Stephen Schaffner, Ph.D.

STEPHEN SCHAFFNER, Ph.D.

Stephen Schaffner is a senior computational biologist in the Infectious Disease and Microbiome Program at the Broad Institute, where he studies the genetics of human infectious disease, including host, viral and malaria genetics.

He has worked extensively in human population genetics, contributing to the first systematic study of human genetic variation, to the International HapMap Project and to the 1000 Genomes Project. He has developed techniques for detecting the effects of positive selection on genetic variation, carried out model-based studies of human demographic history, and developed tools for identifying recent common ancestry in malaria parasites.

Schaffner is a former experimental physicist who joined the Whitehead/MIT Center for Genome Research in 1999, and became part of the Broad Institute at its founding. He earned his Ph.D. in physics at Yale University.

SELECTED PUBLICATIONS

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

Cell. 2016.
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.

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

Cell. 2015.
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

Searching for missing heritability: designing rare variant association studies.

PNAS 111 (4), E455-E464 (2014).
O Zuk, SF Schaffner, K Samocha, R Do, E Hechter, S Kathiresan, MJ Daly, el al.

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

Science. 2014.
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.

Identifying recent adaptations in large-scale genomic data.

Cell. 2013.
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. *Co-first authors

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

Proc Natl Acad Sci U S A. 2012.
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.

Harnessing genomics and genome biology to understand malaria biology

Nat Rev Genet. 2012.
Volkman SK1, Neafsey DE, Schaffner SF, Park DJ, Wirth DF.

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

PLoS Genet. 2011.
Van Tyne D1, 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.

A map of human genome variation from population-scale sequencing.

Nature 467 (7319), 1061-1073 (2010).
1000 Genomes Project Consortium.

A genome-wide map of diversity in Plasmodium falciparum.

Nature Genetics 39 (1), 113-119 (2007).
SK Volkman, PC Sabeti, D DeCaprio, DE Neafsey, SF Schaffner, et al.

Positive natural selection in the human lineage.

Science 312 (5780), 1614-1620 (2006).
PC Sabeti, SF Schaffner, B Fry, J Lohmueller, P Varilly, O Shamovsky, et al.

Calibrating a coalescent simulation of human genome sequence variation.

Genome Research 15 (11), 1576-1583 (2005).
SF Schaffner, C Foo, S Gabriel, D Reich, MJ Daly, D Altshuler.

The international HapMap project.

Nature 426 (6968), 789-796 (2003).
RA Gibbs, JW Belmont, P Hardenbol, TD Willis, F Yu, H Yang, LY Ch'ang, et al.

The structure of haplotype blocks in the human genome.