Print this page

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.

Brian Browning

  • Browning BL and Browning SR. A fast, powerful method for detecting identity by descent, The American Journal of Human Genetics 88, 173-182, 2011.
  • Browning BL and Yu Z. Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies, The American Journal of Human Genetics 85, 847-861, 2009.
  • Browning SR and Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering, The American Journal of Human Genetics 81, 1084-1097, 2007.

Sharon Browning

  • Browning, SR and Thompson, EA. Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies, Genetics, 190, 1521-1531, 2012.
  • Madsen, BE & Browning, SR. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5, e1000384, 2009.
  • Browning, SR & Browning, BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81, 1084-1097, 2007.

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. Comments on the Analysis of Unbalanced Microarray Data. Bioinformatics, 25: 2035-2041, 2009.
  • 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.

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.

Adam Leaché

  • Leaché, AD and Rannala B. The accuracy of species tree estimation under simulation: a comparison of methods, Systematic Biology, 60:126-137, 2011.
  • Leaché, AD and Fujita MK. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus), Proceedings of the Royal Society B: Biological Sciences, 277:3071-3077, 2010.
  • Leaché, AD. Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus), Systematic Biology. 58:547-559, 2009.

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

  • Palacios JA and Minin VN. Integrated nested Laplace approximation for Bayesian nonparametric phylodynamics, Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence, 726-735, 2012.
  • Sawaya SM, Lennon D, Buschiazza G, Gemmell N, Minin VN. Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model, Genome Biology and Evolution, 4: 636-647, 2012.
  • Minin VN, O'Brien JD, Seregin A. Imputation estimators partially correct for model misspecification, Statistical Applications in Genetics and Molecular Biology, 10: Article 17, 2011.

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.

Ali Shojaie

  • Shojaie A, Basu S, and Michailidis G. Adaptive Thresholding for Reconstructing Regulatory Networks from Time Course Gene Expression Data, Statistics In Biosciences, in press.
  • Shojaie A and Michailidis G. Network Enrichment Analysis in Complex Experiments, Statistical Applications in Genetics and Molecular Biology, 9:Article 22, 2010.
  • Shojaie A and Michailidis G. Analysis of Gene Sets Based on The Underlying Regulatory Network, Journal of Computational Biology, 16: 407-426, 2009.

Elizabeth Thompson

  • Brown, MD, Glazner, CG, Zheng, C, and Thompson, EA. Inferring coancestry in population samples in the presence of linkage disequilibrium, Genetics, 190: 1447-1460, 2012.
  • Glazner, CG, and Thompson, EA. Improving pedigree-based linkage analysis by estimating coancestry among families, Statistical Applications in Genetics and Molecular Biology 11: Issue 2, Article 11, 2012.
  • Thompson, EA. The structure of genetic linkage data: from LIPED to 1M SNPs, Human Heredity, 71: 86-96, 2011.

Timothy Thornton

  • Thornton T, Tang H, Hoffmann TJ, Ochs-Balcom HM, Caan BJ, Risch N. Estimating kinship in admixed populations, American Journal of Human Genetics, 91:122-138, 2012.
  • Thornton T., McPeek, MS. ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure. American Journal of Human Genetics, 86, 172-184, 2010.
  • Thornton T, McPeek MS. Case-control association testing with related individuals: a more powerful quasi-likelihood score test. American Journal of Human Genetics 81, 321-337, 2007.

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

  • Skelly, DA, Johansson, M, Madeoy, J, Wakefield, J and Akey, JM. A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-Seq data, in press, Genome Research, 2011.
  • Wakefield, J. Bayesian methods for examining Hardy-Weinberg equilibrium, Biometrics, 66, 257-265, 2010.
  • 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

  • Buckleton, JS, Krawczak, M, and Weir, BS. The interpretation of lineage markers in forensic DNA testing, Forensic Science International: Genetics 5:78-83, 2011.
  • Weir, BS and Laurie CC. Statistical genetics in the genome era, Genetics Research 92:461-470, 2011.
  • Hill, WG and Weir, BS. Variation in actual relationship as a consequence of Mendelian sampling and linkage, Genetics Research 93:47-74, 2011.

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.

Daniela Witten

  • Witten DM, Friedman JH, and Simon N. New insights and faster computations for the graphical lasso. Journal of Computational and Graphical Statistics, 20, 892-900, 2011.
  • Witten DM and Tibshirani R. Penalized classification using Fisher's linear discriminant. Journal of the Royal Statistical Society, Series B, 73, 753-772, 2011.
  • Witten DM, Tibshirani R, and Hastie T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis, Biostatistics, 10, 515-534, 2009.