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Results: 14

1.

Large-scale functional organization of long-range chromatin interaction networks.

Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fullwood MJ, Liu E, Csermely P, Ruan Y.

Cell Rep. 2012 Nov 29;2(5):1207-19. doi: 10.1016/j.celrep.2012.09.022. Epub 2012 Oct 25.

2.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

3.

ChIA-PET analysis of transcriptional chromatin interactions.

Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.

Methods. 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25.

PMID:
22926262
4.

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation.

Goh Y, Fullwood MJ, Poh HM, Peh SQ, Ong CT, Zhang J, Ruan X, Ruan Y.

J Vis Exp. 2012 Apr 30;(62). pii: 3770. doi: 10.3791/3770.

5.

Targeting phosphorylation of eukaryotic initiation factor-2α to treat human disease.

Fullwood MJ, Zhou W, Shenolikar S.

Prog Mol Biol Transl Sci. 2012;106:75-106. doi: 10.1016/B978-0-12-396456-4.00005-5. Review.

PMID:
22340715
6.

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y.

Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014.

7.

Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations.

Fullwood MJ, Lee J, Lin L, Li G, Huss M, Ng P, Sung WK, Shenolikar S.

PLoS One. 2011;6(11):e26054. doi: 10.1371/journal.pone.0026054. Epub 2011 Nov 8.

8.

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK.

Genome Biol. 2010;11(2):R22. doi: 10.1186/gb-2010-11-2-r22. Epub 2010 Feb 25.

9.

Chromatin interaction analysis using paired-end tag sequencing.

Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y.

Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. doi: 10.1002/0471142727.mb2115s89.

PMID:
20069536
10.

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.

11.

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.

Fullwood MJ, Wei CL, Liu ET, Ruan Y.

Genome Res. 2009 Apr;19(4):521-32. doi: 10.1101/gr.074906.107. Review.

12.

ChIP-based methods for the identification of long-range chromatin interactions.

Fullwood MJ, Ruan Y.

J Cell Biochem. 2009 May 1;107(1):30-9. doi: 10.1002/jcb.22116. Review.

13.

The use of multiple displacement amplification to amplify complex DNA libraries.

Fullwood MJ, Tan JJ, Ng PW, Chiu KP, Liu J, Wei CL, Ruan Y.

Nucleic Acids Res. 2008 Mar;36(5):e32. doi: 10.1093/nar/gkn074. Epub 2008 Feb 19.

14.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y.

Nucleic Acids Res. 2006 Jul 13;34(12):e84.

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