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James P. Noonan - Publications

Affiliations: 
Yale University, New Haven, CT 
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44 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
2024 Geller E, Noble MA, Morales M, Gockley J, Emera D, Uebbing S, Cotney JL, Noonan JP. Massively parallel disruption of enhancers active in human neural stem cells. Cell Reports. 43: 113693. PMID 38271204 DOI: 10.1016/j.celrep.2024.113693  0.386
2023 Kocher AA, Dutrow EV, Uebbing S, Yim KM, Rosales Larios MF, Baumgartner M, Nottoli T, Noonan JP. CpG island turnover events predict evolutionary changes in enhancer activity. Biorxiv : the Preprint Server For Biology. PMID 37214934 DOI: 10.1101/2023.05.09.540063  0.673
2023 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, et al. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science (New York, N.Y.). 380: eabn2253. PMID 37104592 DOI: 10.1126/science.abn2253  0.415
2022 Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome. Nature Communications. 13: 304. PMID 35027568 DOI: 10.1038/s41467-021-27899-w  0.463
2021 Uebbing S, Gockley J, Reilly SK, Kocher AA, Geller E, Gandotra N, Scharfe C, Cotney J, Noonan JP. Massively parallel discovery of human-specific substitutions that alter enhancer activity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33372131 DOI: 10.1073/pnas.2007049118  0.373
2019 Stewart TA, Liang C, Cotney JL, Noonan JP, Sanger TJ, Wagner GP. Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings. Nature Communications. 10: 3244. PMID 31324809 DOI: 10.1038/S41467-019-11215-8  0.368
2019 Muhle R, Yim K, Krenzer M, Hill-Teran G, Malison K, Noonan J. 36Single Cell Rna Sequencing Of Embryonic Mouse Cortex Reveals Overlapping And Distinct Patterns Of Asd Risk Gene Expression European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2018.08.043  0.365
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. Current Biology : Cb. 28: 2103-2114.e5. PMID 30008330 DOI: 10.1016/J.Cub.2018.05.015  0.382
2018 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, ... ... Noonan JP, et al. A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies. American Journal of Human Genetics. PMID 29754769 DOI: 10.1016/J.Ajhg.2018.03.023  0.382
2018 Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Reports. 23: 1581-1597. PMID 29719267 DOI: 10.1016/J.Celrep.2018.03.129  0.519
2018 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. Molecular Microbiology. PMID 29608794 DOI: 10.1111/Mmi.13960  0.381
2018 Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP. Disrupting the three-dimensional regulatory topology of thelocus results in overtly normal development. Development (Cambridge, England). PMID 29549111 DOI: 10.1242/Dev.158550  0.477
2017 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, ... ... Noonan JP, et al. Molecular and cellular reorganization of neural circuits in the human lineage. Science (New York, N.Y.). 358: 1027-1032. PMID 29170230 DOI: 10.1126/Science.Aan3456  0.441
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  0.51
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  0.577
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  0.504
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  0.671
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  0.452
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  0.385
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  0.439
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  0.394
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  0.728
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  0.71
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  0.348
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  0.459
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  0.726
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  0.525
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  0.34
2010 Noonan JP. Neanderthal genomics and the evolution of modern humans. Genome Research. 20: 547-53. PMID 20439435 DOI: 10.1101/Gr.076000.108  0.464
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  0.477
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  0.523
2010 Sholtis SJ, Noonan JP. Corrigendum to “Gene regulation and the origins of human biological uniqueness.” [Trends in Genetics, 26/3 (2010) 110–118] Trends in Genetics. 26: 344. DOI: 10.1016/J.Tig.2010.05.002  0.484
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  0.535
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  0.45
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  0.725
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  0.573
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  0.603
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  0.517
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  0.581
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  0.723
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  0.551
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  0.509
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  0.661
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 DOI: 10.1091/Mbc.10.3.665  0.368
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