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Items: 1 to 50 of 111

1.

Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection.

Piantadosi A, Freije CA, Gosmann C, Ye S, Park D, Schaffner SF, Tully DC, Allen TM, Dong KL, Sabeti PC, Kwon DS.

J Virol. 2019 Jan 4;93(2). pii: e00804-18. doi: 10.1128/JVI.00804-18. Print 2019 Jan 15.

2.

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.

Siddle KJ, Eromon P, Barnes KG, Mehta S, Oguzie JU, Odia I, Schaffner SF, Winnicki SM, Shah RR, Qu J, Wohl S, Brehio P, Iruolagbe C, Aiyepada J, Uyigue E, Akhilomen P, Okonofua G, Ye S, Kayode T, Ajogbasile F, Uwanibe J, Gaye A, Momoh M, Chak B, Kotliar D, Carter A, Gladden-Young A, Freije CA, Omoregie O, Osiemi B, Muoebonam EB, Airende M, Enigbe R, Ebo B, Nosamiefan I, Oluniyi P, Nekoui M, Ogbaini-Emovon E, Garry RF, Andersen KG, Park DJ, Yozwiak NL, Akpede G, Ihekweazu C, Tomori O, Okogbenin S, Folarin OA, Okokhere PO, MacInnis BL, Sabeti PC, Happi CT.

N Engl J Med. 2018 Nov 1;379(18):1745-1753. doi: 10.1056/NEJMoa1804498. Epub 2018 Oct 17.

3.

hmmIBD: software to infer pairwise identity by descent between haploid genotypes.

Schaffner SF, Taylor AR, Wong W, Wirth DF, Neafsey DE.

Malar J. 2018 May 15;17(1):196. doi: 10.1186/s12936-018-2349-7.

4.

Plasmepsin II-III copy number accounts for bimodal piperaquine resistance among Cambodian Plasmodium falciparum.

Bopp S, Magistrado P, Wong W, Schaffner SF, Mukherjee A, Lim P, Dhorda M, Amaratunga C, Woodrow CJ, Ashley EA, White NJ, Dondorp AM, Fairhurst RM, Ariey F, Menard D, Wirth DF, Volkman SK.

Nat Commun. 2018 May 2;9(1):1769. doi: 10.1038/s41467-018-04104-z.

5.

Clinical and laboratory predictors of Lassa fever outcome in a dedicated treatment facility in Nigeria: a retrospective, observational cohort study.

Okokhere P, Colubri A, Azubike C, Iruolagbe C, Osazuwa O, Tabrizi S, Chin E, Asad S, Ediale E, Rafiu M, Adomeh D, Odia I, Atafo R, Aire C, Okogbenin S, Pahlman M, Becker-Ziaja B, Asogun D, Fradet T, Fry B, Schaffner SF, Happi C, Akpede G, Günther S, Sabeti PC.

Lancet Infect Dis. 2018 Jun;18(6):684-695. doi: 10.1016/S1473-3099(18)30121-X. Epub 2018 Mar 6. Erratum in: Lancet Infect Dis. 2018 Mar 16;:.

PMID:
29523497
6.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2018 Feb 22;172(5):1132-1134. doi: 10.1016/j.cell.2018.02.021. No abstract available.

PMID:
29474912
7.

Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent.

Taylor AR, Schaffner SF, Cerqueira GC, Nkhoma SC, Anderson TJC, Sriprawat K, Pyae Phyo A, Nosten F, Neafsey DE, Buckee CO.

PLoS Genet. 2017 Oct 27;13(10):e1007065. doi: 10.1371/journal.pgen.1007065. eCollection 2017 Oct.

8.

Zika virus evolution and spread in the Americas.

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC.

Nature. 2017 Jun 15;546(7658):411-415. doi: 10.1038/nature22402. Epub 2017 May 24.

9.

Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG.

Nature. 2017 Jun 15;546(7658):401-405. doi: 10.1038/nature22400. Epub 2017 May 24.

10.

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance.

Cerqueira GC, Cheeseman IH, Schaffner SF, Nair S, McDew-White M, Phyo AP, Ashley EA, Melnikov A, Rogov P, Birren BW, Nosten F, Anderson TJC, Neafsey DE.

Genome Biol. 2017 Apr 28;18(1):78. doi: 10.1186/s13059-017-1204-4.

11.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

12.

Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal.

Wong W, Griggs AD, Daniels RF, Schaffner SF, Ndiaye D, Bei AK, Deme AB, MacInnis B, Volkman SK, Hartl DL, Neafsey DE, Wirth DF.

Genome Med. 2017 Jan 24;9(1):5. doi: 10.1186/s13073-017-0398-0.

13.

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic.

Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J.

Cell. 2016 Nov 3;167(4):1088-1098.e6. doi: 10.1016/j.cell.2016.10.014.

14.

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse.

Lemieux JE, Tran AD, Freimark L, Schaffner SF, Goethert H, Andersen KG, Bazner S, Li A, McGrath G, Sloan L, Vannier E, Milner D, Pritt B, Rosenberg E, Telford S 3rd, Bailey JA, Sabeti PC.

Nat Microbiol. 2016 Jun 13;1(7):16079. doi: 10.1038/nmicrobiol.2016.79.

15.

Genomic Analysis of Viral Outbreaks.

Wohl S, Schaffner SF, Sabeti PC.

Annu Rev Virol. 2016 Sep 29;3(1):173-195. Epub 2016 Aug 3. Review.

16.

Ebola Virus Epidemiology and Evolution in Nigeria.

Folarin OA, Ehichioya D, Schaffner SF, Winnicki SM, Wohl S, Eromon P, West KL, Gladden-Young A, Oyejide NE, Matranga CB, Deme AB, James A, Tomkins-Tinch C, Onyewurunwa K, Ladner JT, Palacios G, Nosamiefan I, Andersen KG, Omilabu S, Park DJ, Yozwiak NL, Nasidi A, Garry RF, Tomori O, Sabeti PC, Happi CT.

J Infect Dis. 2016 Oct 15;214(suppl 3):S102-S109. Epub 2016 Jul 4.

17.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2016 Jun 2;165(6):1519-1529. doi: 10.1016/j.cell.2016.04.027. Erratum in: Cell. 2018 Feb 22;172(5):1132-1134.

18.

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Andersen KG, Shapiro BJ, Matranga CB, Sealfon R, Lin AE, Moses LM, Folarin OA, Goba A, Odia I, Ehiane PE, Momoh M, England EM, Winnicki S, Branco LM, Gire SK, Phelan E, Tariyal R, Tewhey R, Omoniwa O, Fullah M, Fonnie R, Fonnie M, Kanneh L, Jalloh S, Gbakie M, Saffa S, Karbo K, Gladden AD, Qu J, Stremlau M, Nekoui M, Finucane HK, Tabrizi S, Vitti JJ, Birren B, Fitzgerald M, McCowan C, Ireland A, Berlin AM, Bochicchio J, Tazon-Vega B, Lennon NJ, Ryan EM, Bjornson Z, Milner DA Jr, Lukens AK, Broodie N, Rowland M, Heinrich M, Akdag M, Schieffelin JS, Levy D, Akpan H, Bausch DG, Rubins K, McCormick JB, Lander ES, Günther S, Hensley L, Okogbenin S; Viral Hemorrhagic Fever Consortium, Schaffner SF, Okokhere PO, Khan SH, Grant DS, Akpede GO, Asogun DA, Gnirke A, Levin JZ, Happi CT, Garry RF, Sabeti PC.

Cell. 2015 Aug 13;162(4):738-50. doi: 10.1016/j.cell.2015.07.020.

19.

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC.

Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007.

20.

Modeling malaria genomics reveals transmission decline and rebound in Senegal.

Daniels RF, Schaffner SF, Wenger EA, Proctor JL, Chang HH, Wong W, Baro N, Ndiaye D, Fall FB, Ndiop M, Ba M, Milner DA Jr, Taylor TE, Neafsey DE, Volkman SK, Eckhoff PA, Hartl DL, Wirth DF.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7067-72. doi: 10.1073/pnas.1505691112. Epub 2015 May 4.

21.

Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections.

Baniecki ML, Faust AL, Schaffner SF, Park DJ, Galinsky K, Daniels RF, Hamilton E, Ferreira MU, Karunaweera ND, Serre D, Zimmerman PA, Sá JM, Wellems TE, Musset L, Legrand E, Melnikov A, Neafsey DE, Volkman SK, Wirth DF, Sabeti PC.

PLoS Negl Trop Dis. 2015 Mar 17;9(3):e0003539. doi: 10.1371/journal.pntd.0003539. eCollection 2015 Mar.

22.

Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa.

Stremlau MH, Andersen KG, Folarin OA, Grove JN, Odia I, Ehiane PE, Omoniwa O, Omoregie O, Jiang PP, Yozwiak NL, Matranga CB, Yang X, Gire SK, Winnicki S, Tariyal R, Schaffner SF, Okokhere PO, Okogbenin S, Akpede GO, Asogun DA, Agbonlahor DE, Walker PJ, Tesh RB, Levin JZ, Garry RF, Sabeti PC, Happi CT.

PLoS Negl Trop Dis. 2015 Mar 17;9(3):e0003631. doi: 10.1371/journal.pntd.0003631. eCollection 2015 Mar.

23.

Data sharing: Make outbreak research open access.

Yozwiak NL, Schaffner SF, Sabeti PC.

Nature. 2015 Feb 26;518(7540):477-9. doi: 10.1038/518477a. No abstract available.

PMID:
25719649
24.

Clinical illness and outcomes in patients with Ebola in Sierra Leone.

Schieffelin JS, Shaffer JG, Goba A, Gbakie M, Gire SK, Colubri A, Sealfon RS, Kanneh L, Moigboi A, Momoh M, Fullah M, Moses LM, Brown BL, Andersen KG, Winnicki S, Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D, Jalloh S, Fonnie M, Sinnah V, French I, Kovoma A, Kamara FK, Tucker V, Konuwa E, Sellu J, Mustapha I, Foday M, Yillah M, Kanneh F, Saffa S, Massally JL, Boisen ML, Branco LM, Vandi MA, Grant DS, Happi C, Gevao SM, Fletcher TE, Fowler RA, Bausch DG, Sabeti PC, Khan SH, Garry RF; KGH Lassa Fever Program; Viral Hemorrhagic Fever Consortium; WHO Clinical Response Team.

N Engl J Med. 2014 Nov 27;371(22):2092-100. doi: 10.1056/NEJMoa1411680. Epub 2014 Oct 29.

25.

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC.

Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

26.

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.

27.

Searching for missing heritability: designing rare variant association studies.

Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, Daly MJ, Neale BM, Sunyaev SR, Lander ES.

Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):E455-64. doi: 10.1073/pnas.1322563111. Epub 2014 Jan 17.

28.

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.

29.

Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal.

Daniels R, Chang HH, Séne PD, Park DC, Neafsey DE, Schaffner SF, Hamilton EJ, Lukens AK, Van Tyne D, Mboup S, Sabeti PC, Ndiaye D, Wirth DF, Hartl DL, Volkman SK.

PLoS One. 2013 Apr 4;8(4):e60780. doi: 10.1371/journal.pone.0060780. Print 2013.

30.

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.

31.

Epidemiology. Emerging disease or diagnosis?

Gire SK, Stremlau M, Andersen KG, Schaffner SF, Bjornson Z, Rubins K, Hensley L, McCormick JB, Lander ES, Garry RF, Happi C, Sabeti PC.

Science. 2012 Nov 9;338(6108):750-2. doi: 10.1126/science.1225893. No abstract available.

PMID:
23139320
32.

Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite.

Park DJ, Lukens AK, Neafsey DE, Schaffner SF, Chang HH, Valim C, Ribacke U, Van Tyne D, Galinsky K, Galligan M, Becker JS, Ndiaye D, Mboup S, Wiegand RC, Hartl DL, Sabeti PC, Wirth DF, Volkman SK.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):13052-7. doi: 10.1073/pnas.1210585109. Epub 2012 Jul 23.

33.

Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population.

Chang HH, Park DJ, Galinsky KJ, Schaffner SF, Ndiaye D, Ndir O, Mboup S, Wiegand RC, Volkman SK, Sabeti PC, Wirth DF, Neafsey DE, Hartl DL.

Mol Biol Evol. 2012 Nov;29(11):3427-39. doi: 10.1093/molbev/mss161. Epub 2012 Jun 24.

34.

SNP genotyping identifies new signatures of selection in a deep sample of West African Plasmodium falciparum malaria parasites.

Amambua-Ngwa A, Park DJ, Volkman SK, Barnes KG, Bei AK, Lukens AK, Sene P, Van Tyne D, Ndiaye D, Wirth DF, Conway DJ, Neafsey DE, Schaffner SF.

Mol Biol Evol. 2012 Nov;29(11):3249-53. doi: 10.1093/molbev/mss151. Epub 2012 Jun 11.

35.

Harnessing genomics and genome biology to understand malaria biology.

Volkman SK, Neafsey DE, Schaffner SF, Park DJ, Wirth DF.

Nat Rev Genet. 2012 Apr 12;13(5):315-28. doi: 10.1038/nrg3187. Review.

PMID:
22495435
36.

Human cerebral malaria and Plasmodium falciparum genotypes in Malawi.

Milner DA Jr, Vareta J, Valim C, Montgomery J, Daniels RF, Volkman SK, Neafsey DE, Park DJ, Schaffner SF, Mahesh NC, Barnes KG, Rosen DM, Lukens AK, Van Tyne D, Wiegand RC, Sabeti PC, Seydel KB, Glover SJ, Kamiza S, Molyneux ME, Taylor TE, Wirth DF.

Malar J. 2012 Feb 7;11:35. doi: 10.1186/1475-2875-11-35.

37.

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.

38.

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.

39.

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]..

40.

Population genetic study of the brain-derived neurotrophic factor (BDNF) gene.

Petryshen TL, Sabeti PC, Aldinger KA, Fry B, Fan JB, Schaffner SF, Waggoner SG, Tahl AR, Sklar P.

Mol Psychiatry. 2010 Aug;15(8):810-5. doi: 10.1038/mp.2009.24. Epub 2009 Mar 3.

41.

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.

Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA Jr, Lukens A, Rosen D, Daniels R, Houde N, Cortese JF, Tyndall E, Gates C, Stange-Thomann N, Sarr O, Ndiaye D, Ndir O, Mboup S, Ferreira MU, Moraes Sdo L, Dash AP, Chitnis CE, Wiegand RC, Hartl DL, Birren BW, Lander ES, Sabeti PC, Wirth DF.

Genome Biol. 2008;9(12):R171. doi: 10.1186/gb-2008-9-12-r171. Epub 2008 Dec 15.

42.

Genome-wide detection and characterization of positive selection in human populations.

Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES; International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J.

Nature. 2007 Oct 18;449(7164):913-8.

43.

A second generation human haplotype map of over 3.1 million SNPs.

International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J.

Nature. 2007 Oct 18;449(7164):851-61.

44.

Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens".

Yu F, Hill RS, Schaffner SF, Sabeti PC, Wang ET, Mignault AA, Ferland RJ, Moyzis RK, Walsh CA, Reich D.

Science. 2007 Apr 20;316(5823):370.

45.

A genome-wide map of diversity in Plasmodium falciparum.

Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA Jr, Daily JP, Sarr O, Ndiaye D, Ndir O, Mboup S, Duraisingh MT, Lukens A, Derr A, Stange-Thomann N, Waggoner S, Onofrio R, Ziaugra L, Mauceli E, Gnerre S, Jaffe DB, Zainoun J, Wiegand RC, Birren BW, Hartl DL, Galagan JE, Lander ES, Wirth DF.

Nat Genet. 2007 Jan;39(1):113-9. Epub 2006 Dec 10.

PMID:
17159979
46.

Positive natural selection in the human lineage.

Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES.

Science. 2006 Jun 16;312(5780):1614-20. Review.

PMID:
16778047
47.

Searching for signals of evolutionary selection in 168 genes related to immune function.

Walsh EC, Sabeti P, Hutcheson HB, Fry B, Schaffner SF, de Bakker PI, Varilly P, Palma AA, Roy J, Cooper R, Winkler C, Zeng Y, de The G, Lander ES, O'Brien S, Altshuler D.

Hum Genet. 2006 Mar;119(1-2):92-102. Epub 2005 Dec 14.

PMID:
16362345
48.

Calibrating a coalescent simulation of human genome sequence variation.

Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D.

Genome Res. 2005 Nov;15(11):1576-83.

49.

The case for selection at CCR5-Delta32.

Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B, Hutcheson HB, Cullen M, Mikkelsen TS, Roy J, Patterson N, Cooper R, Reich D, Altshuler D, O'Brien S, Lander ES.

PLoS Biol. 2005 Nov;3(11):e378. Epub 2005 Nov 1.

50.

Automated seizure abatement in humans using electrical stimulation.

Osorio I, Frei MG, Sunderam S, Giftakis J, Bhavaraju NC, Schaffner SF, Wilkinson SB.

Ann Neurol. 2005 Feb;57(2):258-68.

PMID:
15668970

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