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Mary K. Kuhner - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
Phylogenetics, Coalescent Theory
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Paulson TG, Galipeau PC, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Hadi K, Shah M, Arora K, Shelton J, Johnson M, Corvelo A, Maley CC, Yao X, Sanghvi R, et al. Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression. Nature Communications. 13: 2300. PMID 35484108 DOI: 10.1038/s41467-022-29767-7  0.529
2021 Smith LP, Yamato JA, Galipeau PC, Paulson TG, Li X, Sanchez CA, Reid BJ, Kuhner MK. Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus. Evolutionary Applications. 14: 399-415. PMID 33664784 DOI: 10.1111/Eva.13125  0.561
2020 Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, ... ... Kuhner MK, et al. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 183: 197-210.e32. PMID 33007263 DOI: 10.1016/j.cell.2020.08.006  0.463
2019 Galipeau PC, Oman KM, Paulson TG, Sanchez CA, Zhang Q, Marty JA, Delrow JJ, Kuhner MK, Vaughan TL, Reid BJ, Li X. Correction to: NSAID use and somatic exomic mutations in Barrett's esophagus. Genome Medicine. 11: 14. PMID 30867038 DOI: 10.1186/S13073-019-0625-Y  0.325
2018 Smith LP, Yamato JA, Kuhner MK. CNValidator: validating somatic copy-number inference. Bioinformatics (Oxford, England). PMID 30541069 DOI: 10.1093/Bioinformatics/Bty1022  0.507
2018 Galipeau PC, Oman KM, Paulson TG, Sanchez CA, Zhang Q, Marty JA, Delrow JJ, Kuhner MK, Vaughan TL, Reid BJ, Li X. NSAID use and somatic exomic mutations in Barrett's esophagus. Genome Medicine. 10: 17. PMID 29486792 DOI: 10.1186/S13073-018-0520-Y  0.343
2018 Martinez P, Mallo D, Paulson TG, Li X, Sanchez CA, Reid BJ, Graham TA, Kuhner MK, Maley CC. Evolution of Barrett's esophagus through space and time at single-crypt and whole-biopsy levels. Nature Communications. 9: 794. PMID 29476056 DOI: 10.1038/S41467-017-02621-X  0.384
2017 Kuhner MK, Yamato J. A Consensus Method for Ancestral Recombination Graphs. Journal of Molecular Evolution. PMID 28285392 DOI: 10.1007/S00239-017-9786-8  0.343
2016 Kostadinov R, Maley CC, Kuhner MK. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content. Plos Computational Biology. 12: e1004413. PMID 27105344 DOI: 10.1371/Journal.Pcbi.1004413  0.708
2016 Kuhner MK, Kostadinov R, Reid BJ. Limitations of the driver/passenger model in cancer prevention. Cancer Prevention Research (Philadelphia, Pa.). PMID 26932841 DOI: 10.1158/1940-6207.Capr-15-0343  0.701
2015 Li X, Paulson TG, Galipeau PC, Sanchez CA, Liu K, Kuhner MK, Maley CC, Self SG, Vaughan TL, Reid BJ, Blount PL. Assessment of esophageal adenocarcinoma risk using somatic chromosome alterations in longitudinal samples in Barrett's esophagus. Cancer Prevention Research (Philadelphia, Pa.). PMID 26130253 DOI: 10.1158/1940-6207.Capr-15-0130  0.39
2014 Zheng C, Kuhner MK, Thompson EA. Bayesian inference of local trees along chromosomes by the sequential Markov coalescent. Journal of Molecular Evolution. 78: 279-92. PMID 24817610 DOI: 10.1007/S00239-014-9620-5  0.416
2014 Zheng C, Kuhner MK, Thompson EA. Joint inference of identity by descent along multiple chromosomes from population samples. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 21: 185-200. PMID 24606562 DOI: 10.1089/Cmb.2013.0140  0.431
2014 Li X, Galipeau PC, Paulson TG, Sanchez CA, Arnaudo J, Liu K, Sather CL, Kostadinov RL, Odze RD, Kuhner MK, Maley CC, Self SG, Vaughan TL, Blount PL, Reid BJ. Temporal and spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett's esophagus. Cancer Prevention Research (Philadelphia, Pa.). 7: 114-27. PMID 24253313 DOI: 10.1158/1940-6207.Capr-13-0289  0.7
2013 Kostadinov RL, Kuhner MK, Li X, Sanchez CA, Galipeau PC, Paulson TG, Sather CL, Srivastava A, Odze RD, Blount PL, Vaughan TL, Reid BJ, Maley CC. NSAIDs modulate clonal evolution in Barrett's esophagus. Plos Genetics. 9: e1003553. PMID 23785299 DOI: 10.1371/Journal.Pgen.1003553  0.704
2013 McGill JR, Walkup EA, Kuhner MK. Correcting coalescent analyses for panel-based SNP ascertainment. Genetics. 193: 1185-96. PMID 23335334 DOI: 10.1534/Genetics.112.146738  0.424
2010 Kostadinov R, Sprouffske K, Merlo L, Kuhner M, Maley C. Abstract 101: The mechanism of clonal expansion determines the tempo and mode of neoplastic progression in Barrett's esophagus Cancer Research. 70: 101-101. DOI: 10.1158/1538-7445.Am10-101  0.72
2009 McCracken KG, Barger CP, Bulgarella M, Johnson KP, Kuhner MK, Moore AV, Peters JL, Trucco J, Valqui TH, Winker K, Wilson RE. Signatures of high-altitude adaptation in the major hemoglobin of five species of andean dabbling ducks. The American Naturalist. 174: 631-50. PMID 19788356 DOI: 10.1086/606020  0.317
2009 McCracken KG, Bulgarella M, Johnson KP, Kuhner MK, Trucco J, Valqui TH, Wilson RE, Peters JL. Gene flow in the face of countervailing selection: adaptation to high-altitude hypoxia in the betaA hemoglobin subunit of yellow-billed pintails in the Andes. Molecular Biology and Evolution. 26: 815-27. PMID 19151158 DOI: 10.1093/Molbev/Msp007  0.324
2009 Kuhner MK. Coalescent genealogy samplers: windows into population history. Trends in Ecology & Evolution. 24: 86-93. PMID 19101058 DOI: 10.1016/J.Tree.2008.09.007  0.358
2009 Smith LP, Kuhner MK. The limits of fine-scale mapping. Genetic Epidemiology. 33: 344-56. PMID 19048633 DOI: 10.1002/Gepi.20387  0.55
2007 Kuhner MK, Smith LP. Comparing likelihood and Bayesian coalescent estimation of population parameters. Genetics. 175: 155-65. PMID 16510781 DOI: 10.1534/Genetics.106.056457  0.54
2006 Kuhner MK. Robustness of coalescent estimators to between-lineage mutation rate variation. Molecular Biology and Evolution. 23: 2355-60. PMID 16956973 DOI: 10.1093/Molbev/Msl106  0.429
2006 Kuhner MK. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics (Oxford, England). 22: 768-70. PMID 16410317 DOI: 10.1093/Bioinformatics/Btk051  0.41
2000 Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of recombination rates from population data. Genetics. 156: 1393-401. PMID 11063710  0.597
2000 Kuhner MK, Felsenstein J. Sampling among haplotype resolutions in a coalescent-based genealogy sampler. Genetic Epidemiology. 19: S15-21. PMID 11055365 DOI: 10.1002/1098-2272(2000)19:1+<::Aid-Gepi3>3.0.Co;2-V  0.605
2000 Kuhner MK, Felsenstein J. Least squares estimation of variance components for linkage Genetic Epidemiology. 19: S1-S7. PMID 11055363 DOI: 10.1002/1098-2272(2000)19:1+<::Aid-Gepi1>3.0.Co;2-0  0.55
2000 Kuhner MK, Beerli P, Yamato J, Felsenstein J. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics. 156: 439-47. PMID 10978306  0.703
1998 Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics. 149: 429-34. PMID 9584114  0.588
1995 Kuhner MK, Yamato J, Felsenstein J. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics. 140: 1421-30. PMID 7498781  0.611
1994 Kuhner MK, Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution. 11: 459-68. PMID 8015439 DOI: 10.1093/Oxfordjournals.Molbev.A040126  0.606
1992 Kuhner MK, Peterson MJ. Genetic exchange in the evolution of the human MHC class II loci. Tissue Antigens. 39: 209-15. PMID 1529428 DOI: 10.1111/J.1399-0039.1992.Tb01937.X  0.312
1991 Kuhner MK, Lawlor DA, Ennis PD, Parham P. Gene conversion in the evolution of the human and chimpanzee MHC class I loci. Tissue Antigens. 38: 152-64. PMID 1801305 DOI: 10.1111/J.1399-0039.1991.Tb01889.X  0.336
1989 Motro U, Thomson G, Kuhner MK, Robinson WP. Affected sib pair IBS methods: detection of linkage and genetic models. Progress in Clinical and Biological Research. 329: 105-10. PMID 2622936  0.451
1989 Thomson G, Robinson WP, Kuhner MK, Joe S, Klitz W. HLA and insulin gene associations with IDDM. Genetic Epidemiology. 6: 155-60. PMID 2567257 DOI: 10.1002/Gepi.1370060129  0.522
1989 Klitz W, Kuhner MK, Robinson W, Esposito M, Thomson G. Clues to IDDM pathogenesis from genetic and serological traits in multiply affected families. Genetic Epidemiology. 6: 117-22. PMID 2567254 DOI: 10.1002/Gepi.1370060122  0.629
1988 Thomson G, Robinson WP, Kuhner MK, Joe S, MacDonald MJ, Gottschall JL, Barbosa J, Rich SS, Bertrams J, Baur MP. Genetic heterogeneity, modes of inheritance, and risk estimates for a joint study of Caucasians with insulin-dependent diabetes mellitus. American Journal of Human Genetics. 43: 799-816. PMID 3057885  0.487
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