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Items: 1 to 20 of 43

1.

Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.

Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082.

2.

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates.

Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J.

Nat Struct Mol Biol. 2011 Feb;18(2):120-7. doi: 10.1038/nsmb.2000. Epub 2010 Dec 23.

PMID:
21183938
3.

A unique chromatin signature uncovers early developmental enhancers in humans.

Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J.

Nature. 2011 Feb 10;470(7333):279-83. doi: 10.1038/nature09692. Epub 2010 Dec 15.

4.

Histone H3K27ac separates active from poised enhancers and predicts developmental state.

Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R.

Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21931-6. doi: 10.1073/pnas.1016071107. Epub 2010 Nov 24.

5.

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity.

Chia NY, Chan YS, Feng B, Lu X, Orlov YL, Moreau D, Kumar P, Yang L, Jiang J, Lau MS, Huss M, Soh BS, Kraus P, Li P, Lufkin T, Lim B, Clarke ND, Bard F, Ng HH.

Nature. 2010 Nov 11;468(7321):316-20. doi: 10.1038/nature09531. Epub 2010 Oct 17.

PMID:
20953172
6.

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

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, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B.

Cell Stem Cell. 2010 May 7;6(5):479-91. doi: 10.1016/j.stem.2010.03.018.

7.

Evolution of the interaction between Runx2 and VDR, two transcription factors involved in osteoblastogenesis.

Marcellini S, Bruna C, HenrĂ­quez JP, Albistur M, Reyes AE, Barriga EH, HenrĂ­quez B, Montecino M.

BMC Evol Biol. 2010 Mar 17;10:78. doi: 10.1186/1471-2148-10-78.

8.

Principles and challenges of genomewide DNA methylation analysis.

Laird PW.

Nat Rev Genet. 2010 Mar;11(3):191-203. doi: 10.1038/nrg2732. Review.

PMID:
20125086
9.

Genome-wide prediction of transcription factor binding sites using an integrated model.

Won KJ, Ren B, Wang W.

Genome Biol. 2010 Jan 22;11(1):R7. doi: 10.1186/gb-2010-11-1-r7.

10.

Modeling disease in human ESCs using an efficient BAC-based homologous recombination system.

Song H, Chung SK, Xu Y.

Cell Stem Cell. 2010 Jan 8;6(1):80-9. doi: 10.1016/j.stem.2009.11.016.

11.

An oestrogen-receptor-alpha-bound human chromatin interactome.

Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y.

Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497.

12.

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):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.

13.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

14.

Systems biology of stem cell fate and cellular reprogramming.

Macarthur BD, Ma'ayan A, Lemischka IR.

Nat Rev Mol Cell Biol. 2009 Oct;10(10):672-81. doi: 10.1038/nrm2766. Epub 2009 Sep 9. Review.

15.

ChIP-seq: advantages and challenges of a maturing technology.

Park PJ.

Nat Rev Genet. 2009 Oct;10(10):669-80. doi: 10.1038/nrg2641. Epub 2009 Sep 8. Review.

16.

Insights from genomic profiling of transcription factors.

Farnham PJ.

Nat Rev Genet. 2009 Sep;10(9):605-16. doi: 10.1038/nrg2636. Epub 2009 Aug 11. Review.

17.

Transcriptional regulatory circuits: predicting numbers from alphabets.

Kim HD, Shay T, O'Shea EK, Regev A.

Science. 2009 Jul 24;325(5939):429-32. doi: 10.1126/science.1171347. Review.

18.

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

Won KJ, Chepelev I, Ren B, Wang W.

BMC Bioinformatics. 2008 Dec 18;9:547. doi: 10.1186/1471-2105-9-547.

19.

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

Whitington T, Perkins AC, Bailey TL.

Nucleic Acids Res. 2009 Jan;37(1):14-25. doi: 10.1093/nar/gkn866. Epub 2008 Nov 6.

20.

STRING 8--a global view on proteins and their functional interactions in 630 organisms.

Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. doi: 10.1093/nar/gkn760. Epub 2008 Oct 21.

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