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Items: 1 to 20 of 59

1.

A literature review at genome scale: improving clinical variant assessment.

Cassa CA, Jordan DM, Adzhubei I, Sunyaev S.

Genet Med. 2018 Feb 1. doi: 10.1038/gim.2017.230. [Epub ahead of print]

2.

Bayesian inference of negative and positive selection in human cancers.

Weghorn D, Sunyaev S.

Nat Genet. 2017 Dec;49(12):1785-1788. doi: 10.1038/ng.3987. Epub 2017 Nov 6.

PMID:
29106416
3.

Lessons from the CAGI-4 Hopkins clinical panel challenge.

Chandonia JM, Adhikari A, Carraro M, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, Lam HYK, Leonardi E, Moult J, Pal LR, Searls DB, Shah S, Sunyaev S, Tosatto SCE, Yin Y, Buckley BA.

Hum Mutat. 2017 Sep;38(9):1155-1168. doi: 10.1002/humu.23225. Epub 2017 Jun 12.

4.

Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society.

Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD, Sunyaev S.

Hum Mutat. 2017 Apr;38(4):460-463. doi: 10.1002/humu.23169. Epub 2017 Feb 14. No abstract available.

PMID:
28054414
5.

Quantifying unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects.

Zou J, Valiant G, Valiant P, Karczewski K, Chan SO, Samocha K, Lek M, Sunyaev S, Daly M, MacArthur DG.

Nat Commun. 2016 Oct 31;7:13293. doi: 10.1038/ncomms13293.

6.

Increasing Generality and Power of Rare-Variant Tests by Utilizing Extended Pedigrees.

Sul JH, Cade BE, Cho MH, Qiao D, Silverman EK, Redline S, Sunyaev S.

Am J Hum Genet. 2016 Oct 6;99(4):846-859. doi: 10.1016/j.ajhg.2016.08.015. Epub 2016 Sep 22.

7.

Widespread macromolecular interaction perturbations in human genetic disorders.

Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

8.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

9.

No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.

Do R, Balick D, Li H, Adzhubei I, Sunyaev S, Reich D.

Nat Genet. 2015 Feb;47(2):126-31. doi: 10.1038/ng.3186. Epub 2015 Jan 12.

10.

Evaluating empirical bounds on complex disease genetic architecture.

Agarwala V, Flannick J, Sunyaev S; GoT2D Consortium, Altshuler D.

Nat Genet. 2013 Dec;45(12):1418-27. doi: 10.1038/ng.2804. Epub 2013 Oct 20.

11.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G.

Nature. 2013 Jul 11;499(7457):214-218. doi: 10.1038/nature12213. Epub 2013 Jun 16.

12.

Sequencing studies in human genetics: design and interpretation.

Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S.

Nat Rev Genet. 2013 Jul;14(7):460-70. doi: 10.1038/nrg3455. Epub 2013 Jun 11. Review.

13.

Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence.

Gokcumen O, Zhu Q, Mulder LC, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Stranger B, Simon V, Lee C.

PLoS Genet. 2013 Apr;9(4):e1003404. doi: 10.1371/journal.pgen.1003404. Epub 2013 Apr 11.

14.

Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis.

Diogo D, Kurreeman F, Stahl EA, Liao KP, Gupta N, Greenberg JD, Rivas MA, Hickey B, Flannick J, Thomson B, Guiducci C, Ripke S, Adzhubey I, Barton A, Kremer JM, Alfredsson L; Consortium of Rheumatology Researchers of North America; Rheumatoid Arthritis Consortium International, Sunyaev S, Martin J, Zhernakova A, Bowes J, Eyre S, Siminovitch KA, Gregersen PK, Worthington J, Klareskog L, Padyukov L, Raychaudhuri S, Plenge RM.

Am J Hum Genet. 2013 Jan 10;92(1):15-27. doi: 10.1016/j.ajhg.2012.11.012. Epub 2012 Dec 20.

15.

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies.

Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P, Sullivan PF, Bergen S, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Purcell SM, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PI, Reich D, Price AL.

Nat Genet. 2012 May 20;44(6):631-5. doi: 10.1038/ng.2283.

16.

Evolution and functional impact of rare coding variation from deep sequencing of human exomes.

Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM; Broad GO; Seattle GO; NHLBI Exome Sequencing Project.

Science. 2012 Jul 6;337(6090):64-9. doi: 10.1126/science.1219240. Epub 2012 May 17.

17.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

18.

Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH Jr, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ.

Nature. 2012 Apr 4;485(7397):242-5. doi: 10.1038/nature11011.

19.

Computational and statistical approaches to analyzing variants identified by exome sequencing.

Stitziel NO, Kiezun A, Sunyaev S.

Genome Biol. 2011 Sep 14;12(9):227. doi: 10.1186/gb-2011-12-9-227. Review.

20.

Progressive multifocal leukoencephalopathy (PML) development is associated with mutations in JC virus capsid protein VP1 that change its receptor specificity.

Gorelik L, Reid C, Testa M, Brickelmaier M, Bossolasco S, Pazzi A, Bestetti A, Carmillo P, Wilson E, McAuliffe M, Tonkin C, Carulli JP, Lugovskoy A, Lazzarin A, Sunyaev S, Simon K, Cinque P.

J Infect Dis. 2011 Jul 1;204(1):103-14. doi: 10.1093/infdis/jir198.

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