Reports and Preprints
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:
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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.
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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.
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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.
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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:
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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.
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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:
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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.
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Conditional tests for localizing trait genes.
- Di, Y., and Thompson, E. A. (2009)
- Human Heredity 68: 139--150
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The IBD process along four chromosomes.
- E. A. Thompson (2008)
- Theoretical Population Biology 73: 369--373
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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
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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:
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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.
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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.
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1953: An unrecognized summit in human genetic linkage analysis
- Thompson, E. A. (2007)
- Statistical Surveys, 1: 1--15.
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Fuzzy p-values in latent variable problems
- Elizabeth A Thompson and Charles J Geyer
- Biometrika, 94: 49--60 (March 2007)
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Accounting for epistasis in linkage analysis of general pedigrees
- Yun Ju Sung and Ellen M. Wijsman
- Human Heredity, 63: 144--152 (Feb 2007)
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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:
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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)
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Improving estimates of genetic maps: A maximum likelihood approach
- Stewart, W. C. L. and Thompson, E. A.
- Biometrics 62: 728--734. (Sept 2006)
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Comment: Fuzzy and Randomized Confidence Intervals and P-Values`
- Thompson, E. A.
- Statistical Science, 20: 382--3831 (Nov 2005)
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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:
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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.)
-
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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)
-
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A score for Bayesian genome screening
- E. Warwick Daw, Ellen M. Wijsman, Elizabeth A. Thompson
- Genetic Epidemiology, 24: 181--190 (April 2003)
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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)
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2000 and earlier:
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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)
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A Coalescent Model of Ancestry for a Rare Allele.
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Jinko Graham and Elizabeth A. Thompson
- Genetics, 156: 375--384. (September 2000)
-
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The Number of Trait Loci in Late-Onset Alzheimer Disease.
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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)
-
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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)
-
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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
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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)
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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)
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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)