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 N_e from temporally spaced samples: Eric C. Anderson, Ellen G. Williamson, and Elizabeth A. Thompson; Genetics, 156: 2109-2118. (December 2000)

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