Publications

2018

Blankvoort S, Witter MP, Noonan J, Cotney J, Kentros C. Marked diversity of unique cortical enhancers enables neuron-specific tools by Enhancer-Driven Gene Expression. Curr. Biol. 28(13):2103-2114 (2018). Article: 10.1016/j.cub.2018.05.015  Data: GSE112897

Liu Y, Cicek AE, Liang Y, Li J, Muhle RA, Krenzer M, Mei Y, Wang Y, Knoblauch N, Morrison J, Jiang Y, Geller E, Li Z, Ionita-Laza I, Wu J, Xia K, Noonan JP, Sun ZS, He X. A statistical framework for mapping risk genes from de novo mutations in whole-genome sequencing studies. Am. J. Hum. Genet. 102(6):1031-1047 (2018). Article: 10.1016/j.ajhg.2018.03.023

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. Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans. Mol. Microbiol. 108(5):473-494 (2018). Article: 10.1111/mmi.13960

Wilderman A, Kron J, VanOudenhove J, Noonan JP, Cotney J. High resolution epigenomic analysis of early human craniofacial development. Cell Rep. 23(5):1581-1597 (2018). Article: 10.1016/j.celrep.2018.03.129  Data: GSE97752

Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP. Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development. Development 145(7) pii: dev158550 (2018). Article: 10.1242/dev.158550  Data: PRJNA388175

2017

Stewart TA, Liang C, Cotney J, Noonan JP, Sanger T, Wagner G. Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings. bioRxiv 224147, December 5, 2017. Available from 10.1101/224147

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. Molecular and cellular reorganization of neural circuits in the human lineage. Science 358 (6366):1027-32 (2017). Article: 10.1126/science.aan3456

2016

Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Origin and evolution of developmental enhancers in the mammalian neocortex. Proc. Natl. Acad. Sci. USA 113(19):E2617-26 (2016). Article: 10.1073/pnas.1603718113  Data: phs001226.v1.p1  GSE63649  Analytical pipeline: https://github.com/yinjun111/emera2016pnas

Reilly SK, Noonan JP. Evolution of gene regulation in humans. Annu. Rev. Genomics Hum. Genet. 17:45-67 (2016). Article: 10.1146/annurev-genom-090314-045935

2015

Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP.  Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 347 (6226):1155-9 (2015). Article: 10.1126/science.1260943   Data: phs001226.v1.p1  GSE63649

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. 6:6404 (2015). Article: 10.1038/ncomms7404  Data: phs001226.v1.p1  GSE57369

Cotney J, Noonan JP.  Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harb. Protoc. 2015(4):419 (2015). Article: 10.1101/pdb.prot084848

2014

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 5(1):22 (2014). Article: 10.1186/2040-2392-5-22

2013

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 155(5):997-1007 (2013). Article: 10.1016/j.cell.2013.10.020

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. 5(10):1926-36 (2013). Article: 10.1093/gbe/evt144

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 154(1):185-96 (2013). Article: 10.1016/j.cell.2013.05.056  Data: phs001226.v1.p1  GSE42413  GSE42237

DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. The genomic landscape of cohesin-associated chromatin interactions. Genome Res. 23(8):1224-34 (2013). Article: 10.1101/gr.156570.113 Data: GSE42237

Oh S, Song S, Grabowski G, Zhao H, Noonan JP. Time series expression analyses using RNA-seq: a statistical approach. Biomed. Res. Int. 2013:203681 (2013). Article: 10.1155/2013/203681

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 339(6123):1077-80 (2013). Article: 10.1126/science.1233009

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 8(1):e53575 (2013). Article: 10.1371/journal.pone.0053575  Data: GSE38820

2012

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. 22(6):1069-80 (2012). Article: 10.1101/gr.129817.111  Data: GSE30641

2011

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. USA. 108(36):14950-5 (2011). Article: 10.1073/pnas.1112213108  Data: GSE30765

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. 24(3):311-20 (2011). Article: 10.1093/protein/gzq112

2010

Noonan JP. Neanderthal genomics and the evolution of modern humans. Genome Res. 20(5):547-53 (2010). Article: 10.1101/gr.076000.108

Sholtis SJ, Noonan JP. Gene regulation and the origins of human biological uniqueness. Trends Genet. 26(3):110-8 (2010). Article: 10.1016/j.tig.2009.12.009

Noonan JP, McCallion AS. Genomics of long-range regulatory elements. Annu. Rev. Genomics Hum. Genet. 11:1-23 (2010). Article: 10.1146/annurev-genom-082509-141651

2009

Noonan JP. Regulatory DNAs and the evolution of human development. Curr. Opin. Genet. Dev. 19(6): 557-64 (2009). Article: 10.1016/j.gde.2009.10.002

2008

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 321(5894):1346-50 (2008). Article: 10.1126/science.1159974

2006

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 314(5802):1113-8 (2006). Article: 10.1126/science.1131412  Data: PRJNA18311

Prabhakar S, Noonan JP, Pääbo S, Rubin EM. Accelerated evolution of conserved noncoding sequences in humans. Science 314(5800):786 (2006). Article: 10.1126/science.1130738

2005

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 309(5734):597-9 (2005). Article: 10.1126/science.1113485  Data: LIBGSS_009950