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Items: 1 to 50 of 58

1.

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.

El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, Kieffer-Kwon P, Kieffer-Kwon KR, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang SC, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nóbrega MA, Aiden EL, Asturias FJ, Casellas R.

Cell. 2019 Aug 22;178(5):1145-1158.e20. doi: 10.1016/j.cell.2019.07.011. Epub 2019 Aug 8.

PMID:
31402173
2.

Gene therapy for pathologic gene expression.

Montefiori LE, Nobrega MA.

Science. 2019 Jan 18;363(6424):231-232. doi: 10.1126/science.aaw0635. No abstract available.

PMID:
30655431
3.

A promoter interaction map for cardiovascular disease genetics.

Montefiori LE, Sobreira DR, Sakabe NJ, Aneas I, Joslin AC, Hansen GT, Bozek G, Moskowitz IP, McNally EM, Nóbrega MA.

Elife. 2018 Jul 10;7. pii: e35788. doi: 10.7554/eLife.35788.

4.

Tbx20 Is Required in Mid-Gestation Cardiomyocytes and Plays a Central Role in Atrial Development.

Boogerd CJ, Zhu X, Aneas I, Sakabe N, Zhang L, Sobreira DR, Montefiori L, Bogomolovas J, Joslin AC, Zhou B, Chen J, Nobrega MA, Evans SM.

Circ Res. 2018 Aug 3;123(4):428-442. doi: 10.1161/CIRCRESAHA.118.311339.

5.

DNA methylation in lung cells is associated with asthma endotypes and genetic risk.

Nicodemus-Johnson J, Myers RA, Sakabe NJ, Sobreira DR, Hogarth DK, Naureckas ET, Sperling AI, Solway J, White SR, Nobrega MA, Nicolae DL, Gilad Y, Ober C.

JCI Insight. 2016 Dec 8;1(20):e90151. doi: 10.1172/jci.insight.90151.

6.

Editorial.

Nóbrega MA, Gómez-Skarmeta JL.

Semin Cell Dev Biol. 2016 Sep;57:1. doi: 10.1016/j.semcdb.2016.07.023. No abstract available.

PMID:
27499506
7.

Probing chromatin landscape reveals roles of endocardial TBX20 in septation.

Boogerd CJ, Aneas I, Sakabe N, Dirschinger RJ, Cheng QJ, Zhou B, Chen J, Nobrega MA, Evans SM.

J Clin Invest. 2016 Aug 1;126(8):3023-35. doi: 10.1172/JCI85350. Epub 2016 Jun 27.

8.

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

Gómez-Marín C, Tena JJ, Acemel RD, López-Mayorga M, Naranjo S, de la Calle-Mustienes E, Maeso I, Beccari L, Aneas I, Vielmas E, Bovolenta P, Nobrega MA, Carvajal J, Gómez-Skarmeta JL.

Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7542-7. doi: 10.1073/pnas.1505463112. Epub 2015 Jun 1.

9.

HIF1α Represses Cell Stress Pathways to Allow Proliferation of Hypoxic Fetal Cardiomyocytes.

Guimarães-Camboa N, Stowe J, Aneas I, Sakabe N, Cattaneo P, Henderson L, Kilberg MS, Johnson RS, Chen J, McCulloch AD, Nobrega MA, Evans SM, Zambon AC.

Dev Cell. 2015 Jun 8;33(5):507-21. doi: 10.1016/j.devcel.2015.04.021. Epub 2015 May 28.

10.

Targeted Germline Modifications in Rats Using CRISPR/Cas9 and Spermatogonial Stem Cells.

Chapman KM, Medrano GA, Jaichander P, Chaudhary J, Waits AE, Nobrega MA, Hotaling JM, Ober C, Hamra FK.

Cell Rep. 2015 Mar 24;10(11):1828-35. doi: 10.1016/j.celrep.2015.02.040. Epub 2015 Mar 12.

11.

Early-life physical activity reverses metabolic and Foxo1 epigenetic misregulation induced by gestational sleep disturbance.

Mutskov V, Khalyfa A, Wang Y, Carreras A, Nobrega MA, Gozal D.

Am J Physiol Regul Integr Comp Physiol. 2015 Mar 1;308(5):R419-30. doi: 10.1152/ajpregu.00426.2014. Epub 2015 Jan 7.

12.

Evidence of non-pancreatic beta cell-dependent roles of Tcf7l2 in the regulation of glucose metabolism in mice.

Bailey KA, Savic D, Zielinski M, Park SY, Wang LJ, Witkowski P, Brady M, Hara M, Bell GI, Nobrega MA.

Hum Mol Genet. 2015 Mar 15;24(6):1646-54. doi: 10.1093/hmg/ddu577. Epub 2014 Nov 14.

13.

Obesity-associated variants within FTO form long-range functional connections with IRX3.

Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gómez-Marín C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF, Lee JH, Puviindran V, Tam D, Shen M, Son JE, Vakili NA, Sung HK, Naranjo S, Acemel RD, Manzanares M, Nagy A, Cox NJ, Hui CC, Gomez-Skarmeta JL, Nóbrega MA.

Nature. 2014 Mar 20;507(7492):371-5. doi: 10.1038/nature13138. Epub 2014 Mar 12.

14.

A common genetic variant within SCN10A modulates cardiac SCN5A expression.

van den Boogaard M, Smemo S, Burnicka-Turek O, Arnolds DE, van de Werken HJ, Klous P, McKean D, Muehlschlegel JD, Moosmann J, Toka O, Yang XH, Koopmann TT, Adriaens ME, Bezzina CR, de Laat W, Seidman C, Seidman JG, Christoffels VM, Nobrega MA, Barnett P, Moskowitz IP.

J Clin Invest. 2014 Apr;124(4):1844-52. doi: 10.1172/JCI73140. Epub 2014 Mar 18.

15.

PU.1 is essential for MLL leukemia partially via crosstalk with the MEIS/HOX pathway.

Zhou J, Wu J, Li B, Liu D, Yu J, Yan X, Zheng S, Wang J, Zhang L, Zhang L, He F, Li Q, Chen A, Zhang Y, Zhao X, Guan Y, Zhao X, Yan J, Ni J, Nobrega MA, Löwenberg B, Delwel R, Valk PJ, Kumar A, Xie L, Tenen DG, Huang G, Wang QF.

Leukemia. 2014 Jul;28(7):1436-48. doi: 10.1038/leu.2013.384. Epub 2013 Dec 26.

16.

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution.

Sakabe NJ, Nobrega MA.

Philos Trans R Soc Lond B Biol Sci. 2013 Nov 11;368(1632):20130022. doi: 10.1098/rstb.2013.0022. Print 2013 Dec 19. Review.

17.

Regulation of MEIS1 by distal enhancer elements in acute leukemia.

Wang QF, Li YJ, Dong JF, Li B, Kaberlein JJ, Zhang L, Arimura FE, Luo RT, Ni J, He F, Wu J, Mattison R, Zhou J, Wang CZ, Prabhakar S, Nobrega MA, Thirman MJ.

Leukemia. 2014 Jan;28(1):138-46. doi: 10.1038/leu.2013.260. Epub 2013 Sep 11.

18.

Effects of unilateral stereotactic posterior striatotomy on harmaline-induced tremor in rats.

Vilela-Filho O, Ferraz FP, Barros BA, Silva LO, Anunciação SF, Souza JT, Silva DJ, Leite MB, Atayde IB, Ragazzo PC, Barreto PG, Nobrega MA, Araujo MR, Santos MR, Ala VH, Queiroz ST.

J Neurosci Res. 2013 Oct;91(10):1328-37. doi: 10.1002/jnr.23249. Epub 2013 Jul 19.

PMID:
23873746
19.

FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA.

Fu Y, Jia G, Pang X, Wang RN, Wang X, Li CJ, Smemo S, Dai Q, Bailey KA, Nobrega MA, Han KL, Cui Q, He C.

Nat Commun. 2013;4:1798. doi: 10.1038/ncomms2822.

20.

Enhancers: five essential questions.

Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G.

Nat Rev Genet. 2013 Apr;14(4):288-95. doi: 10.1038/nrg3458. Review.

21.

TCF7L2 and glucose metabolism: time to look beyond the pancreas.

Nobrega MA.

Diabetes. 2013 Mar;62(3):706-8. doi: 10.2337/db12-1418. No abstract available.

22.

In vitro scan for enhancers at the TCF7L2 locus.

Savic D, Park SY, Bailey KA, Bell GI, Nobrega MA.

Diabetologia. 2013 Jan;56(1):121-5. doi: 10.1007/s00125-012-2730-y. Epub 2012 Sep 26.

23.

TBX5 drives Scn5a expression to regulate cardiac conduction system function.

Arnolds DE, Liu F, Fahrenbach JP, Kim GH, Schillinger KJ, Smemo S, McNally EM, Nobrega MA, Patel VV, Moskowitz IP.

J Clin Invest. 2012 Jul;122(7):2509-18. doi: 10.1172/JCI62617. Epub 2012 Jun 25.

24.

An in vivo cis-regulatory screen at the type 2 diabetes associated TCF7L2 locus identifies multiple tissue-specific enhancers.

Savic D, Bell GI, Nobrega MA.

PLoS One. 2012;7(5):e36501. doi: 10.1371/journal.pone.0036501. Epub 2012 May 10.

25.

Glyoxalase 1 increases anxiety by reducing GABAA receptor agonist methylglyoxal.

Distler MG, Plant LD, Sokoloff G, Hawk AJ, Aneas I, Wuenschell GE, Termini J, Meredith SC, Nobrega MA, Palmer AA.

J Clin Invest. 2012 Jun;122(6):2306-15. doi: 10.1172/JCI61319. Epub 2012 May 15.

26.

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease.

Smemo S, Campos LC, Moskowitz IP, Krieger JE, Pereira AC, Nobrega MA.

Hum Mol Genet. 2012 Jul 15;21(14):3255-63. doi: 10.1093/hmg/dds165. Epub 2012 Apr 27.

27.

A fine-scale chimpanzee genetic map from population sequencing.

Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, Street T, Leffler EM, Bowden R, Aneas I, Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G.

Science. 2012 Apr 13;336(6078):193-8. doi: 10.1126/science.1216872. Epub 2012 Mar 15.

28.

Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.

Sakabe NJ, Aneas I, Shen T, Shokri L, Park SY, Bulyk ML, Evans SM, Nobrega MA.

Hum Mol Genet. 2012 May 15;21(10):2194-204. doi: 10.1093/hmg/dds034. Epub 2012 Feb 10.

29.

Transcriptional enhancers in development and disease.

Sakabe NJ, Savic D, Nobrega MA.

Genome Biol. 2012 Jan 23;13(1):238. doi: 10.1186/gb-2012-13-1-238.

30.

Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function.

Shen T, Aneas I, Sakabe N, Dirschinger RJ, Wang G, Smemo S, Westlund JM, Cheng H, Dalton N, Gu Y, Boogerd CJ, Cai CL, Peterson K, Chen J, Nobrega MA, Evans SM.

J Clin Invest. 2011 Dec;121(12):4640-54. doi: 10.1172/JCI59472. Epub 2011 Nov 14.

31.

Modulation ofTcf7l2 expression alters behavior in mice.

Savic D, Distler MG, Sokoloff G, Shanahan NA, Dulawa SC, Palmer AA, Nobrega MA.

PLoS One. 2011;6(10):e26897. doi: 10.1371/journal.pone.0026897. Epub 2011 Oct 27.

32.

Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature.

Schneider I, Aneas I, Gehrke AR, Dahn RD, Nobrega MA, Shubin NH.

Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12782-6. doi: 10.1073/pnas.1109993108. Epub 2011 Jul 15.

33.

Alterations in TCF7L2 expression define its role as a key regulator of glucose metabolism.

Savic D, Ye H, Aneas I, Park SY, Bell GI, Nobrega MA.

Genome Res. 2011 Sep;21(9):1417-25. doi: 10.1101/gr.123745.111. Epub 2011 Jun 14.

34.

Genome-wide identification of conserved regulatory function in diverged sequences.

Taher L, McGaughey DM, Maragh S, Aneas I, Bessling SL, Miller W, Nobrega MA, McCallion AS, Ovcharenko I.

Genome Res. 2011 Jul;21(7):1139-49. doi: 10.1101/gr.119016.110. Epub 2011 May 31.

35.

The emerging genetic landscape underlying cardiac conduction system function.

Arnolds DE, Chu A, McNally EM, Nobrega MA, Moskowitz IP.

Birth Defects Res A Clin Mol Teratol. 2011 Jun;91(6):578-85. doi: 10.1002/bdra.20800. Epub 2011 Apr 28. Review.

36.

Genome-wide maps of transcription regulatory elements.

Sakabe NJ, Nobrega MA.

Wiley Interdiscip Rev Syst Biol Med. 2010 Jul-Aug;2(4):422-437. doi: 10.1002/wsbm.70. Review.

PMID:
20836039
37.

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer.

Wasserman NF, Aneas I, Nobrega MA.

Genome Res. 2010 Sep;20(9):1191-7. doi: 10.1101/gr.105361.110. Epub 2010 Jul 13.

38.

Journal club. A human geneticist explores the ways that genes are regulated.

Nobrega MA.

Nature. 2010 Jul 1;466(7302):11. doi: 10.1038/466011e. No abstract available.

PMID:
20595974
39.

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.

Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I.

Genome Res. 2010 May;20(5):565-77. doi: 10.1101/gr.104471.109. Epub 2010 Apr 2.

40.

Genome-wide discovery of human heart enhancers.

Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.

Genome Res. 2010 Mar;20(3):381-92. doi: 10.1101/gr.098657.109. Epub 2010 Jan 14.

41.

Distinct genetic regulation of progression of diabetes and renal disease in the Goto-Kakizaki rat.

Nobrega MA, Solberg Woods LC, Fleming S, Jacob HJ.

Physiol Genomics. 2009 Sep 9;39(1):38-46. doi: 10.1152/physiolgenomics.90389.2008. Epub 2009 Jul 7.

PMID:
19584172
42.

Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome.

van Bon BW, Mefford HC, Menten B, Koolen DA, Sharp AJ, Nillesen WM, Innis JW, de Ravel TJ, Mercer CL, Fichera M, Stewart H, Connell LE, Ounap K, Lachlan K, Castle B, Van der Aa N, van Ravenswaaij C, Nobrega MA, Serra-Juhé C, Simonic I, de Leeuw N, Pfundt R, Bongers EM, Baker C, Finnemore P, Huang S, Maloney VK, Crolla JA, van Kalmthout M, Elia M, Vandeweyer G, Fryns JP, Janssens S, Foulds N, Reitano S, Smith K, Parkel S, Loeys B, Woods CG, Oostra A, Speleman F, Pereira AC, Kurg A, Willatt L, Knight SJ, Vermeesch JR, Romano C, Barber JC, Mortier G, Pérez-Jurado LA, Kooy F, Brunner HG, Eichler EE, Kleefstra T, de Vries BB.

J Med Genet. 2009 Aug;46(8):511-23. doi: 10.1136/jmg.2008.063412. Epub 2009 Apr 15.

43.

A molecular pathway including Id2, Tbx5, and Nkx2-5 required for cardiac conduction system development.

Moskowitz IP, Kim JB, Moore ML, Wolf CM, Peterson MA, Shendure J, Nobrega MA, Yokota Y, Berul C, Izumo S, Seidman JG, Seidman CE.

Cell. 2007 Jun 29;129(7):1365-76.

44.

Predicting tissue-specific enhancers in the human genome.

Pennacchio LA, Loots GG, Nobrega MA, Ovcharenko I.

Genome Res. 2007 Feb;17(2):201-11. Epub 2007 Jan 8.

45.

In vivo enhancer analysis of human conserved non-coding sequences.

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM.

Nature. 2006 Nov 23;444(7118):499-502. Epub 2006 Nov 5.

PMID:
17086198
46.

Identifying synonymous regulatory elements in vertebrate genomes.

Ovcharenko I, Nobrega MA.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W403-7.

47.

In vivo characterization of a vertebrate ultraconserved enhancer.

Poulin F, Nobrega MA, Plajzer-Frick I, Holt A, Afzal V, Rubin EM, Pennacchio LA.

Genomics. 2005 Jun;85(6):774-81. Epub 2005 Apr 15.

PMID:
15885503
48.

Evolution and functional classification of vertebrate gene deserts.

Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W, Stubbs L.

Genome Res. 2005 Jan;15(1):137-45. Epub 2004 Dec 8.

49.

Megabase deletions of gene deserts result in viable mice.

Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM.

Nature. 2004 Oct 21;431(7011):988-93.

PMID:
15496924
50.

Exploiting human--fish genome comparisons for deciphering gene regulation.

Ahituv N, Rubin EM, Nobrega MA.

Hum Mol Genet. 2004 Oct 1;13 Spec No 2:R261-6. Review.

PMID:
15358733

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