PubMed

Human DNA methylomes at base resolution show widespread epigenomic differences.

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, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-322. Epub 2009 Oct 14.PMID: 19829295 [PubMed - as supplied by publisher]Related articles

To Tell or Not to Tell: The Community Wants to Know About Expensive Anticancer Drugs As a Potential Treatment Option.

Mileshkin L, Schofield PE, Jefford M, Agalianos E, Levine M, Herschtal A, Savulescu J, Thomson JA, Zalcberg JR.

J Clin Oncol. 2009 Sep 28. [Epub ahead of print]PMID: 19786663 [PubMed - as supplied by publisher]Related articles

Newborn adiposity measured by plethysmography is not predicted by late gestation two-dimensional ultrasound measures of fetal growth.

Moyer-Mileur LJ, Slater H, Thomson JA, Mihalopoulos N, Byrne J, Varner MW.

J Nutr. 2009 Sep;139(9):1772-8. Epub 2009 Jul 29.PMID: 19640967 [PubMed - indexed for MEDLINE]Related articles

The bright side of being blue: depression as an adaptation for analyzing complex problems.

Andrews PW, Thomson JA Jr.

Psychol Rev. 2009 Jul;116(3):620-54. Review.PMID: 19618990 [PubMed - indexed for MEDLINE]Related articles

MicroRNA 92b controls the G1/S checkpoint gene p57 in human embryonic stem cells.

Sengupta S, Nie J, Wagner RJ, Yang C, Stewart R, Thomson JA.

Stem Cells. 2009 Jul;27(7):1524-8.PMID: 19544458 [PubMed - indexed for MEDLINE]Related articles

Exogenous glucose oxidation is reduced with carbohydrate feeding during exercise after starvation.

Rowlands DS, Johnson NA, Thomson JA, Chapman P, Stannard SR.

Metabolism. 2009 Aug;58(8):1161-9. Epub 2009 Jun 18.PMID: 19428033 [PubMed - indexed for MEDLINE]Related articles

MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells.

Xu N, Papagiannakopoulos T, Pan G, Thomson JA, Kosik KS.

Cell. 2009 May 15;137(4):647-58. Epub 2009 Apr 30.PMID: 19409607 [PubMed - indexed for MEDLINE]Related articles

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.

Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.

Bioinformatics. 2009 Jun 1;25(11):1424-5. Epub 2009 Apr 7.PMID: 19351619 [PubMed - indexed for MEDLINE]Related articles

Human induced pluripotent stem cells free of vector and transgene sequences.

Yu J, Hu K, Smuga-Otto K, Tian S, Stewart R, Slukvin II, Thomson JA.

Science. 2009 May 8;324(5928):797-801. Epub 2009 Mar 26.PMID: 19325077 [PubMed - indexed for MEDLINE]Related articlesFree article

Who are we? Where did we come from? How religious identity divides and damns us all.

Thomson JA.

Am J Psychoanal. 2009 Mar;69(1):22-42. Review.PMID: 19295619 [PubMed - indexed for MEDLINE]Related articles

Histone modifications at human enhancers reflect global cell-type-specific gene expression.

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.

Nature. 2009 May 7;459(7243):108-12. Epub 2009 Mar 18.PMID: 19295514 [PubMed - indexed for MEDLINE]Related articles

Functional cardiomyocytes derived from human induced pluripotent stem cells.

Zhang J, Wilson GF, Soerens AG, Koonce CH, Yu J, Palecek SP, Thomson JA, Kamp TJ.

Circ Res. 2009 Feb 27;104(4):e30-41. Epub 2009 Feb 12.PMID: 19213953 [PubMed - indexed for MEDLINE]Related articles

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.

Swaney DL, Wenger CD, Thomson JA, Coon JJ.

Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):995-1000. Epub 2009 Jan 14.PMID: 19144917 [PubMed - indexed for MEDLINE]Related articlesFree article

Induced pluripotent stem cells from a spinal muscular atrophy patient.

Ebert AD, Yu J, Rose FF Jr, Mattis VB, Lorson CL, Thomson JA, Svendsen CN.

Nature. 2009 Jan 15;457(7227):277-80. Epub 2008 Dec 21.PMID: 19098894 [PubMed - indexed for MEDLINE]Related articlesFree article

Protocols for nuclei isolation and nuclear protein extraction from the resurrection plant Xerophyta viscosa for proteomic studies.

Abdalla KO, Thomson JA, Rafudeen MS.

Anal Biochem. 2009 Jan 15;384(2):365-7. Epub 2008 Oct 7.PMID: 18938124 [PubMed - indexed for MEDLINE]Related articles

Secreted proteoglycans directly mediate human embryonic stem cell-basic fibroblast growth factor 2 interactions critical for proliferation.

Levenstein ME, Berggren WT, Lee JE, Conard KR, Llanas RA, Wagner RJ, Smith LM, Thomson JA.

Stem Cells. 2008 Dec;26(12):3099-107. Epub 2008 Sep 18.PMID: 18802039 [PubMed - indexed for MEDLINE]Related articles

Cell type-specific DNA methylation patterns in the human breast.

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, Sukumar S, Parsons R, Richardson AL, Stampfer MR, Gelman RS, Nikolskaya T, Nikolsky Y, Polyak K.

Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):14076-81. Epub 2008 Sep 9.PMID: 18780791 [PubMed - indexed for MEDLINE]Related articlesFree article

NANOG is a direct target of TGFbeta/activin-mediated SMAD signaling in human ESCs.

Xu RH, Sampsell-Barron TL, Gu F, Root S, Peck RM, Pan G, Yu J, Antosiewicz-Bourget J, Tian S, Stewart R, Thomson JA.

Cell Stem Cell. 2008 Aug 7;3(2):196-206.PMID: 18682241 [PubMed - indexed for MEDLINE]Related articlesFree article

Pluripotent stem cell lines.

Yu J, Thomson JA.

Genes Dev. 2008 Aug 1;22(15):1987-97. Review.PMID: 18676805 [PubMed - indexed for MEDLINE]Related articlesFree article

Optical mapping discerns genome wide DNA methylation profiles.

Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou S, Potamousis K, Churas CP, Bergendahl V, Thomson JA, Schwartz DC.

BMC Mol Biol. 2008 Jul 30;9:68.PMID: 18667073 [PubMed - indexed for MEDLINE]Related articlesFree article

Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells.

Dejosez M, Krumenacker JS, Zitur LJ, Passeri M, Chu LF, Songyang Z, Thomson JA, Zwaka TP.

Cell. 2008 Jun 27;133(7):1162-74. Erratum in: Cell. 2008 Aug 22;134(4):692. PMID: 18585351 [PubMed - indexed for MEDLINE]Related articlesFree article

Caspase activity mediates the differentiation of embryonic stem cells.

Fujita J, Crane AM, Souza MK, Dejosez M, Kyba M, Flavell RA, Thomson JA, Zwaka TP.

Cell Stem Cell. 2008 Jun 5;2(6):595-601.PMID: 18522852 [PubMed - indexed for MEDLINE]Related articlesFree article

A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.

Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R.

Nucleic Acids Res. 2008 May;36(9):2926-38. Epub 2008 Apr 1.PMID: 18385155 [PubMed - indexed for MEDLINE]Related articlesFree article

Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells.

Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA.

Cell Stem Cell. 2007 Sep 13;1(3):299-312.PMID: 18371364 [PubMed - indexed for MEDLINE]Related articles

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells.

Phanstiel D, Brumbaugh J, Berggren WT, Conard K, Feng X, Levenstein ME, McAlister GC, Thomson JA, Coon JJ.

Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4093-8. Epub 2008 Mar 7.PMID: 18326628 [PubMed - indexed for MEDLINE]Related articlesFree article

Dielectrophoretic separation of platelets from diluted whole blood in microfluidic channels.

Pommer MS, Zhang Y, Keerthi N, Chen D, Thomson JA, Meinhart CD, Soh HT.

Electrophoresis. 2008 Mar;29(6):1213-8.PMID: 18288670 [PubMed - indexed for MEDLINE]Related articles

Steady-state and pre-steady-state kinetic evaluation of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro cysteine protease: development of an ion-pair model for catalysis.

Solowiej J, Thomson JA, Ryan K, Luo C, He M, Lou J, Murray BW.

Biochemistry. 2008 Feb 26;47(8):2617-30. Epub 2008 Feb 1.PMID: 18237196 [PubMed - indexed for MEDLINE]Related articles

Conserved regulation of MAP kinase expression by PUF RNA-binding proteins.

Lee MH, Hook B, Pan G, Kershner AM, Merritt C, Seydoux G, Thomson JA, Wickens M, Kimble J.

PLoS Genet. 2007 Dec 28;3(12):e233.PMID: 18166083 [PubMed - indexed for MEDLINE]Related articlesFree article

Induced pluripotent stem cell lines derived from human somatic cells.

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.

Science. 2007 Dec 21;318(5858):1917-20. Epub 2007 Nov 20.PMID: 18029452 [PubMed - indexed for MEDLINE]Related articlesFree article

Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant.

Owor BE, Martin DP, Shepherd DN, Edema R, Monjane AL, Rybicki EP, Thomson JA, Varsani A.

J Gen Virol. 2007 Nov;88(Pt 11):3154-65.PMID: 17947543 [PubMed - indexed for MEDLINE]Related articlesFree article

Maize streak virus-resistant transgenic maize: a first for Africa.

Shepherd DN, Mangwende T, Martin DP, Bezuidenhout M, Kloppers FJ, Carolissen CH, Monjane AL, Rybicki EP, Thomson JA.

Plant Biotechnol J. 2007 Nov;5(6):759-67.PMID: 17924935 [PubMed - indexed for MEDLINE]Related articles

The role of biotechnology for agricultural sustainability in Africa.

Thomson JA.

Philos Trans R Soc Lond B Biol Sci. 2008 Feb 27;363(1492):905-13. Review.PMID: 17761472 [PubMed - indexed for MEDLINE]Related articlesFree article

A microarray analysis of the emergence of embryonic definitive hematopoiesis.

Chen D, Wang P, Lewis RL, Daigh CA, Ho C, Chen X, Thomson JA, Kendziorski C.

Exp Hematol. 2007 Sep;35(9):1344-57.PMID: 17761287 [PubMed - indexed for MEDLINE]Related articles

Analysis of multiple single nucleotide polymorphisms closely positioned in the ovine PRNP gene using linear fluorescent probes and melting curve analysis.

French DJ, Jones D, McDowell DG, Thomson JA, Debenham PG.

BMC Infect Dis. 2007 Aug 3;7:90.PMID: 17683552 [PubMed - indexed for MEDLINE]Related articlesFree article

LongSAGE profiling of nine human embryonic stem cell lines.

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, Prabhu AL, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA.

Genome Biol. 2007;8(6):R113.PMID: 17570852 [PubMed - indexed for MEDLINE]Related articlesFree article

Defined substrates for human embryonic stem cell growth identified from surface arrays.

Derda R, Li L, Orner BP, Lewis RL, Thomson JA, Kiessling LL.

ACS Chem Biol. 2007 May 22;2(5):347-55. Epub 2007 May 4.PMID: 17480050 [PubMed - indexed for MEDLINE]Related articles

Protection mechanisms in the resurrection plant Xerophyta viscosa (Baker): both sucrose and raffinose family oligosaccharides (RFOs) accumulate in leaves in response to water deficit.

Peters S, Mundree SG, Thomson JA, Farrant JM, Keller F.

J Exp Bot. 2007;58(8):1947-56. Epub 2007 Apr 23.PMID: 17452754 [PubMed - indexed for MEDLINE]Related articlesFree article

Proteomic analysis of leaf proteins during dehydration of the resurrection plant Xerophyta viscosa.

Ingle RA, Schmidt UG, Farrant JM, Thomson JA, Mundree SG.

Plant Cell Environ. 2007 Apr;30(4):435-46.PMID: 17324230 [PubMed - indexed for MEDLINE]Related articles

Differential requirements for hematopoietic commitment between human and rhesus embryonic stem cells.

Rajesh D, Chinnasamy N, Mitalipov SM, Wolf DP, Slukvin I, Thomson JA, Shaaban AF.

Stem Cells. 2007 Feb;25(2):490-9.PMID: 17284653 [PubMed - indexed for MEDLINE]Related articlesFree article

Nanog and transcriptional networks in embryonic stem cell pluripotency.

Pan G, Thomson JA.

Cell Res. 2007 Jan;17(1):42-9. Review.PMID: 17211451 [PubMed - indexed for MEDLINE]Related articlesFree article

Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes.

Owor BE, Shepherd DN, Taylor NJ, Edema R, Monjane AL, Thomson JA, Martin DP, Varsani A.

J Virol Methods. 2007 Mar;140(1-2):100-5. Epub 2006 Dec 15.PMID: 17174409 [PubMed - indexed for MEDLINE]Related articles

Inhibition of maize streak virus (MSV) replication by transient and transgenic expression of MSV replication-associated protein mutants.

Shepherd DN, Mangwende T, Martin DP, Bezuidenhout M, Thomson JA, Rybicki EP.

J Gen Virol. 2007 Jan;88(Pt 1):325-36.PMID: 17170465 [PubMed - indexed for MEDLINE]Related articlesFree article

Microarray analysis of stem cells and differentiation.

Chang HY, Thomson JA, Chen X.

Methods Enzymol. 2006;420:225-54. Review.PMID: 17161699 [PubMed - indexed for MEDLINE]Related articles

XVSAP1 from Xerophyta viscosa improves osmotic-, salinity- and high-temperature-stress tolerance in Arabidopsis.

Garwe D, Thomson JA, Mundree SG.

Biotechnol J. 2006 Oct;1(10):1137-46.PMID: 17004302 [PubMed - indexed for MEDLINE]Related articles

Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic.

Thomson JA, Perni RB.

Curr Opin Drug Discov Devel. 2006 Sep;9(5):606-17. Review.PMID: 17002221 [PubMed - indexed for MEDLINE]Related articles

A severe de novo methylation of episomal vectors by human ES cells.

Kameda T, Smuga-Otto K, Thomson JA.

Biochem Biophys Res Commun. 2006 Nov 3;349(4):1269-77. Epub 2006 Sep 7.PMID: 16973130 [PubMed - indexed for MEDLINE]Related articles

Addition of gabapentin to a modified FOLFOX regimen does not reduce oxaliplatin-induced neurotoxicity.

Mitchell PL, Goldstein D, Michael M, Beale P, Friedlander M, Zalcberg J, White S, Thomson JA, Clarke S.

Clin Colorectal Cancer. 2006 Jul;6(2):146-51.PMID: 16945171 [PubMed - indexed for MEDLINE]Related articles

Feeder-independent culture of human embryonic stem cells.

Ludwig TE, Bergendahl V, Levenstein ME, Yu J, Probasco MD, Thomson JA.

Nat Methods. 2006 Aug;3(8):637-46. No abstract available. Erratum in: Nat Methods. 2006 Oct;3(10):867. PMID: 16862139 [PubMed - indexed for MEDLINE]Related articles

Genetically modified crops--playing a positive role in sustainable development in Africa.

Thomson JA.

S Afr Med J. 2006 Jun;96(6):509-10. No abstract available. PMID: 16841131 [PubMed - indexed for MEDLINE]Related articlesFree article

Leukosialin (CD43) defines hematopoietic progenitors in human embryonic stem cell differentiation cultures.

Vodyanik MA, Thomson JA, Slukvin II.

Blood. 2006 Sep 15;108(6):2095-105. Epub 2006 Jun 6.PMID: 16757688 [PubMed - indexed for MEDLINE]Related articlesFree article