Reports and Preprints

Some of these publications are NIH grant related, and some are not.
NIH-grant papers|| Other on-line publications

Online Journal Articles (NIH-grant related)

2015

  • Glazner and Thompson

    2014

  • Zheng, Kuhner and Thompson: 2 papers

    2013

  • Sverdlov, S., and Thompson, E. A. (2013) Correlation between relatives given complete geno- types: From identity by descent to identity by function. Theoretical Population Biology 88: 57--67.
  • Koepke, H. A., and Thompson, E. A. (2013) Efficient identification of equivalences in dynamic graphs and pedigree structures. Journal of Computational Biology 20: 551--570.
  • Thompson, E. A. (2013) Identity by descent: Variation in meiosis, across genomes, and in populations. Genetics 194: 301--326.
  • Cheung, C.Y.K., Thompson, E. A., and Wijsman, E. M. (2013) GIGI: An Approach to Effective Imputation of Dense Genotypes on Large Pedigrees. American Journal of Human Genetics 92: 504--516. [PMID: 23561844].
  • Silberstein, M., Weissbrod, O., Otten, L., Tzemach, A., Anisenia, A., Shtark, O., Tuberg, D., Galfrin, E., Gannon, I., Shalata, A., Borochowitz, Z. U., Dechter, R., Thompson, E. and Geiger, D. (2012) A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees. Bioinformatics, doi: 10.1093/bioinformatics/bts658

    2012:

    Computationally efficient multipoint linkage analysis on extended pedigrees for trait models with two contributing major loci
    M. Su and E. A. Thompson (2012)
    Genetic Epiemiology 38: 602--611.
    Inferring coancestry in population samples in the presence of linkage disequilibrium
    M. D. Brown, C. G. Glazner, C. Zheng, and E. A. Thompson (2012)
    Genetics 190: 1447--1460.
    Detecting rare variant associations by identity by descent mapping in case-control studies
    Browning, S. G. and Thompson, E. A. (2012)
    Genetics 190: 1521--1531.
    Improving pedigree-based linkage analysis by estimating coancestry among families
    C. G. Glazner and E. A. Thompson
    Statistical Applications in Genetics and Molecular Biology: 11: Iss. 2, Article 11.
    See also the The files to recreate the analyses.
    See Final submitted PDF of paper.

    2010-2011:

    Inferring coancestry of genome segments in populations
    Thompson, E.A. and Glazner, C. G. (2011).
    ISI contributed paper; Dublin, Ireland.
    The structure of genetic linkage data: from LIPED to 1M SNPs
    Thompson, E.A. (2011)
    Human Heredity 71: 86--96.
    A likelihood-based trait-model-free approach to linkage detection of binary trait
    Basu, S., Stephens, M., Pankow, J.S., and Thompson, E. A. (2010)
    Biometrics 66: 205-213.

    2008-2009:

    Inferring coancestry of genome segments in populations
    Thompson, E. A. (2009)
    Invited Proceedings of the 57th Session of the International Statistical Institute IPM13: Paper 0325. Durban, South Africa.
    Contrasting IBD estimators, association studies, and linkage analyses using the Framingham data.
    Marchani, E.E., Di, Y., Choi, Y., Cheung, C., Su, M., Boehm, F., Thompson, E.A., and Wijsman, E.M. (2009)
    Genetic Analysis Workshop 16. BMC Proceedings 3 (Suppl 7): S102.
    Conditional tests for localizing trait genes.
    Di, Y., and Thompson, E. A. (2009)
    Human Heredity 68: 139--150
    The IBD process along four chromosomes.
    E. A. Thompson (2008)
    Theoretical Population Biology 73: 369--373
    Exact trait-model-free tests for linkage detection in pedigrees
    Basu, S, Di, Y., and Thompson, E. A. (2008)
    Annals of Human Genetics, 72: 676--682
    Multilocus lod scores in large pedigrees: Combination of exact and approximate calculations
    Liping Tong and E. A. Thompson (2008)
    Human Heredity, 65: 142--153

    2007:

    Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors
    Yun Ju Sung, Yanming Di, Audrey Q Fu, Joseph H Rothstein, Weiva Sieh, Liping Tong, Elizabeth A Thompson, and Ellen M Wijsman
    BMC Proceedings 2007, 1(Suppl 1): S93.
    Summary of Genetic Analysis Workshop 15: Group 9 linkage analysis of the CEPH expression data
    Ellen M. Wijsman, Yun Ju Sung, Alfonso Buil, on behalf of Group 9
    Genetic Epidemiology, 31: (Issue S1), S75-S85.
    1953: An unrecognized summit in human genetic linkage analysis
    Thompson, E. A. (2007)
    Statistical Surveys, 1: 1--15.
    Fuzzy p-values in latent variable problems
    Elizabeth A Thompson and Charles J Geyer
    Biometrika, 94: 49--60 (March 2007)
    Accounting for epistasis in linkage analysis of general pedigrees
    Yun Ju Sung and Ellen M. Wijsman
    Human Heredity, 63: 144--152 (Feb 2007)
    MCMC-based linkage analysis for complex traits on general pedigrees: multipoint analysis with a two-locus model and a polygenic component
    Yun Ju Sung, Elizabeth A. Thompson, Ellen M. Wijsman
    Genetic Epidemiology, 31: 103--114 (Feb 2007)

    2005-2006:

    Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain Monte Carlo provides practical approaches for genome scans on general pedigrees
    Ellen M. Wijsman, Joseph H. Rothstein, and Elizabeth A. Thompson
    American Journal of Human Genetics, 79: 846--858 (Nov 2006)
    Improving estimates of genetic maps: A maximum likelihood approach
    Stewart, W. C. L. and Thompson, E. A.
    Biometrics 62: 728--734. (Sept 2006)
    Comment: Fuzzy and Randomized Confidence Intervals and P-Values`
    Thompson, E. A.
    Statistical Science, 20: 382--3831 (Nov 2005)
    MCMC Multilocus Lod Scores: Application of a New Approach
    George, A. W., Wijsman E. M., and Thompson, E. A.
    Human Heredity, 59: 98--108 (April 2005)

    2002, 2003:

    Discovering Disease Genes: Multipoint Linkage Analysis via a New Markov Chain Monte Carlo Approach
    George, A. W. and Thompson, E. A.
    Statistical Science, 18: 515--531 (Dec 2003)
    Genome Sharing in Large Pedigrees: Multiple Imputation of ibd for Linkage Detection
    Thompson, E. A., and Basu, S.
    Human Heredity, 56: 119--125 (November 2003)
    (Also available as ISBN 3-8055-7676-5.)
    Estimation of the inbreeding coefficient through use of genomic data.
    Leutenegger, A.-L., Prum, B., Genin, E., Verny, C., Lemainque, A., Clerget-Darpoux, F., and Thompson, E.A.
    American Journal of Human Genetics, 73: 515-531 (September 2003)
    A score for Bayesian genome screening
    E. Warwick Daw, Ellen M. Wijsman, Elizabeth A. Thompson
    Genetic Epidemiology, 24: 181--190 (April 2003)
    Relationship inference from trios of individuals in the presence of typing error
    Sieberts, S., Wijsman, E.M., and Thompson, E. A.
    American Journal of Human Genetics, 70: 170--180 (January 2002)

    2000 and earlier:

    Bias in multipoint linkage analysis arising from map misspecification
    E. Warwick Daw, Elizabeth A. Thompson, Ellen M. Wijsman
    Genetic Epidemiology, 19: 366--380 (Dec 2000)
    A Coalescent Model of Ancestry for a Rare Allele.
    Jinko Graham and Elizabeth A. Thompson
    Genetics, 156: 375--384. (September 2000)
    The Number of Trait Loci in Late-Onset Alzheimer Disease.
    E. Warwick Daw, Haydeh Payami, Ellen J. Nemens, David Nochlin, Thomas D. Bird, Gerard D. Schellenberg, and Ellen M. Wijsman
    American Journal of Human Genetics, 66: 196--204. (January 2000)
    Multipoint Oligogenic Analysis of Age-at-Onset Data with Applications to Alzheimer Disease Pedigrees
    E. Warwick Daw, Simon C. Heath, Ellen M. Wijsman
    American Journal of Human Genetics, 64: 839-852 (March 1999)
    Disequilibrium Likelihoods for Fine-Scale Mapping of a Rare Allele
    Jinko Graham, Elizabeth Thompson.
    American Journal of Human Genetics, 63: 1517-1530 (November 1998)
    Note that most electronic journals are only available to subscribers, or through Universities having institutional subscriptions.
    For recent articles we have linked to open-access PubMed versions where possible.

    Online Journal Articles ( other)

    Using microsatellite diversity in wild Anegada iguanas (Cyclura pinguis) to establish relatedness in a captive breeding group of this critically endangered species
    Mitchell, A. A., Lau, J., Chemnick, L. G., Thompson, E. A., Alberts, A. C., Ryder, O. A., and Gerber, G. P. (2011)
    Conservation Genetics 12: 771--781

    A two-stage pruning algorithm for likelihood computation for a population tree
    RoyChoudhury, A., Felsenstein, J., and Thompson, E. A. (2008)
    Genetics 180: 1095--1105

    Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population
    Bink, M.C.A.M., Anderson, A.D., van de Weg, W.E., and Thompson, E. A. (2008)
    Theoretical and Applied Genetics 117: 843--855

    Estimation of the inbreeding coefficient through use of genomic data.
    Leutenegger, A., Prum, B., Genin, E., Verny, C., Clerget-Darpoux, F., and Thompson, E. A.
    American Journal of Human Genetics 73: 516--523. (September 2003)

    A model for the length of tracts of identity by descent in finite random mating populations.
    Nicola H. Chapman and Elizabeth A. Thompson
    Theoretical Population Biology 64: 141--150. (September 2003)

    The effect of population history on the lengths of ancestral chromosome segments.
    Nicola H. Chapman and Elizabeth A. Thompson
    Genetics, 162: 449--458. (September 2002)

    A model-based method for identifying species hybrids using multilocus genetic data
    Eric C. Anderson and Elizabeth A. Thompson
    Genetics, 160: 1217-1229. (March 2002)

    Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples
    Eric C. Anderson, Ellen G. Williamson, and Elizabeth A. Thompson
    Genetics, 156: 2109-2118. (December 2000)