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Items: 1 to 20 of 103

1.

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.

2.

Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions.

Li X, Luo OJ, Wang P, Zheng M, Wang D, Piecuch E, Zhu JJ, Tian SZ, Tang Z, Li G, Ruan Y.

Nat Protoc. 2017 May;12(5):899-915. doi: 10.1038/nprot.2017.012. Epub 2017 Mar 30.

PMID:
28358394
3.

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.

4.

Mango: a bias-correcting ChIA-PET analysis pipeline.

Phanstiel DH, Boyle AP, Heidari N, Snyder MP.

Bioinformatics. 2015 Oct 1;31(19):3092-8. doi: 10.1093/bioinformatics/btv336. Epub 2015 Jun 1.

5.

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.

Li G, Cai L, Chang H, Hong P, Zhou Q, Kulakova EV, Kolchanov NA, Ruan Y.

BMC Genomics. 2014;15 Suppl 12:S11. doi: 10.1186/1471-2164-15-S12-S11. Epub 2014 Dec 19.

6.

MICC: an R package for identifying chromatin interactions from ChIA-PET data.

He C, Zhang MQ, Wang X.

Bioinformatics. 2015 Dec 1;31(23):3832-4. doi: 10.1093/bioinformatics/btv445. Epub 2015 Jul 31.

7.

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
8.

Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET).

Choy J, Fullwood MJ.

Methods Mol Biol. 2017;1468:63-89. doi: 10.1007/978-1-4939-4035-6_7.

PMID:
27662871
9.

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.

10.

ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis.

Li G, Chen Y, Snyder MP, Zhang MQ.

Nucleic Acids Res. 2017 Jan 9;45(1):e4. doi: 10.1093/nar/gkw809. Epub 2016 Sep 12.

11.

A Bayesian mixture model for chromatin interaction data.

Niu L, Lin S.

Stat Appl Genet Mol Biol. 2015 Feb;14(1):53-64. doi: 10.1515/sagmb-2014-0029.

PMID:
25485614
12.

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
13.

Statistical models for detecting differential chromatin interactions mediated by a protein.

Niu L, Li G, Lin S.

PLoS One. 2014 May 16;9(5):e97560. doi: 10.1371/journal.pone.0097560. eCollection 2014.

14.

F-Seq: a feature density estimator for high-throughput sequence tags.

Boyle AP, Guinney J, Crawford GE, Furey TS.

Bioinformatics. 2008 Nov 1;24(21):2537-8. doi: 10.1093/bioinformatics/btn480. Epub 2008 Sep 10.

15.

ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

Narlikar L, Jothi R.

Methods Mol Biol. 2012;802:305-22. doi: 10.1007/978-1-61779-400-1_20.

16.

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.

17.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y.

BMC Bioinformatics. 2006 Aug 25;7:390.

18.

High resolution mapping of enhancer-promoter interactions.

Reeder C, Closser M, Poh HM, Sandhu K, Wichterle H, Gifford D.

PLoS One. 2015 May 13;10(5):e0122420. doi: 10.1371/journal.pone.0122420. eCollection 2015.

19.

Mapping regulatory factors by immunoprecipitation from native chromatin.

Orsi GA, Kasinathan S, Zentner GE, Henikoff S, Ahmad K.

Curr Protoc Mol Biol. 2015 Apr 1;110:21.31.1-25. doi: 10.1002/0471142727.mb2131s110.

20.

Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.

Hoffman BG, Jones SJ.

J Endocrinol. 2009 Apr;201(1):1-13. doi: 10.1677/JOE-08-0526. Epub 2009 Jan 9. Review.

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