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Items: 1 to 20 of 101

1.

A compendium of promoter-centered long-range chromatin interactions in the human genome.

Jung I, Schmitt A, Diao Y, Lee AJ, Liu T, Yang D, Tan C, Eom J, Chan M, Chee S, Chiang Z, Kim C, Masliah E, Barr CL, Li B, Kuan S, Kim D, Ren B.

Nat Genet. 2019 Oct;51(10):1442-1449. doi: 10.1038/s41588-019-0494-8. Epub 2019 Sep 9.

PMID:
31501517
2.

The long-range interaction landscape of gene promoters.

Sanyal A, Lajoie BR, Jain G, Dekker J.

Nature. 2012 Sep 6;489(7414):109-13. doi: 10.1038/nature11279.

3.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F; BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.

Cell. 2016 Nov 17;167(5):1369-1384.e19. doi: 10.1016/j.cell.2016.09.037.

4.

Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome.

Jalali S, Singh A, Maiti S, Scaria V.

J Transl Med. 2017 Sep 2;15(1):186. doi: 10.1186/s12967-017-1282-9.

5.

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.

6.

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions.

Schoenfelder S, Javierre BM, Furlan-Magaril M, Wingett SW, Fraser P.

J Vis Exp. 2018 Jun 28;(136). doi: 10.3791/57320.

7.

A high-resolution map of the three-dimensional chromatin interactome in human cells.

Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B.

Nature. 2013 Nov 14;503(7475):290-4. doi: 10.1038/nature12644. Epub 2013 Oct 20.

8.

The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements.

Li Z, Wang M, Lin K, Xie Y, Guo J, Ye L, Zhuang Y, Teng W, Ran X, Tong Y, Xue Y, Zhang W, Zhang Y.

Genome Biol. 2019 Jul 15;20(1):139. doi: 10.1186/s13059-019-1746-8.

9.

Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes.

Alam T, Medvedeva YA, Jia H, Brown JB, Lipovich L, Bajic VB.

PLoS One. 2014 Oct 2;9(10):e109443. doi: 10.1371/journal.pone.0109443. eCollection 2014.

10.

A predictive modeling approach for cell line-specific long-range regulatory interactions.

Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.

Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865. Epub 2015 Sep 3. Erratum in: Nucleic Acids Res. 2016 Feb 29;44(4):1977-8.

11.

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL.

Nature. 2013 Dec 12;504(7479):306-310. doi: 10.1038/nature12716. Epub 2013 Nov 10.

12.

A map of the cis-regulatory sequences in the mouse genome.

Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B.

Nature. 2012 Aug 2;488(7409):116-20. doi: 10.1038/nature11243.

13.

Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response.

Higgins GA, Allyn-Feuer A, Athey BD.

Pharmacogenomics. 2015;16(14):1565-83. doi: 10.2217/pgs.15.105. Epub 2015 Sep 4.

14.

The chromatin accessibility landscape of primary human cancers.

Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY.

Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898.

15.

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

Freire-Pritchett P, Schoenfelder S, Várnai C, Wingett SW, Cairns J, Collier AJ, García-Vílchez R, Furlan-Magaril M, Osborne CS, Fraser P, Rugg-Gunn PJ, Spivakov M.

Elife. 2017 Mar 23;6. pii: e21926. doi: 10.7554/eLife.21926.

16.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.

Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.

17.

HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants.

Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M.

BMC Res Notes. 2016 Mar 11;9:159. doi: 10.1186/s13104-016-1947-0.

18.

An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

Zhao J, Cheng F, Jia P, Cox N, Denny JC, Zhao Z.

Genome Med. 2018 Jan 29;10(1):7. doi: 10.1186/s13073-018-0513-x.

19.

Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.

Paul DS, Albers CA, Rendon A, Voss K, Stephens J; HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P.

Genome Res. 2013 Jul;23(7):1130-41. doi: 10.1101/gr.155127.113. Epub 2013 Apr 9.

20.

Chromatin interaction maps reveal genetic regulation for quantitative traits in maize.

Peng Y, Xiong D, Zhao L, Ouyang W, Wang S, Sun J, Zhang Q, Guan P, Xie L, Li W, Li G, Yan J, Li X.

Nat Commun. 2019 Jun 14;10(1):2632. doi: 10.1038/s41467-019-10602-5.

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