| Year |
Citation |
Score |
| 2025 |
Pal A, Noble MA, Morales M, Pal R, Baumgartner M, Yang JW, Yim KM, Uebbing S, Noonan JP. Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment. Cell. PMID 39889695 DOI: 10.1016/j.cell.2025.01.007 |
0.663 |
|
| 2024 |
Uebbing S, Kocher AA, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan JP. Evolutionary innovations in conserved regulatory elements associate with developmental genes in mammals. Molecular Biology and Evolution. PMID 39302728 DOI: 10.1093/molbev/msae199 |
0.686 |
|
| 2024 |
Baumgartner M, Ji Y, Noonan JP. Reconstructing human-specific regulatory functions in model systems. Current Opinion in Genetics & Development. 89: 102259. PMID 39270593 DOI: 10.1016/j.gde.2024.102259 |
0.65 |
|
| 2024 |
Yim KM, Baumgartner M, Krenzer M, Rosales Larios MF, Hill-Terán G, Nottoli T, Muhle RA, Noonan JP. Cell type-specific dysregulation of gene expression due to haploinsufficiency during mouse cortical development. Biorxiv : the Preprint Server For Biology. PMID 39185167 DOI: 10.1101/2024.08.14.608000 |
0.642 |
|
| 2024 |
Pal A, Noble MA, Morales M, Pal R, Baumgartner M, Yang JW, Yim KM, Uebbing S, Noonan JP. Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. Biorxiv : the Preprint Server For Biology. PMID 39091792 DOI: 10.1101/2024.06.25.600691 |
0.689 |
|
| 2024 |
Noble MA, Ji Y, Yim KM, Yang JW, Morales M, Abu-Shamma R, Pal A, Poulsen R, Baumgartner M, Noonan JP. Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions. Biorxiv : the Preprint Server For Biology. PMID 39005466 DOI: 10.1101/2024.06.30.601407 |
0.679 |
|
| 2024 |
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. Genome Biology. 25: 156. PMID 38872220 DOI: 10.1186/s13059-024-03300-z |
0.596 |
|
| 2024 |
Uebbing S, Kocher AA, Baumgartner M, Ji Y, Bai S, Xing X, Nottoli T, Noonan JP. Evolutionary innovation in conserved regulatory elements across the mammalian tree of life. Biorxiv : the Preprint Server For Biology. PMID 38352419 DOI: 10.1101/2024.01.31.578197 |
0.679 |
|
| 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 |
0.422 |
|
| 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 |
0.682 |
|
| 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 |
0.441 |
|
| 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 |
0.493 |
|
| 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 |
0.397 |
|
| 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 |
0.387 |
|
| 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 |
0.382 |
|
| 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 |
0.4 |
|
| 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 |
0.383 |
|
| 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 |
0.522 |
|
| 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 |
0.48 |
|
| 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 |
0.469 |
|
| 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 |
0.529 |
|
| 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 |
0.584 |
|
| 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 |
0.526 |
|
| 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 |
0.683 |
|
| 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 |
0.432 |
|
| 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 |
0.412 |
|
| 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 |
0.466 |
|
| 2013 |
Pavlicev M, Wagner GP, Noonan JP, HallgrÃmsson 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 |
0.395 |
|
| 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 |
0.755 |
|
| 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 |
0.726 |
|
| 2013 |
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, ... ... 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 |
0.34 |
|
| 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 |
0.456 |
|
| 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 |
0.746 |
|
| 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 |
0.532 |
|
| 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 |
0.339 |
|
| 2010 |
Noonan JP. Neanderthal genomics and the evolution of modern humans. Genome Research. 20: 547-53. PMID 20439435 DOI: 10.1101/Gr.076000.108 |
0.466 |
|
| 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 |
0.484 |
|
| 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 |
0.545 |
|
| 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 |
0.472 |
|
| 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 |
0.544 |
|
| 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 |
0.466 |
|
| 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 |
0.737 |
|
| 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 |
0.57 |
|
| 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 |
0.623 |
|
| 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 |
0.51 |
|
| 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 |
0.583 |
|
| 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 |
0.733 |
|
| 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 |
0.561 |
|
| 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 |
0.511 |
|
| 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 |
0.669 |
|
| 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 |
0.366 |
|
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