Stephen F Schaffner

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
  2. ncbi request reprint Detecting recent positive selection in the human genome from haplotype structure
    Pardis C Sabeti
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 419:832-7. 2002
  3. pmc Calibrating a coalescent simulation of human genome sequence variation
    Stephen F Schaffner
    Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02139, USA
    Genome Res 15:1576-83. 2005
  4. ncbi request reprint Searching for signals of evolutionary selection in 168 genes related to immune function
    Emily C Walsh
    Novartis Institutes for BioMedical Research, 250 Mass Ave, Cambridge, MA 02139, USA
    Hum Genet 119:92-102. 2006
  5. ncbi request reprint Human genome sequence variation and the influence of gene history, mutation and recombination
    David E Reich
    Whitehead Institute MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Genet 32:135-42. 2002
  6. doi request reprint A composite of multiple signals distinguishes causal variants in regions of positive selection
    Sharon R Grossman
    Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 327:883-6. 2010
  7. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
  8. pmc An integrated haplotype map of the human major histocompatibility complex
    Emily C Walsh
    Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
    Am J Hum Genet 73:580-90. 2003
  9. doi request reprint Natural selection in a bangladeshi population from the cholera-endemic ganges river delta
    Elinor K Karlsson
    Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Sci Transl Med 5:192ra86. 2013
  10. pmc Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite
    Daniel J Park
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 109:13052-7. 2012

Detail Information

Publications18

  1. ncbi request reprint The structure of haplotype blocks in the human genome
    Stacey 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...
  2. ncbi request reprint Detecting recent positive selection in the human genome from haplotype structure
    Pardis 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...
  3. pmc Calibrating a coalescent simulation of human genome sequence variation
    Stephen 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...
  4. ncbi request reprint Searching for signals of evolutionary selection in 168 genes related to immune function
    Emily C Walsh
    Novartis Institutes for BioMedical Research, 250 Mass Ave, Cambridge, MA 02139, USA
    Hum Genet 119:92-102. 2006
    ....
  5. ncbi request reprint Human genome sequence variation and the influence of gene history, mutation and recombination
    David E Reich
    Whitehead Institute MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Genet 32:135-42. 2002
    ....
  6. doi request reprint A composite of multiple signals distinguishes causal variants in regions of positive selection
    Sharon 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...
  7. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  8. pmc An integrated haplotype map of the human major histocompatibility complex
    Emily 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...
  9. doi request reprint Natural selection in a bangladeshi population from the cholera-endemic ganges river delta
    Elinor K Karlsson
    Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Sci Transl Med 5:192ra86. 2013
    ..Our findings shed light on the genetic basis of cholera resistance in a population from the Ganges River Delta and present a promising approach for identifying genetic factors influencing susceptibility to infectious diseases. ..
  10. pmc Sequence-based association and selection scans identify drug resistance loci in the Plasmodium falciparum malaria parasite
    Daniel J Park
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 109:13052-7. 2012
    ..falciparum...
  11. ncbi request reprint The X chromosome in population genetics
    Stephen F Schaffner
    Whitehead MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA
    Nat Rev Genet 5:43-51. 2004
  12. pmc Identifying recent adaptations in large-scale genomic data
    Sharon R Grossman
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 152:703-13. 2013
    ..We experimentally characterized one candidate nonsynonymous variant in Toll-like receptor 5 (TLR5) and show that it leads to altered NF-κB signaling in response to bacterial flagellin. PAPERFLICK:..
  13. pmc Integrating common and rare genetic variation in diverse human populations
    David M Altshuler
    Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA
    Nature 467:52-8. 2010
    ....
  14. pmc Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    Daniel 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...
  15. doi request reprint Harnessing genomics and genome biology to understand malaria biology
    Sarah 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
    ....
  16. ncbi request reprint 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...
  17. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly 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...
  18. ncbi request reprint A genome-wide map of diversity in Plasmodium falciparum
    Sarah 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...