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  • Willsey et al 2013

Oran AR, Adams CM, Zhang X-Y, Gennaro VJ, Pfeiffer HK, Mellert HS, Seidel H, Masicoli K, Kaplan J, Gaballa M, Shen C, Rigoutsos I, King M, Cotney J, et al. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget. Impact Journals; 2016 Aug 31;7(45):72395–414.

Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, et al. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nature Communications. 2015;6:6404.

Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, et al. Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science. 2015 Mar 6;347(6226):1155–9.

Cotney JL, Noonan JP. Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harb Protoc. Cold Spring Harbor Laboratory Press; 2015;2015(2):pdb.prot084848.

Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, (16 additional authors), Noonan JP, Roeder K, Devlin B, Sestan N, State MW. (2013). Co-expression networks implicate human mid-fetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 1008-1021.

Cotney, J.*, Leng, J.*, Yin, J., Reilly, S.K., Demare, L.E., Emera, D., Ayoub, A.E., Rakic, P., and Noonan, J.P. (2013). The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 154, 185–196.

Commentary in Nature News & Views: Flicek, P. (2013) Evolutionary biology: The handiwork of tinkering. Nature 500: 158-159.

Demare, L.E., Leng, J., Cotney, J., Reilly, S.K., Yin, J., Sarro, R., and Noonan, J.P. (2013). The genomic landscape of cohesin-associated chromatin interactions. Genome Res 23, 1224–1234.

Clark VE, Erson-Omay EZ, Serin A, Yin J, Cotney J, Ozduman K, Avşar T, Li J, Murray PB, Henegariu O, et al. 2013. Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science 339: 1077–1080.

Bandyopadhyay U*, Cotney J*, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL. 2013. RNA-Seq Profiling of Spinal Cord Motor Neurons from a Presymptomatic SOD1 ALS Mouse. PLoS ONE 8: e53575.

Cotney J, Leng J, Oh S, Demare LE, Reilly SK, Gerstein MB, and Noonan JP. 2012. Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res 22: 1069–1080.

Raimundo N, Song L, Shutt TE, McKay SE, Cotney J, Guan M-X, Gilliland TC, Hohuan D, Santos-Sacchi J, and Shadel GS. 2012. Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness. Cell 148: 716–726.

Surovtseva YV, Shutt TE, Cotney J, Cimen H, Chen SY, Koc EC, and Shadel GS. 2011. Mitochondrial ribosomal protein L12 selectively associates with human mitochondrial RNA polymerase to activate transcription. Proc Natl Acad Sci USA 108: 17921–17926.

Ayoub AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, and Rakic P. 2011. Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing. Proc Natl Acad Sci USA 108: 14950–14955.

Shutt TE, Lodeiro MF, Cotney J, Cameron CE, and Shadel GS. 2010. Core human mitochondrial transcription apparatus is a regulated two-component system in vitro. Proc Natl Acad Sci USA 107: 12133–12138.

Cotney J, McKay SE, and Shadel GS. 2009. 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. Hum Mol Genet 18: 2670–2682.

Cotney J, Wang Z, and Shadel GS. 2007. Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression. Nucleic Acids Res 35: 4042–4054.

Wang Z, Cotney J, and Shadel GS. 2007. Human mitochondrial ribosomal protein MRPL12 interacts directly with mitochondrial RNA polymerase to modulate mitochondrial gene expression. J Biol Chem 282: 12610–12618.

Cotney J, and Shadel GS. 2006. 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. J Mol Evol 63: 707–717.

Pezzementi L, Johnson K, Cotney J, Barker A, and Manning E. Amino acids involved in substrate and inhibitor specificity in cholinesterase 2 from amphioxus. Cholinesterases in the Second Millennium: Biomolecular and Pathological Aspects, (N.C. Inestrosa and E.O. Campos, eds.), 2004. MIFAB: Santiago, Chile, pp. 223-224.

Pezzementi L, Johnson K, Tsigelny I, Cotney J, Manning E, Barker A, and Merritt S. 2003. Amino acids defining the acyl pocket of an invertebrate cholinesterase. Comp. Biochem. Physiol. B, Biochem. Mol. Biol. 136: 813–832.

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