Alkes L Price

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
  2. ncbi request reprint Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
  3. pmc Discerning the ancestry of European Americans in genetic association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 4:e236. 2008
  4. pmc Reconstructing Indian population history
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 461:489-94. 2009
  5. pmc Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium
    Bogdan Pasaniuc
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    PLoS Genet 7:e1001371. 2011
  6. pmc Improved ancestry inference using weights from external reference panels
    Chia Yen Chen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 29:1399-406. 2013
  7. pmc Effects of cis and trans genetic ancestry on gene expression in African Americans
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 4:e1000294. 2008
  8. pmc A genomewide admixture map for Latino populations
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 80:1024-36. 2007
  9. pmc The history of African gene flow into Southern Europeans, Levantines, and Jews
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001373. 2011
  10. pmc Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000519. 2009

Detail Information

Publications28

  1. pmc Identifying repeat domains in large genomes
    Degui 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...
  2. ncbi request reprint Principal components analysis corrects for stratification in genome-wide association studies
    Alkes 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...
  3. pmc Discerning the ancestry of European Americans in genetic association studies
    Alkes 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...
  4. pmc Reconstructing Indian population history
    David 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...
  5. pmc Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium
    Bogdan 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...
  6. pmc Improved ancestry inference using weights from external reference panels
    Chia Yen Chen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 29:1399-406. 2013
    ....
  7. pmc Effects of cis and trans genetic ancestry on gene expression in African Americans
    Alkes 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...
  8. pmc A genomewide admixture map for Latino populations
    Alkes 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...
  9. pmc The history of African gene flow into Southern Europeans, Levantines, and Jews
    Priya 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...
  10. pmc Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000519. 2009
    ....
  11. pmc Informed conditioning on clinical covariates increases power in case-control association studies
    Noah 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...
  12. pmc Using population admixture to help complete maps of the human genome
    Giulio Genovese
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 45:406-14, 414e1-2. 2013
    ..We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies...
  13. pmc Replication and fine mapping of asthma-associated loci in individuals of African ancestry
    David B Kantor
    Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children s Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
    Hum Genet 132:1039-47. 2013
    ..These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry. ..
  14. pmc Analysis of case-control association studies with known risk variants
    Noah 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...
  15. pmc Reconstructing Native American population history
    David 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...
  16. pmc The impact of divergence time on the nature of population structure: an example from Iceland
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000505. 2009
    ....
  17. pmc Population structure and eigenanalysis
    Nick 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...
  18. pmc Pooled association tests for rare variants in exon-resequencing studies
    Alkes 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...
  19. pmc Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001317. 2011
    ....
  20. pmc Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants
    George 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...
  21. pmc Genetic variation in RNASEL associated with prostate cancer risk and progression
    Mara 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...
  22. pmc Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
    Bogdan Pasaniuc
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Genet 44:631-5. 2012
    ....
  23. pmc Two independent alleles at 6q23 associated with risk of rheumatoid arthritis
    Robert 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...
  24. pmc Application of ancestry informative markers to association studies in European Americans
    Michael F Seldin
    Department of Biochemistry, University of California Davis, Davis, California, United States of America
    PLoS Genet 4:e5. 2008
  25. pmc Long-range LD can confound genome scans in admixed populations
    Alkes L Price
    Am J Hum Genet 83:132-5; author reply 135-9. 2008
  26. doi request reprint Principal component analysis of genetic data
    David Reich
    Nat Genet 40:491-2. 2008
  27. ncbi request reprint De novo identification of repeat families in large genomes
    Alkes L Price
    Department of Computer Science and Engineering, University of California San Diego La Jolla, CA 92093 0114, USA
    Bioinformatics 21:i351-8. 2005
    ..We develop a new method for de novo identification of repeat families via extension of consensus seeds; our method enables a rigorous definition of repeat boundaries, a key issue in repeat analysis...
  28. pmc Whole-genome analysis of Alu repeat elements reveals complex evolutionary history
    Alkes 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...