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Systems-level dynamic analyses of fate change in murine embryonic stem cells.

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR.

Nature. 2009 Nov 19;462(7271):358-62. doi: 10.1038/nature08575.


Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.

Markowetz F, Mulder KW, Airoldi EM, Lemischka IR, Troyanskaya OG.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001034. doi: 10.1371/journal.pcbi.1001034.


Transcriptional regulatory mechanisms that govern embryonic stem cell fate.

Das S, Levasseur D.

Methods Mol Biol. 2013;1029:191-203. doi: 10.1007/978-1-62703-478-4_13. Review.


The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network.

Li X, Li L, Pandey R, Byun JS, Gardner K, Qin Z, Dou Y.

Cell Stem Cell. 2012 Aug 3;11(2):163-78. doi: 10.1016/j.stem.2012.04.023.


Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network.

Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E.

Gene. 2013 Dec 1;531(2):212-9. doi: 10.1016/j.gene.2013.09.011. Epub 2013 Sep 13.


Dual roles of histone H3 lysine 9 acetylation in human embryonic stem cell pluripotency and neural differentiation.

Qiao Y, Wang R, Yang X, Tang K, Jing N.

J Biol Chem. 2015 Jan 23;290(4):2508-20. doi: 10.1074/jbc.M114.603761. Epub 2014 Dec 17. Erratum in: J Biol Chem. 2015 Apr 17;290(16):9949.


Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells.

Sun Y, Li H, Liu Y, Shin S, Mattson MP, Rao MS, Zhan M.

Genomics. 2007 Jan;89(1):22-35. Epub 2006 Oct 19.


Epigenetics in embryonic stem cells: regulation of pluripotency and differentiation.

Atkinson S, Armstrong L.

Cell Tissue Res. 2008 Jan;331(1):23-9. Epub 2007 Nov 15. Review.


Proteomic analysis of Sox2-associated proteins during early stages of mouse embryonic stem cell differentiation identifies Sox21 as a novel regulator of stem cell fate.

Mallanna SK, Ormsbee BD, Iacovino M, Gilmore JM, Cox JL, Kyba M, Washburn MP, Rizzino A.

Stem Cells. 2010 Oct;28(10):1715-27. doi: 10.1002/stem.494.


Genome-wide analysis reveals Sall4 to be a major regulator of pluripotency in murine-embryonic stem cells.

Yang J, Chai L, Fowles TC, Alipio Z, Xu D, Fink LM, Ward DC, Ma Y.

Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19756-61. doi: 10.1073/pnas.0809321105. Epub 2008 Dec 5.


Transcriptome analysis in cardiomyocyte-specific differentiation of murine embryonic stem cells reveals transcriptional regulation network.

Gan L, Schwengberg S, Denecke B.

Gene Expr Patterns. 2014 Sep;16(1):8-22. doi: 10.1016/j.gep.2014.07.002. Epub 2014 Jul 21.


Systematic tracking of cell fate changes.

Kim J, Orkin SH.

Nat Biotechnol. 2010 Feb;28(2):146-7. doi: 10.1038/nbt0210-146. No abstract available.


Integrating post-transcriptional regulation into the embryonic stem cell gene regulatory network.

Cassar PA, Stanford WL.

J Cell Physiol. 2012 Feb;227(2):439-49. doi: 10.1002/jcp.22787. Review.


Quantitative proteome analysis of pluripotent cells by iTRAQ mass tagging reveals post-transcriptional regulation of proteins required for ES cell self-renewal.

O'Brien RN, Shen Z, Tachikawa K, Lee PA, Briggs SP.

Mol Cell Proteomics. 2010 Oct;9(10):2238-51. doi: 10.1074/mcp.M110.000281. Epub 2010 May 31.


Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis.

Karantzali E, Schulz H, Hummel O, Hubner N, Hatzopoulos A, Kretsovali A.

Genome Biol. 2008 Apr 4;9(4):R65. doi: 10.1186/gb-2008-9-4-r65.


Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.

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, Lobanenkov VV, Stewart R, Thomson JA, Ren B.

Cell Res. 2011 Oct;21(10):1393-409. doi: 10.1038/cr.2011.146. Epub 2011 Aug 30.


Time scales in epigenetic dynamics and phenotypic heterogeneity of embryonic stem cells.

Sasai M, Kawabata Y, Makishi K, Itoh K, Terada TP.

PLoS Comput Biol. 2013;9(12):e1003380. doi: 10.1371/journal.pcbi.1003380. Epub 2013 Dec 12.


Critical components of the pluripotency network are targets for the p300/CBP interacting protein (p/CIP) in embryonic stem cells.

Chitilian JM, Thillainadesan G, Manias JL, Chang WY, Walker E, Isovic M, Stanford WL, Torchia J.

Stem Cells. 2014 Jan;32(1):204-15. doi: 10.1002/stem.1564.


Involvement of histone acetylation of Sox17 and Foxa2 promoters during mouse definitive endoderm differentiation revealed by microRNA profiling.

Fu S, Fei Q, Jiang H, Chuai S, Shi S, Xiong W, Jiang L, Lu C, Atadja P, Li E, Shou J.

PLoS One. 2011;6(11):e27965. doi: 10.1371/journal.pone.0027965. Epub 2011 Nov 23.


The transcriptional regulation of pluripotency.

Yeo JC, Ng HH.

Cell Res. 2013 Jan;23(1):20-32. doi: 10.1038/cr.2012.172. Epub 2012 Dec 11. Review.

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