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Genomic control of transcription in the brain

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Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A. Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet. 2014 Sep 4;10(9):e1004610. PMID: 25188404. 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. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun;24(6):920-9. PMID: 24752179 Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio LA, Puelles L, Visel A, Rubenstein JL. Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron. 2014 Jun 4;82(5):989-1003. PMID: 24814534 Dickel, DE, Zhu Y, Nord AS, Wylie J, Akiyama JA, Plajzer-Frick I, Bruneau BG, Cisel A, Pennacchio LA. Function-based Identification of Mammalian Enhancers. Nat Methods 2014 May;11(5):566-71. PMID: 24658141 Nord AS, Lee M, King MC, Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics. 2011 Apr 12;12:184. PMCID: PMC3088570 Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JLR, Rubin EM, Pennacchio LA, Visel A. Rapid and Pervasive Changes in Genome-Wide Enhancer Usage During Mammalian Development. Cell. 2013. Dec 19;155(7): 1521-31 PMID: 24360275 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. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013. Oct 25;342(6157):1241006. PMID: 24159046 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. A high-resolution enhancer atlas of the developing telencephalon. Cell. 2013 Feb 14;152(4):895-908. PMCID: PMC3660042 Nord AS, Roeb W, Dickel DE, Walsh T, Kusenda M, O'Connor KL, Malhotra D, McCarthy SE, Stray SM, Taylor SM, Sebat J; STAART Psychopharmacology Network, King B, King MC, McClellan JM. Reduced transcript expression of genes affected by inherited and de novo CNVs in autism. Eur J Hum Genet. 2011 Jun;19(6):727-31. PMCID: PMC3110052 Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008 Apr 25;320(5875):539-43. PMID: 18369103 Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007 Jul 18;2(7):e617. PMCID: PMC1910612 Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D642-8. PMCID: PMC1347459

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