Publications

Cotney JL, Noonan JP: Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harb Protoc. 2015 Apr 1; 2015 Apr 1. PMID: 25834253

Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP: The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun. 2015 Mar 10; 2015 Mar 10. PMID: 25752243

Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP: Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science. 2015 Mar 6. PMID: 25745175

Cotney JL, Noonan JP: Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harb Protoc. 2015 Feb 2; 2015 Feb 2. PMID: 25646502

Liu L, Lei J, Sanders SJ, Willsey AJ, Kou Y, Cicek AE, Klei L, Lu C, He X, Li M, Muhle RA, Ma'ayan A, Noonan JP, Sestan N, McFadden KA, State MW, Buxbaum JD, Devlin B, Roeder K: DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. Mol Autism. 2014 Mar 6; 2014 Mar 6. PMID: 24602502

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, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW: Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell. 2013 Nov 21. PMID: 24267886

DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP: The genomic landscape of cohesin-associated chromatin interactions. Genome Res. 2013 Aug; 2013 May 23. PMID: 23704192

Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP: The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell. 2013 Jul 3. PMID: 23827682

Clark VE, Erson-Omay EZ, Serin A, Yin J, Cotney J, Ozduman K, Avşar T, Li J, Murray PB, Henegariu O, Yilmaz S, Günel JM, Carrión-Grant G, Yilmaz B, Grady C, Tanrikulu B, Bakircioğlu M, Kaymakçalan H, Caglayan AO, Sencar L, Ceyhun E, Atik AF, Bayri Y, Bai H, Kolb LE, Hebert RM, Omay SB, Mishra-Gorur K, Choi M, Overton JD, Holland EC, Mane S, State MW, Bilgüvar K, Baehring JM, Gutin PH, Piepmeier JM, Vortmeyer A, Brennan CW, Pamir MN, Kiliç T, Lifton RP, Noonan JP, Yasuno K, Günel M: Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science. 2013 Mar 1; 2013 Jan 24. PMID: 23348505

Oh S, Song S, Grabowski G, Zhao H, Noonan JP: Time series expression analyses using RNA-seq: a statistical approach. Biomed Res Int. 2013; 2013 Mar 24. PMID: 23586021

Pavlicev M, Wagner GP, Noonan JP, Hallgrímsson B, Cheverud JM: Genomic correlates of relationship QTL involved in fore- versus hind limb divergence in mice. Genome Biol Evol. 2013. PMID: 24065733

Bandyopadhyay U, Cotney J, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL: RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse. PLoS One. 2013; 2013 Jan 3. PMID: 23301088

Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP: Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. Genome Res. 2012 Jun; 2012 Mar 15. PMID: 22421546

Ayoub AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, Rakic P: Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing. Proc Natl Acad Sci U S A. 2011 Sep 6; 2011 Aug 22. PMID: 21873192

Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, Dimaio D: Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering. Protein Eng Des Sel. 2011 Mar; 2010 Dec 10. PMID: 21149273

Noonan JP: Neanderthal genomics and the evolution of modern humans. Genome Res. 2010 May. PMID: 20439435

Sholtis SJ, Noonan JP: Gene regulation and the origins of human biological uniqueness. Trends Genet. 2010 Mar; 2010 Jan 26. PMID: 20106546

Noonan JP, McCallion AS: Genomics of long-range regulatory elements. Annu Rev Genomics Hum Genet. 2010. PMID: 20438361

Noonan JP: Regulatory DNAs and the evolution of human development. Curr Opin Genet Dev. 2009 Dec; 2009 Nov 11. PMID: 19913404

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: Human-specific gain of function in a developmental enhancer. Science. 2008 Sep 5. PMID: 18772437

Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM: Sequencing and analysis of Neanderthal genomic DNA. Science. 2006 Nov 17. PMID: 17110569

Prabhakar S, Noonan JP, Pääbo S, Rubin EM: Accelerated evolution of conserved noncoding sequences in humans. Science. 2006 Nov 3. PMID: 17082449

Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G, Krause J, Detter JC, Pääbo S, Rubin EM: Genomic sequencing of Pleistocene cave bears. Science. 2005 Jul 22; 2005 Jun 2. PMID: 15933159

Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM: Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res. 2004 Dec; 2004 Nov 15. PMID: 15545497

Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM: The DNA sequence and comparative analysis of human chromosome 5. Nature. 2004 Sep 16. PMID: 15372022

Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM: Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res. 2004 Mar. PMID: 14993203

Noonan JP, Li J, Nguyen L, Caoile C, Dickson M, Grimwood J, Schmutz J, Feldman MW, Myers RM: Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster. Am J Hum Genet. 2003 Mar; 2003 Feb 7. PMID: 12577201

Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T: Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Res. 2001 Mar. PMID: 11230163

Yankiwski V, Noonan JP, Neff NF: The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability. BMC Cell Biol. 2001; 2001 Jul 2. PMID: 11472631

Pickering TD, Gurwitz JH, Zaleznik D, Noonan JP, Avorn J: The appropriateness of oral fluoroquinolone-prescribing in the long-term care setting. J Am Geriatr Soc. 1994 Jan. PMID: 8277111

Gurwitz JH, Noonan JP, Soumerai SB: Reducing the use of H2-receptor antagonists in the long-term-care setting. J Am Geriatr Soc. 1992 Apr. PMID: 1348256

Gurwitz JH, Noonan JP, Sanchez M, Prather W: Barium enemas in the frail elderly. Am J Med. 1992 Jan. PMID: 1731508

Boucher RE, Noonan JP: Adaptive detection and removal of non-gaussian spikes from gaussian data. IEEE Trans Pattern Anal Mach Intell. 1982 Feb. PMID: 21869017

Noonan JP, Ananth J: Compulsive water drinking and water intoxication. Compr Psychiatry. 1977 Mar-Apr. PMID: 837668

Ananth J, Sangani H, Noonan JP: Amantadine in drug-induced extrapyramidal signs: a comparative study. Int J Clin Pharmacol Biopharm. 1975 Jun. PMID: 239908