• Slukvin I, Uenishi G, Jung HS, Kumar A, Park MA, Hadland BK, McLeod E, Raymond M, Moskvin O, Swanson S, Tamplin OJ, Zon LI, Thomson JA, Berstein I. “NOTCH signaling specifies arterial-type definitive hemogenic endothelium from human pluripotent stem cells.” Nature Comm. Accepted (2018).
  • Howden SE, Thomson JA, Little MH. “Simultaneous reprogramming and gene editing of human fibroblasts.” Nat Protoc. 2018 May;13(5):875-898. Epub 2018 Apr 5. Pub Med.
  • Miller AZ, Swanson SA, Thomson JA, Vereide DT. “Expandable arterial endothelial precursors derived from human CD34+ progenitors differ in their proclivity to undergo the endothelial-to-mesenchymal transition.” Scientific Reports. 2018 Jan 9;10(1):73-86. Pub Med.
  • Brown ME, Zhou Y, McIntosh B, Norman IG, Lou HE, Biermann M, Sullivan JA, Kamp TJ, Thomson JA, Anagnostopoulos PV, Burlingham WJ. “A humanized mouse model generated using surplus neonatal tissue.” Stem Cell Reports. Accepted (2018).


  • Phillips MJ, Jiang P, Howden S, Barney P, Min J, York NW, Chu LF, Capowski EE, Cash A, Jain S, Barlow K, Tabassum T, Stewart R, Pattnaik BR, Thomson JA, Gamm DM. “A novel approach to single cell RNA-seq analysis facilitates in silico gene reporting of human pluripotent stem cell-derived retinal cell types.” Stem Cells. 2017 Dec 12. [Epub ahead of print]. Pub Med.
  • Yu E, Mi HY, Zhang J, Thomson JA, Turng LS. “Development of biomimetic thermoplastic polyurethane/fibroin small-diameter vascular grafts via a novel electrospinning approach.” J Biomed Mater Res A. 2018 Apr;106(4):985-996. Epub 2017 Dec 5. PMID: 29143442. Pub Med.
  • Vermilyea SC, Guthrie S, Meyer M, Smuga-Otto K, Braun K, Howden S, Thomson JA, Zhang SC, Emborg ME, Golos TG. “Induced pluripotent stem cell-derived dopaminergic neurons from adult common marmoset fibroblasts.” Stem Cells Dev. 2017 Sep 1;26(17):1225-1235. doi: 10.1089/scd.2017.0069. Epub 2017 Jul 24. PubMed PMID: 28635509; Pub Med.
  • Jiang P, Hou Z, Bolin J, Thomson J, Stewart R. “RNA-seq of human neural progenitor cells exposed to lead (Pb) reveals transcriptome dynamics, splicing alterations and disease risk associations.” Toxicol Sci. 2017 Sep 1;159(1):251-265. Pub Med.
  • Zhang J, Chu LF, Hou Z, Schwartz MP, Hacker T, Vickerman V, Swanson S, Leng N, Nguyen BK, Elwell A, Bolin J, Brown ME, Stewart R, Burlingham WJ, Murphy WL, Thomson JA. “Functional characterization of human pluripotent stem cell-derived arterial endothelial cells.” Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6072-E6078. doi: 10.1073/pnas.1702295114. Epub 2017 Jul 10. Pub Med.
  • Bacher R, Chu LF, Leng N, Gasch A, Thomson JA, Stewart R, Newton M. “SCnorm: robust normalization of single-cell RNA-seq data.” Nature Methods. 2017 Jun;14(6):584-586. Pub Med.
  • Zhang J, Schwartz MP, Hou Z, Yongsheng B, Ardalani H, Swanson S, Steill J, Ruotti V, Elwell A, Nguyen BK, Bolin J, Stewart R, Thomson JA, Murphy WL. “A genome-wide analysis of human pluripotent stem cell-derived endothelial cells in synthetic hydrogels or standard 2D and 3D culture platforms.” Stem Cell Reports. 2017 Mar 10. pii: S2213-6711(17)30081-4. Pub Med.
  • Barry C, Schmitz MT, Jiang P, Schwartz MP, Duffin BM, Swanson S, Bacher R, Bolin JM, Elwell AL, McIntosh BE, Stewart R, Thomson JA. “Species-specific developmental timing is maintained by pluripotent stem cells ex utero.” Dev Biol. 2017 Feb 6. pii: S0012-1606(16)30812-0. Pub Med.


  • Eguchi A, Wleklinski MJ, Spurgat MC, Heiderscheit EA, Kropornicka AS, Vu CK, Bhimsaria D, Swanson SA, Stewart R, Kamp TJ. Slukvin Igor, Thomson JA, Dutton JR, Ansari A. “Reprogramming cell fate with a genome-scale library of artificial transcription factors.” PNAS. 2016 Dec 20; 113(51):E8257-E8266. Pub Med.
  • Erwin SG, Bhimsaria D, Rodriguez-Martinez JA, Grieshop MP, Swanson SA, Stewart R, Thomson JA, Ramanathan P, Ansari AZ. “COSMIC-seq analysis reveals genome-wide binding of polyamides to clustered sites in diverse chromatin states.” Proc Natl Acad Sci USA. 2016 Nov 22;113(47):E7418-E7427. Pub Med.
  • Lee WH, Higuchi H, Ikeda S, Macke E, Takimoto T, Pattnaik B, Liu C, Chu LF, Siepka SM, Krentz KJ, Rubinstein CD, Kalejta RF, Thomson JA, Mullins R, Takahashi JS, Pinto L, Ikeda A. “Mouse Tmem135 mutation reveals a mechanism involving mitochondrial dynamics that leads to age-dependent retinal pathologies.” Elife, 2016 Nov 15;5. pii: e19264. PMID: 27863209. Pub Med.
  • Korthauer KD, Chu LF, Newton MA, Li Y, Thomson JA, Stewart R, Kendziorski C. “A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.” Genome Biol. 2016 Oct 25;17(1):222. Pub Med.
  • Baik J, Magli A, Tahara N, Swanson S, Koyano-Nakagawa N, Borges L, Stewart R, Garry D, Kawakami Y, Thomson J, Perlingeiro R. “Endoglin Integrates BMP and Wnt Signaling to Induce Hematopoiesis through JDP2.” Nat Commun. 2016 Oct 7;7:13101. Pub Med.
  • 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 Biol. 2016 Aug 17;17(1):173. Pub Med.
  • Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R. “Analysis of embryonic development in the unsequenced axolotl: waves of transciptomic upheaval and stability.” Dev Biol. 2016 Jul 27. pii: S0012-1606(15)30261-X. Pub Med.
  • Kwong C, Thomson JA, Caldwell MD, Peissig P, Stewart R, Page CD. “Baseline Regularization for Computational Drug Repositioning with Longitudinal Observation Data.” IJCAI: Proceedings of the Conference Sponsored by the International Joint Conferences on Artificial Intelligence. 2016 Jul;2016:2521-2528. Pub Med.
  • Capowski EE, Wright LS, Liang K, Phillips MJ, Wallace K, Petelinski A, Hagstrom A, Pinilia I, Borys K, Lien J, Min JH, Keles S, Thomson JA, Gamm DM. “Regulation of WNT signaling by VSX2 during optic vesicle patterning in human induced pluripotent stem cells.” Stem Cells. 2016 Jun 14. Pub Med.
  • Jiang P, Thomson JA, Stewart R. “Quality control of single-cell RNA-seq by SinQC.” Bioinformatics. 2016 Aug 15;32(16):2514-6. Pub Med.
  • Zanotelli MR, Ardalani H, Zhang J, Hou Z, Nguyen EH, Swanson SA, Nguyen BK, Bolin JM, ElwellA, Bischel LL, Xie AW, Stewart R, Beebe DJ, Thomson JA, Schwartz MP, Murphy WL. “Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels.” Acta Biomater. 2016 Apr 15;35:32-41. Pub Med.
  • Lalit PA, Salick MR, Nelson DO, Squirrell JM, Shafer CM, Patel NG, Saeed I, Schmuck EG, Markandeya YS, Wong R, Lea MR, Eliceiri KW, Hacker TA, Crone WC, Kyba M, Garry DJ, Stewart R, Thomson JA, Downs KM, Lyons GE, Kamp TJ. “Lineage reprogramming of fibroblasts to proliferative induced cardiac progenitor cells by defined factors.” Cell Stem Cell, 2016 Mar 3;18(3):354-67. Pub Med.
  • D’Souza SS, Maufort J, Kumar A, Zhang J, Smuga-Otto K, Thomson JA, Slukvin II. “GSK3β Inhibition promotes efficient myeloid and lymphoid hematopoiesis from non-human primate-induced pluripotent stem cells.” Stem Cell Reports. 2016 Feb 9;6(2):243-56. Pub Med.
  • 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, 2016 May 1;32(9):1408-10. Pub Med.
  • Chan SS, Hagen HR, Swanson SA, Stewart R, Boll KA, Aho J, Thomson JA, Kyba M. “Development of Bipotent Cardiac/Skeletal Myogenic Progenitors from Mesp1+ Mesoderm.” Stem Cell Reports, 2016 Jan 12;6:26-34. Pub Med.


  • Cho M, Oh SS, Nie J, Stewart R, Radeke M, Eisenstein M, Coffey P, Thomson JA, Soh HT. “Array-Based Discovery of Aptamer Pairs.” Analytical Chemistry, 2015 Jan 6;87(1):821-8. Pub Med.
  • Raval KK, White BC, deLange WJ, Yu J, 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.” Journal of Biological Chemistry, 2015 Jan 30;290(5):3121-36. Pub Med.
  • McIntosh BE, Brown ME, Duffin BM, Maufort JP, Vereide DT, Slukvin II, Thomson JA. “Non-irradiated NOD,B6.SCID Il2rg-/- KitW41/W41 (NBSGW) Mice Support Multi-lineage Engraftment of Human Hematopoietic Cells.” Stem Cell Reports, 2015 Feb 10; 4(2): 171-180. Pub Med.
  • Dixon JR, Inkyung J, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal T, Xie W, Dioa T, Liang J, Zhao H, Lobanenkov VV, Ecker J, Thomson JA, Ren B. “Chromatin Architecture Reorganization During Stem Cell Differentiation.” Nature, 2015 Feb 19;518(7539):331-6. Pub Med.
  • Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, et al. “Integrative analysis of 111 reference human epigenomes.” Nature, 2015 Feb 19;518(7539):317-30. Pub Med.
  • 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, 2015 Mar;25(3):390-3. Pub Med.
  • Hou Z, Jiang P, Swanson SA, Elwell A, Nguyen BK, Bolin J, Stewart R, Thomson JA. “A cost effective RNA sequencing protocol for large-scale gene expression studies.” Scientific Reports, 2015 Apr 1;5:9570. Pub Med.
  • Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey C, Stewart R, Kendziorski C. “EBSeq-HMM: A Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.” Bioinformatics, 2015 Apr 5. Pub Med.
  • Belair DG, Whisler JA, Valdez J, Velazquez J, Molenda JA, Vickerman V, Lewis R, Daigh C, Hansen TD, Mann DA, Thomson JA, Griffith LG, Kamm RD, Schwartz MP, Murphy WL. “Human vascular tissue models formed from human induced pluripotent stem cell derived endothelial cells.” Stem Cell Reviews and Reports, 2015 Jun;11(3):511-25. doi: 10.1007/s12015-014-9549-5. Pub Med.
  • Leng N, Chu LF, Barry C, Li Y,  Choi J, Li X, Jiang P, Stewart R, Thomson JA, Kendziorski C. “Oscope identifies oscillatory genes in unsynchronized single cell RNA-seq experiments.” Nat Methods. 2015 Oct;12(10):947-50. doi: 10.1038/nmeth.3549. Pub Med.
  • Pellett S, Schwartz MP, Tepp WH, Josephson R, Scherf JM, Pier CL, Thomson JA, Murphy WL, Johnson EA. “Human Induced Pluripotent Stem Cell Derived Neuronal Cells Cultured on Chemically-Defined Hydrogels for Sensitive In Vitro Detection of Botulinum Neurotoxin.” Sci Rep. 2015 Sep 28;5:14566. doi: 10.1038/srep14566. Pub Med.
  • Schwartz MP, Hou Z, Propson NE, Zhang J, Engstrom C, Costa VS, Jiang P, Nguyen BK, Bolin J, Daly W, Wang Y, Stewart R, Page CD, Murphy WL, Thomson JA. “Human pluripotent stem cell-derived neural constructs for predicting neurotoxicity.” Proc Natl Acad Sci USA 2015 Sep 21. pii 201516645. Pub Med.
  • Friend K, Brooks HA, Propson NE, Thomson JA, Kimble J. “Embryonic stem cell growth factors regulate eIF2α phosphorylation.” PLoS One. 2015 Sep 25;10(9):e0139076. doi: 10.1371/journal.pone.0139076. eCollection 2015. Pub Med.
  • Suknuntha K, Ishii Y, Tao L, Hu K, McIntosh BE, Yang DT, Swanson S, Stewart R, Wang JY, Thomson JA, Slukvin I. “Discovery of survival factor for primitive chronic myeloid leukemia cells using induced pluripotent stem cells.” Stem Cell Research, 2015 Nov;15(3):678-93. doi: 10.1016/j.scr.2015.10.015. Epub 2015 Oct 31. Pub Med.
  • Howden SE, Maufort JP, Duffin B, Elefanty AG, Stanley EG, Thomson JA. “Simultaneous Reprogramming and Gene Correction of Patient Fibroblasts.” Stem Cell Reports, 2015 Dec 8;5(6):1109-18. doi: 10.1016/j.stemcr.2015.10.009. Epub 2015 Nov 12. Pub Med.


  • Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. “NANOG is multiply-phosphorylated and directly modified by ERK2 and CDK1.” Stem Cell Reports, 2014 Jan 14;2(1):18-25. Pub Med.
  • 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, Gamm DM. “Modeling human retinal development with patient-specific iPS cells reveals multiple roles for VSX2.” Stem Cells. 2014 Feb 15. Pub Med.
  • 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 ES cells.” Stem Cells, 2014 Mar 26. Pub Med.
  • Sengupta S, Johnson BP, Swanson SA, Stewart R, Bradfield CA, Thomson JA. “Aggregate Culture of Human Embryonic Step Cell-Derived Hepatocytes in Suspension are an Improved In Vitro Model for Drug Metabolism and Toxicity Testing.” Toxicol Sci. 2014 Apr 29. Pub Med.
  • Jiang P, 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, in press (2014).
  • Howden SE, Thomson JA. “Gene Targeting of Human Pluripotent Stem Cells by Homologous Recombination.” Methods in Molecular Biology, 1114: 37-55 (2014). Pub Med.
  • Elcheva I, Brok-Volchanskaya V, Kumar A, Liu P, Lee J, Tong D, Vodyanik M, Swanson S, Stewart R, Kyba M, Yakubov E, Cooke JP, Thomson JA, Slukvin I. “Direct Induction of Hematoendothelial Programs in Human Pluripotent Stem Cells by Transcriptional Regulators.” Nature Communications, 2014 Jul 14; 5:4372. Pub Med.


  • Stewart R, Rascon AR, Tian S, Nie J, Probasco MD, Bolin JM, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN. “Comparative RNA-Seq Analysis in the Unsequenced Axolotl: Burst of Oncogene Expression Defines One of Three Phases of Gene Expression in the Blastema.” PLoS Computational Biology 9(3): e1002936 (2013).
  • Yu J, Thomson JA. “Chapter 33,” in Principles of Tissue Engineering, 4th ed., edited by Robert Lanza. Elsevier Academic Press (2013).
  • Leng N, Dawson J, Thomson JA, Ruotti V, Rissman A, Smits B, Haag J, Gould M, Stewart R, Kendziorski C. “EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments.” Bioinformatics, 29 (8): 1035-43 (2013). Pub Med.
  • Wei X, Lister R, Schultz M, Rajagopal N, Hou Z, Ray P, Whitaker J, Tian S, Hawkins RD, Leung D, Wang T, Yang H, Swanson SA, Yun Z, Lee AY, Kim A, Nery J, Urich MA, Kuan S, Yen S, Klugman S, et al. “Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells.” Cell, 153(5):1134-1148 (2013). Pub Med.
  • Meyer S, Maufort J, 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(8): e71798 (2013). Pub Med.
  • 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(Suppl 1) (2013). NIHMS ID: 550666.
  • Hou Z, Zhang Y, Propson NE, Howden SE, Chu L, Sontheimer EJ, Thomson, JA. “Efficient Genome Engineering in Human Pluripotent Stem Cells Using Cas9 from Neisseria meningitides.” Proc Natl Acad Sci, USA, 110 (39): 15644-9 (2013). Pub Med.
  • Lagree S, Hou Z, Thomson JA, Stewart R, Gasch A, Roy S. “Integrated module and gene-specific regulatory inference implicates upstream signaling networks.” PLOS Computational Biology, 9(10): e1003252 (2013). Pub Med.
  • Cho M, Oh SS, Nie J, Stewart R, Eisenstein MS, Chambers J, Marth J, Walker F, Thomson JA, Soh H. “Quantitative Selection and Parallel Characterization of Aptamers.” Proc Natl Acad Sci, USA, 110 (46): 18460-5 (2013). Pub Med.


  • 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. Pub Med.
  • 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 (2012): 30(3): 461-470. Pub Med.
  • Chen G, Gulbranson D, Yu, P, Hou Z, Thomson JA. “Thermal stability of FGF protein is a determinant factor in regulating self-renewal, differentiation and reprogramming in human pluripotent stem cells.” Stem Cells (2012): 30(4):623-630. Pub Med.
  • The Huntington’s Disease iPSC Consortium (Thomson JA). “Induced Pluripotent Stem Cells from Patients with Huntington’s Disease Show CAG Repeat-Associated Phenotypes.” Cell Stem Cell (2012): 11(2): 264-278.
  • Soh H, Gong Q, Rossi J, Zhou J, Ahmad K, Csordas A, Wang J, Stewart R, Thomson JA, Nie J. “Selection strategy to generate multivalent aptamer sets that bind to distinct sites on protein targets.” Analytical Chemistry (2012): 84(12): 5365-71. Pub Med.
  • 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. Pub Med.
  • Choi K-D, Vodyanik MA, Togaratti P, Suknuntha K, Samarjeet F, Probasco MD, 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 (2012): 2(3):553-67. Pub Med.
  • Beers J, Gulbranson DR, George N, Jones J, Thomson JA, Chen G. “An enzyme-free dissociation method for passaging and colony expansion of human pluripotent stem cells in chemically defined conditions.” Nature Protocols (7): 2029-2040 (2012). Pub Med.
  • Zhang J, Klos M, Lian X, Wilson GF, Herman AM, Raval KK, Ding S, Barron MR, Soerens AG, Yu J, Burlingham WJ, Lozonschi L, Hu J, Palecek SP, Lyon GE, Thomson JA, Herron TJ, Jalife J, Kamp TJ. “Extracellular Matrix Promotes Highly Efficient Cardiac Differentiation of Human Pluripotent Stem Cells: The Matrix Sandwich Method.” Circulation Research (2012): 111(9):1125-36. Pub Med.
  • Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin J, Swanson S, Stewart R, Thomson JA, Roberts RW, Soh H, Sun R. “Single-round, Multiplexed antibody mimetic design through mRNA display.” Angewandte Chemie (2012): 51(50):12499-553.