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Items: 9

1.

Cosi2: an efficient simulator of exact and approximate coalescent with selection.

Shlyakhter I, Sabeti PC, Schaffner SF.

Bioinformatics. 2014 Dec 1;30(23):3427-9. doi: 10.1093/bioinformatics/btu562. Epub 2014 Aug 22.

2.

Natural selection in a bangladeshi population from the cholera-endemic ganges river delta.

Karlsson EK, Harris JB, Tabrizi S, Rahman A, Shlyakhter I, Patterson N, O'Dushlaine C, Schaffner SF, Gupta S, Chowdhury F, Sheikh A, Shin OS, Ellis C, Becker CE, Stuart LM, Calderwood SB, Ryan ET, Qadri F, Sabeti PC, Larocque RC.

Sci Transl Med. 2013 Jul 3;5(192):192ra86. doi: 10.1126/scitranslmed.3006338.

3.

Identifying recent adaptations in large-scale genomic data.

Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL; 1000 Genomes Project, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2013 Feb 14;152(4):703-13. doi: 10.1016/j.cell.2013.01.035.

4.

Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.

Van Tyne D, Park DJ, Schaffner SF, Neafsey DE, Angelino E, Cortese JF, Barnes KG, Rosen DM, Lukens AK, Daniels RF, Milner DA Jr, Johnson CA, Shlyakhter I, Grossman SR, Becker JS, Yamins D, Karlsson EK, Ndiaye D, Sarr O, Mboup S, Happi C, Furlotte NA, Eskin E, Kang HM, Hartl DL, Birren BW, Wiegand RC, Lander ES, Wirth DF, Volkman SK, Sabeti PC.

PLoS Genet. 2011 Apr;7(4):e1001383. doi: 10.1371/journal.pgen.1001383. Epub 2011 Apr 21.

5.

Integrating common and rare genetic variation in diverse human populations.

International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE.

Nature. 2010 Sep 2;467(7311):52-8. doi: 10.1038/nature09298.

6.

A composite of multiple signals distinguishes causal variants in regions of positive selection.

Grossman SR, Shlyakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC.

Science. 2010 Feb 12;327(5967):883-6. doi: 10.1126/science.1183863. Epub 2010 Jan 7. Erratum in: Science. 2012 Feb17;335(6070):796. Shylakhter, Ilya [corrected to Shlyakhter, Ilya]..

7.

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.

Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB.

Genome Biol. 2009;10(10):R103. doi: 10.1186/gb-2009-10-10-r103. Epub 2009 Oct 1.

8.

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):810-20. doi: 10.1101/gr.7337908. Epub 2008 Mar 13.

9.

An empirical examination of factors influencing prediction of carcinogenic hazard across species.

Gray GM, Li P, Shlyakhter I, Wilson R.

Regul Toxicol Pharmacol. 1995 Dec;22(3):283-91.

PMID:
8837853

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