M Stephens

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. ncbi request reprint Automating sequence-based detection and genotyping of SNPs from diploid samples
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 38:375-81. 2006
  2. pmc A comparison of bayesian methods for haplotype reconstruction from population genotype data
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 73:1162-9. 2003
  3. pmc Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 76:449-62. 2005
  4. pmc A new statistical method for haplotype reconstruction from population data
    M Stephens
    Department of Statistics, University of Oxford
    Am J Hum Genet 68:978-89. 2001
  5. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
  6. pmc Association mapping in structured populations
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Am J Hum Genet 67:170-81. 2000
  7. pmc Imputation-based analysis of association studies: candidate regions and quantitative traits
    Bertrand Servin
    Department of Statistics, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 3:e114. 2007
  8. pmc Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    Na Li
    Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
    Genetics 165:2213-33. 2003
  9. ncbi request reprint Probabilistic segmentation and intensity estimation for microarray images
    Raphael Gottardo
    Department of Statistics, University of Washington, Box 354322, Seattle, 98195 4322, USA
    Biostatistics 7:85-99. 2006
  10. pmc Assigning African elephant DNA to geographic region of origin: applications to the ivory trade
    Samuel K Wasser
    Department of Biology, Center for Conservation Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 101:14847-52. 2004

Detail Information

Publications33

  1. ncbi request reprint Automating sequence-based detection and genotyping of SNPs from diploid samples
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 38:375-81. 2006
    ..9% genotyping accuracy. This algorithm is implemented in a software package, PolyPhred version 5.0, which is freely available for academic use...
  2. pmc A comparison of bayesian methods for haplotype reconstruction from population genotype data
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 73:1162-9. 2003
    ..The new algorithm is included in the software package PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/software.html)...
  3. pmc Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 76:449-62. 2005
    ..Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site...
  4. pmc A new statistical method for haplotype reconstruction from population data
    M Stephens
    Department of Statistics, University of Oxford
    Am J Hum Genet 68:978-89. 2001
    ..Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources...
  5. pmc Inference of population structure using multilocus genotype data
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Genetics 155:945-59. 2000
    ..g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html...
  6. pmc Association mapping in structured populations
    J K Pritchard
    Department of Statistics, University of Oxford, United Kingdom
    Am J Hum Genet 67:170-81. 2000
    ..It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations...
  7. pmc Imputation-based analysis of association studies: candidate regions and quantitative traits
    Bertrand Servin
    Department of Statistics, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 3:e114. 2007
    ..Methods described here are implemented in a software package, Bim-Bam, available from the Stephens Lab website http://stephenslab.uchicago.edu/software.html...
  8. pmc Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    Na Li
    Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
    Genetics 165:2213-33. 2003
    ..We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping...
  9. ncbi request reprint Probabilistic segmentation and intensity estimation for microarray images
    Raphael Gottardo
    Department of Statistics, University of Washington, Box 354322, Seattle, 98195 4322, USA
    Biostatistics 7:85-99. 2006
    ..These approaches produce comparable results, and both appear to offer some advantages over other methods. We use an HIV experiment to compare our approach to two commercial software products: Spot and Arrayvision...
  10. pmc Assigning African elephant DNA to geographic region of origin: applications to the ivory trade
    Samuel K Wasser
    Department of Biology, Center for Conservation Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 101:14847-52. 2004
    ....
  11. pmc Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban
    Samuel K Wasser
    Center for Conservation Biology, Department of Biology, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 104:4228-33. 2007
    ..Such outcomes demonstrate the potential of genetic analyses to help combat the expanding wildlife trade by identifying origin(s) of large seizures of contraband ivory. Broader applications to wildlife trade are discussed...
  12. pmc Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data
    Arindam Roychoudhury
    Department of Statistics, University of Washington, Seattle, Washington 98195 4322, USA
    Genetics 176:1363-6. 2007
    ....
  13. pmc Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein
    Alexander P Reiner
    University of Washington, Department of Epidemiology, Seattle, WA 98195, USA
    Am J Hum Genet 82:1193-201. 2008
    ....
  14. doi request reprint Combating the illegal trade in African elephant ivory with DNA forensics
    Samuel K Wasser
    Center for Conservation Biology, Department of Biology, University of Washington, Seattle, WA 98195 1800, USA
    Conserv Biol 22:1065-71. 2008
    ..These smuggling strategies could not have been detected by forensic information, which typically begins only at the shipping source...
  15. ncbi request reprint msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
    Garrett Hellenthal
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Bioinformatics 23:520-1. 2007
    ..Availability: The source code for msHOT is available at http://home.uchicago.edu/~rhudson1, along with accompanying instructions...
  16. pmc A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase
    Paul Scheet
    Department of Statistics, University of Washington, Seattle, 98195 4322, USA
    Am J Hum Genet 78:629-44. 2006
    ..The methods described in this article are implemented in a software package, fastPHASE, which is available from the Stephens Lab Web site...
  17. ncbi request reprint Automating resequencing-based detection of insertion-deletion polymorphisms
    Tushar R Bhangale
    Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 38:1457-62. 2006
    ..Using this approach, we identify indels in the HapMap ENCODE regions, providing the first report of these polymorphisms in this data set...
  18. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
    ..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...
  19. ncbi request reprint Times on trees, and the age of an allele
    M Stephens
    Department of Statistics, University of Oxford, Oxford, United Kingdom
    Theor Popul Biol 57:109-19. 2000
    ..In particular we use results from the first part of the paper to derive explicit formulae for the density of the age of a mutant allele, conditional on its frequency in either a sample or the population...
  20. ncbi request reprint Insights into recombination from population genetic variation
    Garrett Hellenthal
    Department of Statistics, University of Washington, Seattle, WA 98195, USA
    Curr Opin Genet Dev 16:565-72. 2006
    ....
  21. ncbi request reprint Evidence for substantial fine-scale variation in recombination rates across the human genome
    Dana C Crawford
    Department of Genome Sciences, University of Washington, Box 354322, Seattle, Washington 98195, USA
    Nat Genet 36:700-6. 2004
    ..No primary sequence characteristics are consistently associated with precise hot-spot location, although G+C content and nucleotide diversity are correlated with local recombination rate...
  22. ncbi request reprint Traces of human migrations in Helicobacter pylori populations
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
    Science 299:1582-5. 2003
    ..Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade...
  23. pmc Linkage disequilibrium-based quality control for large-scale genetic studies
    Paul Scheet
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS Genet 4:e1000147. 2008
    ..Our method is implemented in the software package fastPHASE, available from the Stephens Lab website (http://stephenslab.uchicago.edu/software.html)...
  24. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
    Genetics 164:1567-87. 2003
    ..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu...
  25. 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
    ....
  26. 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...
  27. pmc High-resolution mapping of expression-QTLs yields insight into human gene regulation
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, IL, USA
    PLoS Genet 4:e1000214. 2008
    ..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
  28. pmc Absence of the TAP2 human recombination hotspot in chimpanzees
    Susan E Ptak
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    PLoS Biol 2:e155. 2004
    ....
  29. ncbi request reprint Identification of biological relationships from text documents using efficient computational methods
    Mathew Palakal
    Department of Computer and Information Science, Indiana University Purdue University Indianapolis, 723 West Michigan St SL 280, Indianapolis, IN 46202 USA
    J Bioinform Comput Biol 1:307-42. 2003
    ..For the thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81 percent. These results are promising for multi-object identification and relationship finding from biological documents...
  30. pmc RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    John C Marioni
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:1509-17. 2008
    ..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology...
  31. ncbi request reprint Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion
    Thomas De Raedt
    Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
    Nat Genet 38:1419-23. 2006
    ..This apparent conservation of patterns of recombination hotspots in moderately diverged paralogous regions contrasts with recent evidence that these patterns are not conserved in less-diverged orthologous regions of chimpanzees...
  32. ncbi request reprint A multi-level text mining method to extract biological relationships
    Mathew Palakal
    Department of Computer and Information Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
    Proc IEEE Comput Soc Bioinform Conf 1:97-108. 2002
    ..For a corpus of thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81%. The approach is both adaptable and scalable to new problems as opposed to rule-based methods...
  33. ncbi request reprint Global effect of PEG-IFN-alpha and ribavirin on gene expression in PBMC in vitro
    Milton W Taylor
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    J Interferon Cytokine Res 24:107-18. 2004
    ....