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Items: 23

1.

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.

McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, McCallion AS.

Am J Hum Genet. 2018 Dec 6;103(6):874-892. doi: 10.1016/j.ajhg.2018.10.018. Epub 2018 Nov 29.

PMID:
30503521
2.

Enhancer redundancy provides phenotypic robustness in mammalian development.

Osterwalder M, Barozzi I, Tissières V, Fukuda-Yuzawa Y, Mannion BJ, Afzal SY, Lee EA, Zhu Y, Plajzer-Frick I, Pickle CS, Kato M, Garvin TH, Pham QT, Harrington AN, Akiyama JA, Afzal V, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA.

Nature. 2018 Feb 8;554(7691):239-243. doi: 10.1038/nature25461. Epub 2018 Jan 31.

3.

Ultraconserved Enhancers Are Required for Normal Development.

Dickel DE, Ypsilanti AR, Pla R, Zhu Y, Barozzi I, Mannion BJ, Khin YS, Fukuda-Yuzawa Y, Plajzer-Frick I, Pickle CS, Lee EA, Harrington AN, Pham QT, Garvin TH, Kato M, Osterwalder M, Akiyama JA, Afzal V, Rubenstein JLR, Pennacchio LA, Visel A.

Cell. 2018 Jan 25;172(3):491-499.e15. doi: 10.1016/j.cell.2017.12.017. Epub 2018 Jan 18.

4.

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.

Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama JA, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio LA.

PLoS Comput Biol. 2017 Aug 21;13(8):e1005720. doi: 10.1371/journal.pcbi.1005720. eCollection 2017 Aug.

5.

HAND2 Target Gene Regulatory Networks Control Atrioventricular Canal and Cardiac Valve Development.

Laurent F, Girdziusaite A, Gamart J, Barozzi I, Osterwalder M, Akiyama JA, Lincoln J, Lopez-Rios J, Visel A, Zuniga A, Zeller R.

Cell Rep. 2017 May 23;19(8):1602-1613. doi: 10.1016/j.celrep.2017.05.004.

6.

Progressive Loss of Function in a Limb Enhancer during Snake Evolution.

Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio LA, Visel A.

Cell. 2016 Oct 20;167(3):633-642.e11. doi: 10.1016/j.cell.2016.09.028.

7.

Genome-wide compendium and functional assessment of in vivo heart enhancers.

Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio LA.

Nat Commun. 2016 Oct 5;7:12923. doi: 10.1038/ncomms12923.

8.

Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease.

Chatterjee S, Kapoor A, Akiyama JA, Auer DR, Lee D, Gabriel S, Berrios C, Pennacchio LA, Chakravarti A.

Cell. 2016 Oct 6;167(2):355-368.e10. doi: 10.1016/j.cell.2016.09.005. Epub 2016 Sep 29.

9.

A distal 594 bp ECR specifies Hmx1 expression in pinna and lateral facial morphogenesis and is regulated by the Hox-Pbx-Meis complex.

Rosin JM, Li W, Cox LL, Rolfe SM, Latorre V, Akiyama JA, Visel A, Kuramoto T, Bobola N, Turner EE, Cox TC.

Development. 2016 Jul 15;143(14):2582-92. doi: 10.1242/dev.133736. Epub 2016 Jun 10.

10.

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease.

He A, Gu F, Hu Y, Ma Q, Ye LY, Akiyama JA, Visel A, Pennacchio LA, Pu WT.

Nat Commun. 2014 Sep 24;5:4907. doi: 10.1038/ncomms5907.

11.

Tissue-specific RNA expression marks distant-acting developmental enhancers.

Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A.

PLoS Genet. 2014 Sep 4;10(9):e1004610. doi: 10.1371/journal.pgen.1004610. eCollection 2014 Sep.

12.

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.

Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA.

Genome Res. 2014 Jun;24(6):920-9. doi: 10.1101/gr.168930.113. Epub 2014 Apr 21.

13.

Function-based identification of mammalian enhancers using site-specific integration.

Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, Plajzer-Frick I, Kirkpatrick A, Göttgens B, Bruneau BG, Visel A, Pennacchio LA.

Nat Methods. 2014 May;11(5):566-71. doi: 10.1038/nmeth.2886. Epub 2014 Mar 23.

14.

Rapid and pervasive changes in genome-wide enhancer usage during mammalian development.

Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JL, Rubin EM, Pennacchio LA, Visel A.

Cell. 2013 Dec 19;155(7):1521-31. doi: 10.1016/j.cell.2013.11.033.

15.

Fine tuning of craniofacial morphology by distant-acting enhancers.

Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A.

Science. 2013 Oct 25;342(6157):1241006. doi: 10.1126/science.1241006.

16.

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants.

Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N; NISC Comparative Sequencing Program, Black BL, Visel A, Pennacchio LA, Collins FS; National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program Authors; NISC Comparative Sequencing Program Authors.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17921-6. doi: 10.1073/pnas.1317023110. Epub 2013 Oct 14.

17.

A high-resolution enhancer atlas of the developing telencephalon.

Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL.

Cell. 2013 Feb 14;152(4):895-908. doi: 10.1016/j.cell.2012.12.041. Epub 2013 Jan 31.

18.

Large-scale discovery of enhancers from human heart tissue.

May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA, Visel A.

Nat Genet. 2011 Dec 4;44(1):89-93. doi: 10.1038/ng.1006.

19.

ChIP-Seq identification of weakly conserved heart enhancers.

Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel A, Pennacchio LA.

Nat Genet. 2010 Sep;42(9):806-10. doi: 10.1038/ng.650. Epub 2010 Aug 22.

20.

Functional autonomy of distant-acting human enhancers.

Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA.

Genomics. 2009 Jun;93(6):509-13. doi: 10.1016/j.ygeno.2009.02.002. Epub 2009 Mar 5.

21.

ChIP-seq accurately predicts tissue-specific activity of enhancers.

Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA.

Nature. 2009 Feb 12;457(7231):854-8. doi: 10.1038/nature07730.

22.

Human-specific gain of function in a developmental enhancer.

Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP.

Science. 2008 Sep 5;321(5894):1346-50. doi: 10.1126/science.1159974.

23.

Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA.

Nat Genet. 2008 Feb;40(2):158-60. doi: 10.1038/ng.2007.55. Epub 2008 Jan 6.

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