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Items: 1 to 20 of 42

1.

A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies.

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, Wu J, Xia K, Noonan JP, Sun ZS, He X.

Am J Hum Genet. 2018 Jun 7;102(6):1031-1047. doi: 10.1016/j.ajhg.2018.03.023. Epub 2018 May 10.

PMID:
29754769
2.

High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development.

Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J.

Cell Rep. 2018 May 1;23(5):1581-1597. doi: 10.1016/j.celrep.2018.03.129.

3.

Genome-wide analysis of the regulation of Cu metabolism in Cryptococcus neoformans.

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.

Mol Microbiol. 2018 Jun;108(5):473-494. doi: 10.1111/mmi.13960. Epub 2018 Apr 24.

PMID:
29608794
4.

Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development.

Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP.

Development. 2018 Apr 9;145(7). pii: dev158550. doi: 10.1242/dev.158550.

5.

Molecular and cellular reorganization of neural circuits in the human lineage.

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.

Science. 2017 Nov 24;358(6366):1027-1032. doi: 10.1126/science.aan3456.

6.

Evolution of Gene Regulation in Humans.

Reilly SK, Noonan JP.

Annu Rev Genomics Hum Genet. 2016 Aug 31;17:45-67. doi: 10.1146/annurev-genom-090314-045935. Epub 2016 Apr 21. Review.

PMID:
27147089
7.

Origin and evolution of developmental enhancers in the mammalian neocortex.

Emera D, Yin J, Reilly SK, Gockley J, Noonan JP.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):E2617-26. doi: 10.1073/pnas.1603718113. Epub 2016 Apr 25.

8.

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

Cotney JL, Noonan JP.

Cold Spring Harb Protoc. 2015 Apr 1;2015(4):419. doi: 10.1101/pdb.err087585. No abstract available.

9.

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.

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.

Nat Commun. 2015 Mar 10;6:6404. doi: 10.1038/ncomms7404.

10.

Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.

Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP.

Science. 2015 Mar 6;347(6226):1155-9. doi: 10.1126/science.1260943.

11.

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

Cotney JL, Noonan JP.

Cold Spring Harb Protoc. 2015 Feb 2;2015(2):191-9. doi: 10.1101/pdb.prot084848. Erratum in: Cold Spring Harb Protoc. 2015 Apr;2015(4):419.

PMID:
25646502
12.

DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics.

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.

Mol Autism. 2014 Mar 6;5(1):22. doi: 10.1186/2040-2392-5-22.

13.

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.

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.

Cell. 2013 Nov 21;155(5):997-1007. doi: 10.1016/j.cell.2013.10.020.

14.

Genomic correlates of relationship QTL involved in fore- versus hind limb divergence in mice.

Pavlicev M, Wagner GP, Noonan JP, Hallgrímsson B, Cheverud JM.

Genome Biol Evol. 2013;5(10):1926-36. doi: 10.1093/gbe/evt144.

15.

The evolution of lineage-specific regulatory activities in the human embryonic limb.

Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP.

Cell. 2013 Jul 3;154(1):185-96. doi: 10.1016/j.cell.2013.05.056.

16.

The genomic landscape of cohesin-associated chromatin interactions.

DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP.

Genome Res. 2013 Aug;23(8):1224-34. doi: 10.1101/gr.156570.113. Epub 2013 May 23.

17.

Time series expression analyses using RNA-seq: a statistical approach.

Oh S, Song S, Grabowski G, Zhao H, Noonan JP.

Biomed Res Int. 2013;2013:203681. doi: 10.1155/2013/203681. Epub 2013 Mar 24.

18.

Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO.

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.

Science. 2013 Mar 1;339(6123):1077-80. doi: 10.1126/science.1233009. Epub 2013 Jan 24.

19.

RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse.

Bandyopadhyay U, Cotney J, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL.

PLoS One. 2013;8(1):e53575. doi: 10.1371/journal.pone.0053575. Epub 2013 Jan 3.

20.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Cotney J, Leng J, Oh S, DeMare LE, Reilly SK, Gerstein MB, Noonan JP.

Genome Res. 2012 Jun;22(6):1069-80. doi: 10.1101/gr.129817.111. Epub 2012 Mar 15.

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