Research Topics
Species | Alkes L PriceSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
Research Grants
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Detail Information
Publications
Identifying repeat domains in large genomesDegui Zhi
Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
Genome Biol 7:R7. 2006..Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries...
Principal components analysis corrects for stratification in genome-wide association studiesAlkes L Price
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Genet 38:904-9. 2006..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...- Discerning the ancestry of European Americans in genetic association studiesAlkes L Price
Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS Genet 4:e236. 2008..We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data... - Reconstructing Indian population historyDavid Reich
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 461:489-94. 2009..We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically... - Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer ConsortiumBogdan Pasaniuc
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
PLoS Genet 7:e1001371. 2011..Our methods and our publicly available software are broadly applicable to GWAS in admixed populations... - Effects of cis and trans genetic ancestry on gene expression in African AmericansAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
PLoS Genet 4:e1000294. 2008..Both effects are highly significant, and we estimate that 12+/-3% of all heritable variation in human gene expression is due to cis variants... - A genomewide admixture map for Latino populationsAlkes L Price
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Am J Hum Genet 80:1024-36. 2007..We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America... - Sensitive detection of chromosomal segments of distinct ancestry in admixed populationsAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
PLoS Genet 5:e1000519. 2009.... - The history of African gene flow into Southern Europeans, Levantines, and JewsPriya Moorjani
Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS Genet 7:e1001373. 2011..For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas... 
Using population admixture to help complete maps of the human genomeGiulio Genovese
1 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA 3 Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA 4 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Genet 45:406-14. 2013..We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies...- Reconstructing Native American population historyDavid Reich
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 488:370-4. 2012..A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America... - Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individualsAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
PLoS Genet 7:e1001317. 2011.... - Pooled association tests for rare variants in exon-resequencing studiesAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
Am J Hum Genet 86:832-8. 2010..We used a rigorous population-genetics simulation framework to evaluate the power of the method, and we applied the method to empirical sequencing data from three disease studies... - The impact of divergence time on the nature of population structure: an example from IcelandAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
PLoS Genet 5:e1000505. 2009.... - Population structure and eigenanalysisNick Patterson
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
PLoS Genet 2:e190. 2006..This means that we can predict the dataset size needed to detect structure... - Analysis of case-control association studies with known risk variantsNoah Zaitlen
Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
Bioinformatics 28:1729-37. 2012..Roughly, this method estimates model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature... - Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variantsGeorge Ayodo
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Am J Hum Genet 81:234-42. 2007..This empirically demonstrates that combining association analysis with evidence of natural selection can increase power to detect risk variants by orders of magnitude--up to P=.000018 for HBB and P=.00043 for CD36... - Informed conditioning on clinical covariates increases power in case-control association studiesNoah Zaitlen
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
PLoS Genet 8:e1003032. 2012..This suggests that applying our method to existing and future association studies of these diseases may identify novel disease loci... - Genetic variation in RNASEL associated with prostate cancer risk and progressionMara S Meyer
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
Carcinogenesis 31:1597-603. 2010..The results of this study support a link between RNASEL and prostate cancer and suggest that the association may be mediated through inflammation. These novel findings warrant replication in future studies... - Extremely low-coverage sequencing and imputation increases power for genome-wide association studiesBogdan Pasaniuc
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
Nat Genet 44:631-5. 2012.... - Long-range LD can confound genome scans in admixed populationsAlkes L Price
Am J Hum Genet 83:132-5; author reply 135-9. 2008 - Two independent alleles at 6q23 associated with risk of rheumatoid arthritisRobert M Plenge
Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
Nat Genet 39:1477-82. 2007..We show that these two SNP associations are statistically independent, are each reproducible in the comparison of our data and WTCCC data, and define risk and protective haplotypes for rheumatoid arthritis at 6q23... - Application of ancestry informative markers to association studies in European AmericansMichael F Seldin
Department of Biochemistry, University of California Davis, Davis, California, United States of America
PLoS Genet 4:e5. 2008 - De novo identification of repeat families in large genomesAlkes L Price
Department of Computer Science and Engineering, University of California San Diego La Jolla, CA 92093-0114, USA
Bioinformatics 21:i351-8. 2005..AVAILABILITY: Source code is available for download at http://www-cse.ucsd.edu/groups/bioinformatics/software.html.. - Principal component analysis of genetic dataDavid Reich
Nat Genet 40:491-2. 2008 - Whole-genome analysis of Alu repeat elements reveals complex evolutionary historyAlkes L Price
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0114, USA
Genome Res 14:2245-52. 2004..We apply a novel method to identify and statistically validate 213 Alu subfamilies. We build an evolutionary tree of these subfamilies and conclude that the history of Alu evolution is more complex than previous studies had indicated...
Research Grants
- Diverse implications of population structure for identifying human disease genesAlkes Price; Fiscal Year: 2007....