Publications

2024

Massively parallel disruption of enhancers active in human neural stem cells.Geller E, Noble MA, Morales M, Gockley J, Emera D, Uebbing S, Cotney JL, Noonan JP. Cell Rep. 2024 Feb 27; 2024 Jan 23. PMID: 38271204.
Evolutionary innovation in conserved regulatory elements across the mammalian tree of life.Uebbing S, Kocher AA, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan JP. bioRxiv. 2024 Jan 31; 2024 Jan 31. PMID: 38352419.

2023

CpG island turnover events predict evolutionary changes in enhancer activity.Kocher AA, Dutrow EV, Uebbing S, Yim KM, Larios MFR, Baumgartner M, Nottoli T, Noonan JP. bioRxiv. 2023 May 16; 2023 May 16. PMID: 37214934.
The functional and evolutionary impacts of human-specific deletions in conserved elements.Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK. Science. 2023 Apr 28; 2023 Apr 28. PMID: 37104592.
A systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension.Gunawardhana KL, Hong L, Rugira T, Uebbing S, Kucharczak J, Mehta S, Karunamuni DR, Cabera-Mendoza B, Gandotra N, Scharfe C, Polimanti R, Noonan JP, Mani A. J Clin Invest. 2023 Feb 15; 2023 Feb 15. PMID: 36602864.

2022

Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome.Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. Nat Commun. 2022 Jan 13; 2022 Jan 13. PMID: 35027568.

2021

Massively parallel discovery of human-specific substitutions that alter enhancer activity.Uebbing S, Gockley J, Reilly SK, Kocher AA, Geller E, Gandotra N, Scharfe C, Cotney J, Noonan JP. Proc Natl Acad Sci U S A. 2021 Jan 12. PMID: 33372131.

2019

Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings.Stewart TA, Liang C, Cotney JL, Noonan JP, Sanger TJ, Wagner GP. Nat Commun. 2019 Jul 19; 2019 Jul 19. PMID: 31324809.

2018

A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies.Liu Y, Liang Y, Cicek AE, Li Z, Li J, Muhle RA, Krenzer M, Mei Y, Wang Y, Knoblauch N, Morrison J, Zhao S, Jiang Y, Geller E, Ionita-Laza I, Wu J, Xia K, Noonan JP, Sun ZS, He X. Am J Hum Genet. 2018 Jun 7; 2018 May 10. PMID: 29754769.
Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans.Garcia-Santamarina S, Festa RA, Smith AD, Yu CH, Probst C, Ding C, Homer CM, Yin J, Noonan JP, Madhani H, Perfect JR, Thiele DJ. Mol Microbiol. 2018 Jun; 2018 Apr 24. PMID: 29608794.
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development.Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. Cell Rep. 2018 May 1. PMID: 29719267.
Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development.Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP. Development. 2018 Apr 9; 2018 Apr 9. PMID: 29549111.

2017

Molecular and cellular reorganization of neural circuits in the human lineage.Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Science. 2017 Nov 24. PMID: 29170230.

2016

Evolution of Gene Regulation in Humans.Reilly SK, Noonan JP. Annu Rev Genomics Hum Genet. 2016 Aug 31; 2016 Apr 21. PMID: 27147089.
Origin and evolution of developmental enhancers in the mammalian neocortex.Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Proc Natl Acad Sci U S A. 2016 May 10; 2016 Apr 25. PMID: 27114548.

2015

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.Cotney JL, Noonan JP. Cold Spring Harb Protoc. 2015 Apr 1; 2015 Apr 1. PMID: 25834253.
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.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. Nat Commun. 2015 Mar 10; 2015 Mar 10. PMID: 25752243.
Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP. Science. 2015 Mar 6. PMID: 25745175.
Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.Cotney JL, Noonan JP. Cold Spring Harb Protoc. 2015 Feb 2; 2015 Feb 2. PMID: 25646502.

2014

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics.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. Mol Autism. 2014 Mar 6; 2014 Mar 6. PMID: 24602502.

2013

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.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. Cell. 2013 Nov 21. PMID: 24267886.
The genomic landscape of cohesin-associated chromatin interactions.DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. Genome Res. 2013 Aug; 2013 May 23. PMID: 23704192.
The evolution of lineage-specific regulatory activities in the human embryonic limb.Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. Cell. 2013 Jul 3. PMID: 23827682.
Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO.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. Science. 2013 Mar 1; 2013 Jan 24. PMID: 23348505.
Genomic correlates of relationship QTL involved in fore- versus hind limb divergence in mice.Pavlicev M, Wagner GP, Noonan JP, Hallgrímsson B, Cheverud JM. Genome Biol Evol. 2013. PMID: 24065733.
Time series expression analyses using RNA-seq: a statistical approach.Oh S, Song S, Grabowski G, Zhao H, Noonan JP. Biomed Res Int. 2013; 2013 Mar 24. PMID: 23586021.
RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse.Bandyopadhyay U, Cotney J, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL. PLoS One. 2013; 2013 Jan 3. PMID: 23301088.

2012

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

2011

Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing.Ayoub AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, Rakic P. Proc Natl Acad Sci U S A. 2011 Sep 6; 2011 Aug 22. PMID: 21873192.
Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering.Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, Dimaio D. Protein Eng Des Sel. 2011 Mar; 2010 Dec 10. PMID: 21149273.

2010

Neanderthal genomics and the evolution of modern humans.Noonan JP. Genome Res. 2010 May. PMID: 20439435.
Gene regulation and the origins of human biological uniqueness.Sholtis SJ, Noonan JP. Trends Genet. 2010 Mar; 2010 Jan 26. PMID: 20106546.
Genomics of long-range regulatory elements.Noonan JP, McCallion AS. Annu Rev Genomics Hum Genet. 2010. PMID: 20438361.

2009

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

2008

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

2006

Sequencing and analysis of Neanderthal genomic DNA.Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM. Science. 2006 Nov 17. PMID: 17110569.
Accelerated evolution of conserved noncoding sequences in humans.Prabhakar S, Noonan JP, Pääbo S, Rubin EM. Science. 2006 Nov 3. PMID: 17082449.

2005

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

2004

Coelacanth genome sequence reveals the evolutionary history of vertebrate genes.Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM. Genome Res. 2004 Dec; 2004 Nov 15. PMID: 15545497.
The DNA sequence and comparative analysis of human chromosome 5.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. Nature. 2004 Sep 16. PMID: 15372022.
Gene conversion and the evolution of protocadherin gene cluster diversity.Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM. Genome Res. 2004 Mar. PMID: 14993203.

2003

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

2001

Comparative DNA sequence analysis of mouse and human protocadherin gene clusters.Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T. Genome Res. 2001 Mar. PMID: 11230163.
The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability.Yankiwski V, Noonan JP, Neff NF. BMC Cell Biol. 2001; 2001 Jul 2. PMID: 11472631.

1994

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

1992

Reducing the use of H2-receptor antagonists in the long-term-care setting.Gurwitz JH, Noonan JP, Soumerai SB. J Am Geriatr Soc. 1992 Apr. PMID: 1348256.
Barium enemas in the frail elderly.Gurwitz JH, Noonan JP, Sanchez M, Prather W. Am J Med. 1992 Jan. PMID: 1731508.

1982

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

1977

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

1975

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