Stephen F Schaffner
Affiliation: Massachusetts Institute of Technology
- The structure of haplotype blocks in the human genomeStacey B Gabriel
Whitehead/MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
- Detecting recent positive selection in the human genome from haplotype structurePardis C Sabeti
Whitehead Institute/MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 419:832-7. 2002..More generally, the method could be used to scan the entire genome for evidence of recent positive selection...
- Calibrating a coalescent simulation of human genome sequence variationStephen F Schaffner
Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02139, USA
Genome Res 15:1576-83. 2005..We anticipate that this model, for which software is publicly available, and others like it will have numerous applications in empirical studies of human genetics...
- Searching for signals of evolutionary selection in 168 genes related to immune functionEmily C Walsh
Novartis Institutes for BioMedical Research, 250 Mass Ave, Cambridge, MA 02139, USA
Hum Genet 119:92-102. 2006....
- Human genome sequence variation and the influence of gene history, mutation and recombinationDavid E Reich
Whitehead Institute/MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
Nat Genet 32:135-42. 2002....
- A composite of multiple signals distinguishes causal variants in regions of positive selectionSharon R Grossman
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Science 327:883-6. 2010..CMS can not just identify individual loci but implicates precise variants selected by evolution...
- An integrated haplotype map of the human major histocompatibility complexEmily C Walsh
Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
Am J Hum Genet 73:580-90. 2003..Furthermore, these data show that multi-SNP haplotypes will likely be a valuable means for refining association signals in this region...
- Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasiteDaniel J Park
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 109:13052-7. 2012..falciparum...
- Genome-wide detection and characterization of positive selection in human populationsPardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007....
- The X chromosome in population geneticsStephen F Schaffner
Whitehead/MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA
Nat Rev Genet 5:43-51. 2004
- Integrating common and rare genetic variation in diverse human populationsDavid M Altshuler
Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA
Nature 467:52-8. 2010....
- Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergenceDaniel E Neafsey
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Genome Biol 9:R171. 2008..To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum...
- Harnessing genomics and genome biology to understand malaria biologySarah K Volkman
Department of Immunology and Infectious Disease, Harvard School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, USA
Nat Rev Genet 13:315-28. 2012....
- A second generation human haplotype map of over 3.1 million SNPsKelly A Frazer
The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
Nature 449:851-61. 2007..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
- Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens"Fuli Yu
Department of Genetics, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
Science 316:370. 2007..However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection...
- A genome-wide map of diversity in Plasmodium falciparumSarah K Volkman
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
Nat Genet 39:113-9. 2007..We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite...