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Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer.Oran, Amanda R; Adams, Clare M; Zhang, Xiao-Yong; Gennaro, Victoria J; Pfeiffer, Harla K; Mellert, Hestia S; Seidel, Hans E; Mascioli, Kirsten; Kaplan, Jordan; Gaballa, Mahmoud R; Shen, Chen; Rigoutsos, Isidore; King, Michael P; Cotney, Justin L; Arnold, Jamie J; Sharma, Suresh D; Martinez-Outschoorn, Ubaldo E; Vakoc, Christopher R; Chodosh, Lewis A; Thompson, James E; Bradner, James E; Cameron, Craig E; Shadel, Gerald S; Eischen, Christine M; McMahon, Steven B Oncotarget 2016 Aug;
Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.Cotney, Justin L; Noonan, James P Cold Spring Harbor protocols 2015 Apr;2015(4):419
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.Cotney, Justin; Muhle, Rebecca A; Sanders, Stephan J; Liu, Li; Willsey, A Jeremy; Niu, Wei; Liu, Wenzhong; Klei, Lambertus; Lei, Jing; Yin, Jun; Reilly, Steven K; Tebbenkamp, Andrew T; Bichsel, Candace; Pletikos, Mihovil; Sestan, Nenad; Roeder, Kathryn; State, Matthew W; Devlin, Bernie; Noonan, James P Nature communications 2015 Mar;66404
Evolutionary changes in promoter and enhancer activity during human corticogenesis.Reilly, Steven K; Yin, Jun; Ayoub, Albert E; Emera, Deena; Leng, Jing; Cotney, Justin; Sarro, Richard; Rakic, Pasko; Noonan, James P Science (New York, N.Y.) 2015 Mar;347(6226):1155-9
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.Willsey, A Jeremy; Sanders, Stephan J; Li, Mingfeng; Dong, Shan; Tebbenkamp, Andrew T; Muhle, Rebecca A; Reilly, Steven K; Lin, Leon; Fertuzinhos, Sofia; Miller, Jeremy A; Murtha, Michael T; Bichsel, Candace; Niu, Wei; Cotney, Justin; Ercan-Sencicek, A Gulhan; Gockley, Jake; Gupta, Abha R; Han, Wenqi; He, Xin; Hoffman, Ellen J; Klei, Lambertus; Lei, Jing; Liu, Wenzhong; Liu, Li; Lu, Cong; Xu, Xuming; Zhu, Ying; Mane, Shrikant M; Lein, Ed S; Wei, Liping; Noonan, James P; Roeder, Kathryn; Devlin, Bernie; Sestan, Nenad; State, Matthew W Cell 2013 Nov;155(5):997-1007
The genomic landscape of cohesin-associated chromatin interactions.DeMare, Laura E; Leng, Jing; Cotney, Justin; Reilly, Steven K; Yin, Jun; Sarro, Richard; Noonan, James P Genome research 2013 Aug;23(8):1224-34
The evolution of lineage-specific regulatory activities in the human embryonic limb.Cotney, Justin; Leng, Jing; Yin, Jun; Reilly, Steven K; DeMare, Laura E; Emera, Deena; Ayoub, Albert E; Rakic, Pasko; Noonan, James P Cell 2013 Jul;154(1):185-96
Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO.Clark, Victoria E; Erson-Omay, E Zeynep; Serin, Akdes; Yin, Jun; Cotney, Justin; Ozduman, Koray; Avsar, Timu?in; Li, Jie; Murray, Phillip B; Henegariu, Octavian; Yilmaz, Saliha; Günel, Jennifer Moliterno; Carrión-Grant, Geneive; Yilmaz, Baran; Grady, Conor; Tanrikulu, Bahattin; Bakircioglu, Mehmet; Kaymak?alan, Hande; Caglayan, Ahmet Okay; Sencar, Leman; Ceyhun, Emre; Atik, A Fatih; Bayri, Yasar; Bai, Hanwen; Kolb, Luis E; Hebert, Ryan M; Omay, S Bulent; Mishra-Gorur, Ketu; Choi, Murim; Overton, John D; Holland, Eric C; Mane, Shrikant; State, Matthew W; Bilgüvar, Kaya; Baehring, Joachim M; Gutin, Philip H; Piepmeier, Joseph M; Vortmeyer, Alexander; Brennan, Cameron W; Pamir, M Necmettin; Kili?, Türker; Lifton, Richard P; Noonan, James P; Yasuno, Katsuhito; Günel, Murat Science (New York, N.Y.) 2013 Mar;339(6123):1077-80
RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse.Bandyopadhyay, Urmi; Cotney, Justin; Nagy, Maria; Oh, Sunghee; Leng, Jing; Mahajan, Milind; Mane, Shrikant; Fenton, Wayne A; Noonan, James P; Horwich, Arthur L PloS one 2013 Jan;8(1):e53575
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.Cotney, Justin; Leng, Jing; Oh, Sunghee; DeMare, Laura E; Reilly, Steven K; Gerstein, Mark B; Noonan, James P Genome research 2012 Jun;22(6):1069-80
Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness.Raimundo, Nuno; Song, Lei; Shutt, Timothy E; McKay, Sharen E; Cotney, Justin; Guan, Min-Xin; Gilliland, Thomas C; Hohuan, David; Santos-Sacchi, Joseph; Shadel, Gerald S Cell 2012 Feb;148(4):716-26
Mitochondrial ribosomal protein L12 selectively associates with human mitochondrial RNA polymerase to activate transcription.Surovtseva, Yulia V; Shutt, Timothy E; Cotney, Justin; Cimen, Huseyin; Chen, Sophia Y; Koc, Emine C; Shadel, Gerald S Proceedings of the National Academy of Sciences of the United States of America 2011 Nov;108(44):17921-6
Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing.Ayoub, Albert E; Oh, Sunghee; Xie, Yanhua; Leng, Jing; Cotney, Justin; Dominguez, Martin H; Noonan, James P; Rakic, Pasko Proceedings of the National Academy of Sciences of the United States of America 2011 Sep;108(36):14950-5
Core human mitochondrial transcription apparatus is a regulated two-component system in vitro.Shutt, Timothy E; Lodeiro, Maria F; Cotney, Justin; Cameron, Craig E; Shadel, Gerald S Proceedings of the National Academy of Sciences of the United States of America 2010 Jul;107(27):12133-8
Elucidation of separate, but collaborative functions of the rRNA methyltransferase-related human mitochondrial transcription factors B1 and B2 in mitochondrial biogenesis reveals new insight into maternally inherited deafness.Cotney, Justin; McKay, Sharen E; Shadel, Gerald S Human molecular genetics 2009 Jul;18(14):2670-82
Human mitochondrial ribosomal protein MRPL12 interacts directly with mitochondrial RNA polymerase to modulate mitochondrial gene expression.Wang, Zhibo; Cotney, Justin; Shadel, Gerald S The Journal of biological chemistry 2007 Apr;282(17):12610-8
Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression.Cotney, Justin; Wang, Zhibo; Shadel, Gerald S Nucleic acids research 2007 Jan;35(12):4042-54
Evidence for an early gene duplication event in the evolution of the mitochondrial transcription factor B family and maintenance of rRNA methyltransferase activity in human mtTFB1 and mtTFB2.Cotney, Justin; Shadel, Gerald S Journal of molecular evolution 2006 Nov;63(5):707-17
Amino acids defining the acyl pocket of an invertebrate cholinesterase.Pezzementi, Leo; Johnson, Kimberly; Tsigelny, Igor; Cotney, Justin; Manning, Elizabeth; Barker, Andrew; Merritt, Sarah Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 2003 Dec;136(4):813-32
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