S. F. Schaffner
A5062342817- Particle physics theoretical and experimental studies
- Quantum Chromodynamics and Particle Interactions
- High-Energy Particle Collisions Research
- Malaria Research and Control
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Mosquito-borne diseases and control
- Neutrino Physics Research
- Dark Matter and Cosmic Phenomena
- Viral Infections and Vectors
- Viral Infections and Outbreaks Research
- Particle Accelerators and Free-Electron Lasers
- SARS-CoV-2 and COVID-19 Research
- Genetic Associations and Epidemiology
- Atomic and Subatomic Physics Research
- COVID-19 epidemiological studies
- Particle Detector Development and Performance
- Evolution and Genetic Dynamics
- Viral gastroenteritis research and epidemiology
- Superconducting Materials and Applications
- Animal Virus Infections Studies
- Black Holes and Theoretical Physics
- Genetic Mapping and Diversity in Plants and Animals
- vaccines and immunoinformatics approaches
- SARS-CoV-2 detection and testing
Broad Institute
2016-2025
Harvard University
2014-2024
Massachusetts Institute of Technology
2000-2024
Kansas State University
2023
Brigham and Women's Hospital
2023
Center for Systems Biology
2014-2021
State Street (United States)
2021
Harvard University Press
1992-2020
Princeton University
2001-2014
Howard Hughes Medical Institute
2007
Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and ancestral haplotypes which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases human genome) in samples from Africa, Europe, Asia. We show that genome can be parsed objectively into blocks: sizable over there is little evidence for historical recombination within...
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 genomes from 78 patients in Leone to ~2000× coverage. observed a rapid accumulation of interhost intrahost genetic variation, allowing us characterize patterns viral transmission over the initial weeks epidemic. This West African variant likely diverged central lineages around 2004, crossed Guinea May 2014, has exhibited sustained human-to-human subsequently, with no...
Significance Discovering the genetic basis of common diseases, such as diabetes, heart disease, and schizophrenia, is a key goal in biomedicine. Genomic studies have revealed thousands variants underlying but these explain only portion heritability. Rare are also likely to play an important role, few examples known thus far, initial discovery efforts with small sample sizes had limited success. In this paper, we describe analytical framework for design rare variant association disease. It...
Population genetic models play an important role in human research, connecting empirical observations about sequence variation with hypotheses underlying historical and biological causes. More specifically, are used to compare measures of variation, linkage disequilibrium (LD), selection expectations under a “null” distribution. In the absence detailed information demographic history, mutation recombination rates, simulations have necessity arbitrary models, usually simple ones. With advent...
Limited clinical and laboratory data are available on patients with Ebola virus disease (EVD). The Kenema Government Hospital in Sierra Leone, which had an existing infrastructure for research regarding viral hemorrhagic fever, has received cared EVD since the beginning of outbreak Leone May 2014.
The human genome contains hundreds of regions whose patterns genetic variation indicate recent positive natural selection, yet for most the underlying gene and advantageous mutation remain unknown. We developed a method, composite multiple signals (CMS), that combines tests selection increases resolution by up to 100-fold. By applying CMS candidate from International Haplotype Map, we localized population-specific selective 55 kilobases (median), identifying known novel causal variants. can...
We have observed the decays ${\mathit{B}}^{0}$\ensuremath{\rightarrow}${\mathit{K}}^{\mathrm{*}}$(892${)}^{0}$\ensuremath{\gamma} and ${\mathit{B}}^{\mathrm{\ensuremath{-}}}$\ensuremath{\rightarrow}${\mathit{K}}^{\mathrm{*}}$(892${)}^{\mathrm{\ensuremath{-}}}$\ensuremath{\gamma}, which are evidence for quark-level process b\ensuremath{\rightarrow}s\ensuremath{\gamma}. The average branching fraction is...
Although several hundred regions of the human genome harbor signals positive natural selection, few relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from 1000 Genomes (1000G) Project composite multiple (CMS) test, we investigated 412 candidate leveraged functional annotation, protein structure modeling, epigenetics, association studies to identify extensively annotate causal variants. The resulting catalog provides a tractable list for...