Mary Sara McPeek's Publications


Last updated 10 January 2025
  1. Zhou H., McPeek M. S. (2024) Overcoming the “feast or famine” effect: improved interaction testing in genome-wide association studies bioRxiv doi: 10.1101/2024.02.13.580168

  2. Akinbiyi T., McPeek M. S., Abney M. (2024) ADELLE: A global testing method for Trans-eQTL mapping PLoS Genetics 21 (1): e1011563 doi.org/10.1371/journal.pgen.1011563

  3. Mbatchou J., McPeek M. S. (2024) JASPER: fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression American Journal of Human Genetics 111: 1750-1769 doi.org/10.1016/j.ajhg.2024.06.010

  4. Mbatchou J., Abney M., McPeek M. S. (2023) BRASS: permutation methods for binary traits in genetic association studies with structured samples PLoS Genetics 19(11):e1011020 doi.org/10.1371/journal.pgen.1011020

  5. Weine E., McPeek M. S., Abney M. (2023) Application of equal local levels to improve Q-Q plot testing bands with R package qqconf Journal of Statistical Software 106: 1-31 doi.org/10.18637/jss.v106.i10

  6. Conomos M.P., Reiner A.P., McPeek M.S., Thornton T.A. Genome-wide control of population structure and relatedness in genetic association studies via linear mixed models with orthogonally partitioned structure https://www.biorxiv.org/content/10.1101/409953v1

  7. Wu X., McPeek M. S. (2018) L-GATOR: genetic association testing for a longitudinally-measured quantitative trait in samples with related individuals American Journal of Human Genetics 102: 547-591

  8. Wang M., Roux F., Bartoli C., Huard-Chauveau C., Meyer C., Lee H., Roby D., McPeek M.S., Bergelson J. (2018) Two-way mixed-effects methods for joint association mapping analysis using both host and pathogen genomes PNAS vol. 115 no. 24 E5440-E5449

  9. Zhong S., Jiang D., McPeek M. S. (2016) CERAMIC: Case-Control Association Testing in Samples with Related Individuals Based on Retrospective Mixed Model Analysis with Adjustment for Covariates PLoS Genetics 12(10):.e1006329. doi:10.1371/journal.pgen.1006329

  10. Wang M., Jakobsdottir J., Smith A. V., McPeek M. S. (2016) G-STRATEGY: Optimal Selection of Individuals for Sequencing in Genetic Association Studies Genetic Epidemiology 40:446-460 | DOI: 10.1002/gepi.21982

  11. Jiang D., Zhong S., McPeek M. S. (2016) Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn's Disease American Journal of Human Genetics 98: 243-255

  12. Jiang D., Mbatchou J., McPeek M. S. (2015) "Retrospective Association Analysis of Binary Traits: Overcoming Some Limitations of the Additive Polygenic Model" Human Heredity 80: 187-195

  13. Jiang D., McPeek M. S. (2014) Robust Rare Variant Association Testing for Quantitative Traits in Samples with Related Individuals Genetic Epidemiology 38: 10-20

  14. Jakobsdottir J., McPeek M. S. (2013) MASTOR: Mixed-Model Association Mapping of Quantitative Traits in Samples with Related Individuals American Journal of Human Genetics 92: 652-666

  15. Thornton T., Zhang Q., Cai X., Ober C., McPeek M. S. (2012) XM: Association Testing on the X-Chromosome in Case-Control Samples with Related Individuals Genetic Epidemiology 36: 438-450

  16. McPeek M. S. (2012) BLUP Genotype Imputation for Case-Control Association Testing with Related Individuals and Missing Data Journal of Computational Biology 19: 756-765

  17. McPeek M. S. (2012) Genetic Recombination in Selected Works of Terry Speed, Sandrine Dudoit, ed., Springer-Verlag New York Publishers

  18. Thornton T., McPeek M. S. (2010) ROADTRIPS: Case-control association testing with partially or completely unknown population and pedigree structure American Journal of Human Genetics 86: 172-184

  19. Zhang J., Niyogi P., McPeek M. S. (2009) Laplacian eigenfunctions learn population structure PLoS ONE 4(12) e7928

  20. Wang Z., McPeek M. S. (2009) ATRIUM: Testing Untyped SNPs in Case-Control Association Studies with Related Individuals American Journal of Human Genetics 85: 667-678

  21. Wang Z., McPeek M. S. (2009) An Incomplete-Data Quasi-Likelihood Approach to Haplotype-Based Genetic Association Studies on Related Individuals, (2009) Journal of the American Statistical Association 104: 1251-1260

  22. Wang H.-Y., Fu Y., McPeek M. S., Lu X., Nuzhdin S., Su A., Lu J., Wu M.-L., Wu C.-I. (2008) Complex genetic interactions underlying expression differences between Drosophila races --- Analysis of chromosome substitutions PNAS 105: 6362-6367

  23. Thornton T., McPeek M. S. (2007) Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test American Journal of Human Genetics 81: 321-337

  24. Pluzhnikov A., Nolan D. K., Tan Z., McPeek M. S., Ober C (2007) Correlation of Intergenerational Family Sizes Suggests a Genetic Component to Reproductive Fitness American Journal of Human Genetics 81: 165-169

  25. Tong L., Mets L., McPeek M. S (2007) Likelihood-Based Inference for Multi-Color Optical Mapping Statistical Applications in Genetics and Molecular Biology 6(1) article 5

  26. Zheng M., McPeek M. S. (2007) Multipoint Linkage Disequilibrium Mapping with Haplotype Block Structure American Journal of Human Genetics 80: 112-125

  27. Armstrong N. J., McPeek M. S., Speed T. P. (2006) Incorporating interference into linkage analysis for experimental crosses Biostatistics 7: 374-386

  28. Zhang J., Schneider D., Ober C., McPeek M. S. (2005) Multilocus linkage disequilibrium mapping by the decay of haplotype sharing with samples of related individuals Genetic Epidemiology 29: 128-140

  29. Bourgain C., Abney M., Schneider D., Ober C., McPeek M. S. (2004) Testing for Hardy-Weinberg in samples with related individuals Genetics 168:2349-2361

  30. Weiss L. A., Veenstra-VanderWeele J., Newman D. L., Kim S.-J., Dytch H., McPeek M. S., Cheng S., Ober C., Cook E. H. Jr., Abney M. (2004) Genome-wide association study identifies ITGB3 as a QTL for whole blood serotonin European Journal of Human Genetics 12:949-954

  31. Newman D. L., Hoffjan S., Bourgain C., Abney M., Nicolae R. I., Profits E. T., Grow M. A., Walker K., Steiner L., Parry R., Reynolds R., McPeek M. S., Cheng S., Ober C. (2004) Are common disease susceptibility alleles the same in outbred and founder populations? European Journal of Human Genetics 12:584-590

  32. McPeek M. S., Wu X., Ober C. (2004) Best linear unbiased allele-frequency estimation in complex pedigrees Biometrics 60:359-367 Erratum

  33. Zheng M., McPeek M. S. (2004) Parametric bootstrap for assessment of goodness of fit of models for block haplotype structure Springer Lecture Notes in Computer Science Series 2983, S. Istrail, M. S. Waterman, A. G. Clark, eds., pp. 113-123

  34. Bourgain C., Hoffjan S., Nicolae R., Newman D., Steiner L., Walker K., Reynolds R., Ober C., McPeek M. S. (2003) Novel case-control test in a founder population identifies P-selectin as an atopy susceptibility locus American Journal of Human Genetics 73:612-626

    Typos in published version

  35. Strahs A., McPeek M. S. (2003) Multipoint fine-scale linkage disequilibrium mapping: importance of modeling background LD IMS Lecture Notes Monograph Series, Volume 40 Science and Statistics: A Festschrift for Terry Speed, Darlene R. Goldstein, ed., pp. 343-366

  36. Newman D. L., Abney M., Dytch H., Parry R., McPeek M. S., Ober C. (2003) Major loci influencing serum triglyceride levels on 2q14 9p21 localized by homozygosity-by-descent mapping in a large Hutterite pedigree Human Molecular Genetics 12:137-144

  37. Sun L., Wilder K., McPeek M. S. (2002) Enhanced pedigree error detection Human Heredity 54:99-110

  38. McPeek M. S. (2002) Inference on pedigree structure from genome screen data Statistica Sinica 12:311-335

  39. Abney M., Ober C., McPeek M. S. (2002) Quantitative trait homozygosity and association mapping and empirical genome-wide significance in large complex pedigrees: fasting serum insulin level in the Hutterites American Journal of Human Genetics 70:920-934 Errata and typos

  40. Sun L., Cox N. J., McPeek M. S. (2002) A statistical method for identification of polymorphisms that explain a linkage result American Journal of Human Genetics 70: 399-411

  41. Newman D. L., Abney M., McPeek M. S., Ober C., Cox N. J. (2001) The importance of genealogy in determining genetic associations with complex traits Am J Hum Genet 69:1146-1148

  42. Sun L., Abney M., McPeek M. S. (2001) Detection of misspecified relationships in inbred and outbred pedigrees Genetic Epidemiology 21: S36-S41, Figure 1

  43. Ober C., Abney M., McPeek M. S. (2001) The genetic dissection of complex traits in a founder population Am J Hum Genet 69:1068-1079

  44. Abney M., McPeek M. S., Ober C. (2001) Broad and narrow heritabilities of quantitative traits in a founder population Am J Hum Genet 68:1302-1307

  45. McPeek M. S. (2000) From mouse to human: fine mapping of quantitative trait loci in a model organism PNAS 97:12389-12390

  46. McPeek, M. S., Sun L. (2000) Statistical tests for detection of misspecified relationships by use of genome-screen data Am J Hum Genet 66:1076-1094 Errata and typos

  47. Abney, M., McPeek, M. S., Ober C. (2000) Estimation of variance components of quantitative traits in inbred populations Am J Hum Genet 66:629-650

  48. Girardet A., McPeek M. S., Leeflang E. P., Munier F., Arnheim N., Claustres M., Pellestor F. (2000) Meiotic segregation analysis of RB1 alleles in retinoblastoma pedigrees by use of single-sperm typing Am J Hum Genet 66:167-175

  49. McPeek M. S. (1999) SPERMSEG: analysis of segregation distortion in single sperm data Am J Hum Genet 65:1195-1197

  50. McPeek, M. S., Strahs, A. (1999) Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping Am J Hum Genet 65:858-875 Errata and typos

  51. Grewal, R. P., Cancel G., Leeflang E. P., Duerr A., McPeek M. S., Draghinas D., Xiang Y., Stevanin G., Alnot M.-O., Brice A., Arnheim N. (1999) French Machado-Joseph Disease patients do not exhibit gametic segregation distortion: a sperm typing analysis Hum Mol Genet 8:1779-1784

  52. McPeek M. S. (1999) Optimal allele-sharing statistics for genetic mapping using affected relatives Genet Epi 16:225-249 Typo in published version

  53. McPeek M. S. (1996) Introduction to recombination and linkage analysis IMA Volumes in Mathematics and its Applications, Volume 81, Genetic mapping and DNA sequencing, T. P. Speed and M. S. Waterman, eds., Springer-Verlag New York Publishers

  54. Leeflang, E., McPeek, M. S., Arnheim, N. (1996) Analysis of meiotic segregation using single-sperm typing: meiotic drive at the Myotonic Dystrophy locus Am J Hum Genet 59:896-904

  55. Zhao, H., McPeek, M. S., Speed, T. (1995) Statistical analysis of chromatid interference Genetics 139:1057-1065

  56. Zhao, H., Speed, T., McPeek, M.S. (1995) Statistical analysis of crossover interference using the chi-square model Genetics 139:1045-1056

  57. McPeek, M. S., Speed, T. (1995) Modeling interference in genetic recombination Genetics 139:1031-1044

  58. McPeek M. S. (1995) Constrained maximum likelihood estimation for ordering three genetic loci with a small-sample robustness result for the no-interference model. Techincal report #410, Department of Statistics, University of Chicago (1995)

  59. Scherer, S., McPeek, M. S., Speed, T. (1994) Atypical regions in large genomic DNA sequences PNAS 91:7134-7138

  60. Applications of Statistics to Modeling Genetic Recombination and Ordering Chromosome Markers by Linkage Analysis. Ph.D. thesis, Department of Statistics, University of California at Berkeley (1993)

  61. Evans, S., McPeek, M. S., Speed, T. (1993)A characterisation of crossover models that possess map functions Theor. Popul. Biol. 43: 80-90, with S.N. Evans and T.P. Speed

  62. Speed, T., McPeek, M. S., Evans, S. (1992) Robustness of the no-interference model for ordering markers PNAS 89:3103-3106

  63. Guerra, R., McPeek, M. S., Speed, T., Stewart, M. (1992) A Bayesian analysis for mapping from radiation hybrid data Cytogenetics and Cell Genetics 59: 104-106