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 2024.01.31.578197. Article: https://www.biorxiv.org/content/10.1101/2024.01.31.578197v1 Code: https://github.com/severinEvo/Uebbing_et_al_acceleration Data: https://zenodo.org/records/10600206
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 Rep. 43, 113693 (2024). Article: https://doi.org/10.1016/j.celrep.2024.113693 Data: GSE138823 Code: https://zenodo.org/records/10258136
2021-23
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 2023.05.09.540063; doi: https://doi.org/10.1101/2023.05.09.540063
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. Nat. Commun. 13, 304 (2022). Article: https://www.nature.com/articles/s41467-021-27899-w Data: GSE141471
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. Proc. Natl. Acad. Sci. USA 118(2):e2007049118 (2021). Article: 10.1073/pnas.2007049118 Data: GSE140983 Code: https://github.com/NoonanLab/Uebbing_Gockley_et_al_MPRA Featured in PNAS Highlights: https://www.pnas.org/content/118/2/eiti0221118
2019
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 neurodevelopmental enhancer activity. bioRxiv 865519. Available from: doi.org/10.1101/865519. Now published in PNAS: 10.1073/pnas.2007049118
Geller E, Gockley J, Emera D, Uebbing S, Cotney J, Noonan JP. Massively parallel disruption of enhancers active during human corticogenesis. bioRxiv 852673. Available from: https://www.biorxiv.org/content/10.1101/852673v1. Now published in Cell Reports: https://doi.org/10.1016/j.celrep.2024.113693
Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. The Human Accelerated Region HACNS1 modifies developmental gene expression in humanized mice. bioRxiv 873075. Available from: https://www.biorxiv.org/content/10.1101/2019.12.11.873075v2. Now published in Nature Communications: https://www.nature.com/articles/s41467-021-27899-w
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. Nat. Commun. 10 (1), 3244 (2019). Article: 10.1038/s41467-019-11215-8
2018
Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM et al. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362(6420) pii:eaat7615 (2018). Article: 10.1126/science.aat7615 Data: www.synapse.org/#!Synapse:syn4921369/wiki/235539
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
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