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References for PMC Articles for PubMed (Select 19619308)


WGCNA: an R package for weighted correlation network analysis.

Langfelder P, Horvath S.

BMC Bioinformatics. 2008 Dec 29;9:559. doi: 10.1186/1471-2105-9-559.


Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

Presson AP, Sobel EM, Papp JC, Suarez CJ, Whistler T, Rajeevan MS, Vernon SD, Horvath S.

BMC Syst Biol. 2008 Nov 6;2:95. doi: 10.1186/1752-0509-2-95.


Two supporting factors greatly improve the efficiency of human iPSC generation.

Zhao Y, Yin X, Qin H, Zhu F, Liu H, Yang W, Zhang Q, Xiang C, Hou P, Song Z, Liu Y, Yong J, Zhang P, Cai J, Liu M, Li H, Li Y, Qu X, Cui K, Zhang W, Xiang T, Wu Y, Zhao Y, Liu C, Yu C, Yuan K, Lou J, Ding M, Deng H.

Cell Stem Cell. 2008 Nov 6;3(5):475-9. doi: 10.1016/j.stem.2008.10.002. No abstract available.


Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation.

Duncan EM, Muratore-Schroeder TL, Cook RG, Garcia BA, Shabanowitz J, Hunt DF, Allis CD.

Cell. 2008 Oct 17;135(2):284-94. doi: 10.1016/j.cell.2008.09.055.


Functional organization of the transcriptome in human brain.

Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH.

Nat Neurosci. 2008 Nov;11(11):1271-82. doi: 10.1038/nn.2207. Epub 2008 Oct 12.


Regulatory networks define phenotypic classes of human stem cell lines.

Müller FJ, Laurent LC, Kostka D, Ulitsky I, Williams R, Lu C, Park IH, Rao MS, Shamir R, Schwartz PH, Schmidt NO, Loring JF.

Nature. 2008 Sep 18;455(7211):401-5. doi: 10.1038/nature07213. Epub 2008 Aug 24.


Geometric interpretation of gene coexpression network analysis.

Horvath S, Dong J.

PLoS Comput Biol. 2008 Aug 15;4(8):e1000117. doi: 10.1371/journal.pcbi.1000117.


Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH.

Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043.


Nuclear pore composition regulates neural stem/progenitor cell differentiation in the mouse embryo.

Lupu F, Alves A, Anderson K, Doye V, Lacy E.

Dev Cell. 2008 Jun;14(6):831-42. doi: 10.1016/j.devcel.2008.03.011.


Stem-cell-based therapy and lessons from the heart.

Passier R, van Laake LW, Mummery CL.

Nature. 2008 May 15;453(7193):322-9. doi: 10.1038/nature07040. Review.


Regenerative medicine and human models of human disease.

Chien KR.

Nature. 2008 May 15;453(7193):302-5. doi: 10.1038/nature07037.


Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation.

Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G.

Cell Stem Cell. 2008 Feb 7;2(2):160-9. doi: 10.1016/j.stem.2007.12.011.


Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment.

Walker E, Ohishi M, Davey RE, Zhang W, Cassar PA, Tanaka TS, Der SD, Morris Q, Hughes TR, Zandstra PW, Stanford WL.

Cell Stem Cell. 2007 Jun 7;1(1):71-86. doi: 10.1016/j.stem.2007.04.002.


Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution.

Maherali N, Sridharan R, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R, Plath K, Hochedlinger K.

Cell Stem Cell. 2007 Jun 7;1(1):55-70. doi: 10.1016/j.stem.2007.05.014.


An extended transcriptional network for pluripotency of embryonic stem cells.

Kim J, Chu J, Shen X, Wang J, Orkin SH.

Cell. 2008 Mar 21;132(6):1049-61. doi: 10.1016/j.cell.2008.02.039. Erratum in: Cell. 2008 Jun 27;133(7):1290.


A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.

Keller MP, Choi Y, Wang P, Davis DB, Rabaglia ME, Oler AT, Stapleton DS, Argmann C, Schueler KL, Edwards S, Steinberg HA, Chaibub Neto E, Kleinhanz R, Turner S, Hellerstein MK, Schadt EE, Yandell BS, Kendziorski C, Attie AD.

Genome Res. 2008 May;18(5):706-16. doi: 10.1101/gr.074914.107. Epub 2008 Mar 17.


Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling.

Shieh GS, Chen CM, Yu CY, Huang J, Wang WF, Lo YC.

BMC Bioinformatics. 2008 Mar 3;9:134. doi: 10.1186/1471-2105-9-134.


Selective blockade of microRNA processing by Lin28.

Viswanathan SR, Daley GQ, Gregory RI.

Science. 2008 Apr 4;320(5872):97-100. doi: 10.1126/science.1154040. Epub 2008 Feb 21.


Generation of human induced pluripotent stem cells from dermal fibroblasts.

Lowry WE, Richter L, Yachechko R, Pyle AD, Tchieu J, Sridharan R, Clark AT, Plath K.

Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):2883-8. doi: 10.1073/pnas.0711983105. Epub 2008 Feb 15.


A core Klf circuitry regulates self-renewal of embryonic stem cells.

Jiang J, Chan YS, Loh YH, Cai J, Tong GQ, Lim CA, Robson P, Zhong S, Ng HH.

Nat Cell Biol. 2008 Mar;10(3):353-60. doi: 10.1038/ncb1698. Epub 2008 Feb 10.

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