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StatGen Research

Here are three recent publications of each member of the StatGen faculty. To learn more about statistical genetics research at UW, please go directly to the faculty home pages.

Josh Akey

  • Biswas S, Storey JD, Akey JM. Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis. BMC Bioinformatics, 9:244, 2008.
  • Akey JM, Swanson WJ, Madeoy J, Eberle M, Shriver MD. TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations. Human Molecular Genetics, 15:2106-13,2006.
  • Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biology, 2:e286, 2004

Karen Edwards

  • Edwards KL, Hutter CM, Yin Wan J, Kim H, Monks SA. Genome-wide Linkage Scan for the Metabolic Syndrome: The GENNID Study. Obesity (Silver Spring), 2008.
  • Harrison TA, Burke W, Edwards KL. The asthma consultative process: a collaborative approach to integrating genomics into public health practice. Preventing Chronic Disease, 2, A27, 2005.
  • Kim H, Hutter CM, Monks SA, Edwards KL. Comparison of single-nucleotide polymorphisms and microsatellites in detecting quantitative trait loci for alcoholism: The Collaborative Study on the Genetics of Alcoholism. BMC Genetics, 6 Suppl 1, S5, 2005.

Joe Felsenstein

  • Felsenstein J. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist, 171:713-25, 2008.
  • Felsenstein J. Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Molecular Biology and Evolution, 23:691-700, 2006.
  • Felsenstein, J. Using the quantitative genetic threshold model for inferences between and within species. Philosophical Transactions of the Royal Society of London, series B 360: 1427-1434, 2005.

Phil Green

  • Saunders CT and Green P. Insights from modeling protein evolution with context-dependent mutation and asymmetric amino acid selection. Molecular Biology and Evolution, 24: 2632-2647, 2007.
  • Baek D, Davis C, Ewing B, Gordon D and Green P. Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Research, 17:145-155, 2007.
  • Hwang DG and Green P. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proceedings of the National Academy of Sciences U.S.A., 101:13994-14001, 2004.

Gail Jarvik

  • Carlson CS, Heagerty PJ, Nord AS, Pritchard DK, Ranchalis J, Boguch JM, Duan H, Hatsukami TS, Schwartz SM, Rieder MJ, Nickerson DA, Jarvik GP. TagSNP evaluation for the association of 42 inflammation loci and vascular disease: Evidence of IL6, FGB, ALOX5, NFKBIA, and IL4R loci effects. Human Genetics, 121, 65-75, 2007.
  • Badzioch MB, Goode EL, Jarvik GP. The role of parametric linkage methods in complex trait analyses using microsatellites. BMC Genetics, 6 (Suppl1), S48, 2005.
  • Jarvik GP, Hatsukami TS, Carlson CS, Richter RJ, Jampsa R, Brophy VH, Margolin S, Rieder MJ, Nickerson DA, Schellenberg GD, Heagerty PJ, Furlong CE. Novel paraoxonase (PON1) nonsense and missense mutations predicted by functional genomic assay of PON1 status. Pharmacogenetics, 13, 291-295, 2003.

Kathleen Kerr

  • Kerr KF. Extended analysis of benchmark datasets for Agilent two-color microarrays. BMC Bioinformatics, 8, 371, 2007.
  • Kerr MK. Design considerations for efficient and effective microarray studies. Biometrics, 59, 822-828, 2003.
  • Kerr MK. Linear models for microarray data analysis: Hidden similarities and differences, Journal of Computational Biology 10, 891-901, 2003.

Mary Kuhner

  • Kuhner MK, Smith LP. Comparing likelihood and Bayesian coalescent estimation of population parameters. Genetics, 175, 155-65, 2007.
  • Kuhner MK. Robustness of coalescent estimators to between-lineage mutation rate variation. Mol Biol Evol. 23, 2355-2360, 2006.
  • Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of recombination rates from population data. Genetics, 156, 1393-1401, 2000.

Barbara McKnight

  • McKnight B, Tierney C, McGorray SP, Day NE. Likelihood-based inference for the genetic relative risk based on affected-sibling-pair marker data. Biometrics, 54, 426-443, 1998.
  • Siegmund K, McKnight B. Modeling hazard functions in families. Genetic Epidemiology, 15, 147-171, 1998.
  • Tierney C, McKnight B. Power of affected sibling method tests for linkage. Human Heredity, 43, 276-287, 1993.

Vladimir Minin

  • Minin VN, Bloomquist EW, Suchard MA. Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Molecular Biology and Evolution, 25, 1459-1471, 2008.
  • Minin VN and Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. Journal of Mathematical Biology, 56, 391-412, 2008.
  • Minin VN, Dorman KS, Fang F, and Suchard MA. Phylogenetic mapping of recombination hot-spots in HIV via spatially smoothed change-point processes. Genetics, 175, 1773-1785, 2007.

Debbie Nickerson

  • Howie BN, Carlson CS, Rieder MJ, Nickerson DA. Efficient selection of tagging single-nucleotide polymorphisms in multiple populations. Human Genetics, 120, 58-68, 2006.
  • Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nature Genetics, 38, 375-381, 2006.
  • Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA. Genomic regions exhibiting positive selection identified from dense genotype data. Genome Research, 1553-1565, 2005.

Elizabeth Thompson

  • Tong L and Thompson EA. Multilocus lod scores in large pedigrees: Combination of exact and approximate calculations. Human Heredity, 65, 142-153, 2008.
  • Thompson EA and Geyer CJ. Fuzzy p-values in latent variable problems, Biometrika, 90, 49-60, 2007.
  • Stewart WCL and Thompson EA. Improving estimates of genetic maps: A maximum likelihood approach. Biometrics, 62, 728-734, 2006.

Barbara Trask

  • Rudd MK, Friedman C, Parghi SS, Linardopoulou EV, Hsu L, Trask BJ. Elevated rates of sister chromatid exchange at chromosome ends. PLoS Genetics, 3, e32, 2007.
  • Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication, Nature, 437, 94-100, 2005.
  • Lane RP, Young J, Newman T, Trask BJ. Species specificity in rodent pheromone receptor repertoires. Genome Res, 14, 603-608, 2004.

Jon Wakefield

  • Wakefield J. Bayes factors for genome-wide association studies: comparison with p-values. Genetic Epidemiology, published online ahead of print, DOI:10.1002/gepi.20359.
  • Li S, Wakefield J, Self S. A Trans-dimensional Bayesian model for pattern recognition in DNA sequences. Biostatistics, published online ahead of print, DOI:10.1093/biostatistics/kxm058.
  • Wakefield J. A Bayesian measure of the probability of false discovery in genetic epidemiology studies. American Journal of Human Genetics, 81, 208-227, 2007.

Bruce Weir

  • Weir BS. Linkage disequilibrium and association tests. Annual Reviews of Genomics and Human Genetics 9, 129-142, 2008.
  • Hill WG and Weir BS. Prediction of multi-locus inbreeding coefficients and relation to linkage disequilibrium in random mating populations. Theoretical Population Biology, 72, 179-185, 2007.
  • Weir BS. The rarity of DNA profiles. Annals of Applied Statistics 1, 358-370, 2007.

Ellen Wijsman

  • Igo RP Jr and Wijsman EM. Empirical significance values for linkage analysis: trait simulation using posterior model distributions from MCMC oligogenic segregation analysis. Genetic Epidemiology, 32, 119-131, 2008.
  • Sung YJ and Wijsman EM. Accounting for epistasis in linkage analysis of general pedigrees. Human Heredity, 63, 144-152, 2007.
  • Sung YJ, Dawson G, Munson J, Estes A, Schellenberg GD, Wijsman EM. Genetic investigation of quantitative traits related to autism: use of multivariate polygenic models with ascertainment adjustment. American Journal of Human Genetics, 76, 68-81, 2005.