A severe de novo methylation of episomal vectors by human ES cells. Biochemical and Biophysical Research Communications. 349: 1269-77. PMID 16973130 DOI: 10.1016/j.bbrc.2006.08.175  0.48
2006 Ludwig TE, Bergendahl V, Levenstein ME, Yu J, Probasco MD, Thomson JA. Feeder-independent culture of human embryonic stem cells. Nature Methods. 3: 637-46. PMID 16862139 DOI: 10.1038/nmeth902  0.48
2006 Vodyanik MA, Thomson JA, Slukvin II. Leukosialin (CD43) defines hematopoietic progenitors in human embryonic stem cell differentiation cultures. Blood. 108: 2095-105. PMID 16757688 DOI: 10.1182/blood-2006-02-003327  0.48
2006 Ludwig TE, Levenstein ME, Jones JM, Berggren WT, Mitchen ER, Frane JL, Crandall LJ, Daigh CA, Conard KR, Piekarczyk MS, Llanas RA, Thomson JA. Derivation of human embryonic stem cells in defined conditions. Nature Biotechnology. 24: 185-7. PMID 16388305 DOI: 10.1038/nbt1177  0.48
2006 Levenstein ME, Ludwig TE, Xu RH, Llanas RA, VanDenHeuvel-Kramer K, Manning D, Thomson JA. Basic fibroblast growth factor support of human embryonic stem cell self-renewal. Stem Cells (Dayton, Ohio). 24: 568-74. PMID 16282444 DOI: 10.1634/stemcells.2005-0247  0.48
2006 Narayan AD, Chase JL, Lewis RL, Tian X, Kaufman DS, Thomson JA, Zanjani ED. Human embryonic stem cell-derived hematopoietic cells are capable of engrafting primary as well as secondary fetal sheep recipients. Blood. 107: 2180-3. PMID 16278307 DOI: 10.1182/blood-2005-05-1922  0.48
2005 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. Nature Methods. 2: 185-90. PMID 15782187 DOI: 10.1038/nmeth744  0.48
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