Mary K. Kuhner - Publications

University of Washington, Seattle, Seattle, WA 
Phylogenetics, Coalescent Theory

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
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  1
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  1
2018 Smith LP, Yamato JA, Kuhner MK. CNValidator: validating somatic copy-number inference. Bioinformatics (Oxford, England). PMID 30541069 DOI: 10.1093/Bioinformatics/Bty1022  1
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  0.92
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  1
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  1
2015 Kuhner MK, Yamato J. Assessing Differences Between Ancestral Recombination Graphs. Journal of Molecular Evolution. 80: 258-64. PMID 25841763 DOI: 10.1007/S00239-015-9676-X  1
2015 Kuhner MK, Yamato J. Practical performance of tree comparison metrics. Systematic Biology. 64: 205-14. PMID 25378436 DOI: 10.1093/Sysbio/Syu085  1
2014 Kuhner MK, McGill J. Correcting for sequencing error in maximum likelihood phylogeny inference. G3 (Bethesda, Md.). 4: 2545-52. PMID 25378476 DOI: 10.1534/G3.114.014365  1
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  1
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  1
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  1
2013 McGill JR, Walkup EA, Kuhner MK. GraphML specializations to codify ancestral recombinant graphs. Frontiers in Genetics. 4: 146. PMID 23967010 DOI: 10.3389/Fgene.2013.00146  1
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  1
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  1
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  1
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  1
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  1
2009 Smith LP, Kuhner MK. The limits of fine-scale mapping. Genetic Epidemiology. 33: 344-56. PMID 19048633 DOI: 10.1002/Gepi.20387  1
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  1
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  1
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  1
2000 Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of recombination rates from population data. Genetics. 156: 1393-401. PMID 11063710  1
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  1
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  1
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  1
1998 Kuhner MK, Yamato J, Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics. 149: 429-34. PMID 9584114  1
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  1
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  1
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  1
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  1
1990 Kuhner M, Watts S, Klitz W, Thomson G, Goodenow RS. Gene conversion in the evolution of both the H-2 and Qa class I genes of the murine major histocompatibility complex Genetics. 126: 1115-1126. PMID 2076814  1
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  1
1989 Kuhner MK, Goodenow RS. DNA sequences of mouse H-2 and Qa genes. Immunogenetics. 30: 458-64. PMID 2592022 DOI: 10.1007/Bf02421178  1
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  1
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  1
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  1
Show low-probability matches.