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Items: 9

1.

Sequential regulatory activity prediction across chromosomes with convolutional neural networks.

Kelley DR, Reshef YA, Bileschi M, Belanger D, McLean CY, Snoek J.

Genome Res. 2018 May;28(5):739-750. doi: 10.1101/gr.227819.117. Epub 2018 Mar 27.

2.

Quantifying prion disease penetrance using large population control cohorts.

Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, McLean CY, Tung JY, Yu LP, Gambetti P, Blevins J, Zhang S, Cohen Y, Chen W, Yamada M, Hamaguchi T, Sanjo N, Mizusawa H, Nakamura Y, Kitamoto T, Collins SJ, Boyd A, Will RG, Knight R, Ponto C, Zerr I, Kraus TF, Eigenbrod S, Giese A, Calero M, de Pedro-Cuesta J, Haïk S, Laplanche JL, Bouaziz-Amar E, Brandel JP, Capellari S, Parchi P, Poleggi A, Ladogana A, O'Donnell-Luria AH, Karczewski KJ, Marshall JL, Boehnke M, Laakso M, Mohlke KL, Kähler A, Chambert K, McCarroll S, Sullivan PF, Hultman CM, Purcell SM, Sklar P, van der Lee SJ, Rozemuller A, Jansen C, Hofman A, Kraaij R, van Rooij JG, Ikram MA, Uitterlinden AG, van Duijn CM; Exome Aggregation Consortium (ExAC), Daly MJ, MacArthur DG.

Sci Transl Med. 2016 Jan 20;8(322):322ra9. doi: 10.1126/scitranslmed.aad5169.

3.

Diagnosis of Parkinson's disease on the basis of clinical and genetic classification: a population-based modelling study.

Nalls MA, McLean CY, Rick J, Eberly S, Hutten SJ, Gwinn K, Sutherland M, Martinez M, Heutink P, Williams NM, Hardy J, Gasser T, Brice A, Price TR, Nicolas A, Keller MF, Molony C, Gibbs JR, Chen-Plotkin A, Suh E, Letson C, Fiandaca MS, Mapstone M, Federoff HJ, Noyce AJ, Morris H, Van Deerlin VM, Weintraub D, Zabetian C, Hernandez DG, Lesage S, Mullins M, Conley ED, Northover CA, Frasier M, Marek K, Day-Williams AG, Stone DJ, Ioannidis JP, Singleton AB; Parkinson's Disease Biomarkers Program and Parkinson's Progression Marker Initiative investigators.

Lancet Neurol. 2015 Oct;14(10):1002-9. doi: 10.1016/S1474-4422(15)00178-7. Epub 2015 Aug 10.

4.

Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis.

Durand EY, Eriksson N, McLean CY.

Mol Biol Evol. 2014 Aug;31(8):2212-22. doi: 10.1093/molbev/msu151. Epub 2014 Apr 30.

5.

A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae.

Reno PL, McLean CY, Hines JE, Capellini TD, Bejerano G, Kingsley DM.

PLoS One. 2013 Dec 19;8(12):e84258. doi: 10.1371/journal.pone.0084258. eCollection 2013.

6.

Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.

Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJM, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF.

Science. 2014 Jan 10;343(6167):189-193. doi: 10.1126/science.1239947. Epub 2013 Dec 12.

7.

PRISM offers a comprehensive genomic approach to transcription factor function prediction.

Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G.

Genome Res. 2013 May;23(5):889-904. doi: 10.1101/gr.139071.112. Epub 2013 Feb 4.

8.

Human-specific loss of regulatory DNA and the evolution of human-specific traits.

McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM.

Nature. 2011 Mar 10;471(7337):216-9. doi: 10.1038/nature09774.

9.

GREAT improves functional interpretation of cis-regulatory regions.

McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.

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