James P. Noonan - Publications

Affiliations: 
Yale University, New Haven, CT 

34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Reilly SK, Noonan JP. Evolution of Gene Regulation in Humans. Annual Review of Genomics and Human Genetics. PMID 27147089 DOI: 10.1146/annurev-genom-090314-045935  0.56
2016 Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Origin and evolution of developmental enhancers in the mammalian neocortex. Proceedings of the National Academy of Sciences of the United States of America. PMID 27114548 DOI: 10.1073/pnas.1603718113  0.6
2015 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, ... ... Noonan JP, et al. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nature Communications. 6: 6404. PMID 25752243 DOI: 10.1038/ncomms7404  0.6
2015 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 (New York, N.Y.). 347: 1155-9. PMID 25745175 DOI: 10.1126/science.1260943  0.6
2015 Cotney JL, Noonan JP. Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing. Cold Spring Harbor Protocols. 2015: 191-9. PMID 25646502 DOI: 10.1101/pdb.prot084848  0.6
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, et al. DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. Molecular Autism. 5: 22. PMID 24602502 DOI: 10.1186/2040-2392-5-22  0.6
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, ... ... Noonan JP, et al. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell. 155: 997-1007. PMID 24267886 DOI: 10.1016/j.cell.2013.10.020  0.6
2013 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 Biology and Evolution. 5: 1926-36. PMID 24065733 DOI: 10.1093/gbe/evt144  0.6
2013 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: 185-96. PMID 23827682 DOI: 10.1016/j.cell.2013.05.056  0.6
2013 DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. The genomic landscape of cohesin-associated chromatin interactions. Genome Research. 23: 1224-34. PMID 23704192 DOI: 10.1101/gr.156570.113  0.6
2013 Oh S, Song S, Grabowski G, Zhao H, Noonan JP. Time series expression analyses using RNA-seq: a statistical approach. Biomed Research International. 2013: 203681. PMID 23586021 DOI: 10.1155/2013/203681  0.6
2013 Clark VE, Erson-Omay EZ, Serin A, Yin J, Cotney J, Ozduman K, AvÅŸar T, Li J, Murray PB, Henegariu O, Yilmaz S, Günel JM, Carrión-Grant G, Yilmaz B, Grady C, ... ... Noonan JP, et al. Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science (New York, N.Y.). 339: 1077-80. PMID 23348505 DOI: 10.1126/science.1233009  0.6
2013 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: e53575. PMID 23301088 DOI: 10.1371/journal.pone.0053575  0.6
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 Research. 22: 1069-80. PMID 22421546 DOI: 10.1101/gr.129817.111  0.6
2012 Oh S, Zhao H, Noonan JP. Time course RNA-seq: A potential avenue with somewhat different approach in tandem of differential analysis Proceedings - 2012 6th International Conference On Complex, Intelligent, and Software Intensive Systems, Cisis 2012. 580-587. DOI: 10.1109/CISIS.2012.204  0.6
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. Proceedings of the National Academy of Sciences of the United States of America. 108: 14950-5. PMID 21873192 DOI: 10.1073/pnas.1112213108  0.6
2011 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 Engineering, Design & Selection : Peds. 24: 311-20. PMID 21149273 DOI: 10.1093/protein/gzq112  0.6
2010 Noonan JP. Neanderthal genomics and the evolution of modern humans. Genome Research. 20: 547-53. PMID 20439435 DOI: 10.1101/gr.076000.108  0.6
2010 Noonan JP, McCallion AS. Genomics of long-range regulatory elements. Annual Review of Genomics and Human Genetics. 11: 1-23. PMID 20438361 DOI: 10.1146/annurev-genom-082509-141651  0.6
2010 Sholtis SJ, Noonan JP. Gene regulation and the origins of human biological uniqueness. Trends in Genetics : Tig. 26: 110-8. PMID 20106546 DOI: 10.1016/j.tig.2009.12.009  0.6
2009 Noonan JP. Regulatory DNAs and the evolution of human development. Current Opinion in Genetics & Development. 19: 557-64. PMID 19913404 DOI: 10.1016/j.gde.2009.10.002  0.6
2009 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. Response to comment on "human-specific gain of function in a developmental enhancer" Science. 323: 714d. DOI: 10.1126/science.1166571  0.6
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 (New York, N.Y.). 321: 1346-50. PMID 18772437 DOI: 10.1126/science.1159974  0.6
2007 Rubin EM, Noonan JP. Response [5] Science. 315: 1664. DOI: 10.1126/science.315.5819.1664  0.6
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 (New York, N.Y.). 314: 1113-8. PMID 17110569 DOI: 10.1126/science.1131412  0.6
2006 Prabhakar S, Noonan JP, Pääbo S, Rubin EM. Accelerated evolution of conserved noncoding sequences in humans. Science (New York, N.Y.). 314: 786. PMID 17082449 DOI: 10.1126/science.1130738  0.6
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 (New York, N.Y.). 309: 597-9. PMID 15933159 DOI: 10.1126/science.1113485  0.6
2004 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 Research. 14: 2397-405. PMID 15545497 DOI: 10.1101/gr.2972804  0.6
2004 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, ... ... Noonan JP, et al. The DNA sequence and comparative analysis of human chromosome 5. Nature. 431: 268-74. PMID 15372022 DOI: 10.1038/nature02919  0.6
2004 Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM. Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Research. 14: 354-66. PMID 14993203 DOI: 10.1101/gr.2133704  0.6
2003 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. American Journal of Human Genetics. 72: 621-35. PMID 12577201 DOI: 10.1086/368060  0.6
2001 Yankiwski V, Noonan JP, Neff NF. The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability. Bmc Cell Biology. 2: 11. PMID 11472631 DOI: 10.1186/1471-2121-2-11  0.6
2001 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 Research. 11: 389-404. PMID 11230163 DOI: 10.1101/gr.167301  0.6
1999 Neff NF, Ellis NA, Ye TZ, Noonan J, Huang K, Sanz M, Proytcheva M. The DNA helicase activity of BLM is necessary for the correction of the genomic instability of bloom syndrome cells. Molecular Biology of the Cell. 10: 665-76. PMID 10069810  0.6
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