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Coalescent genealogy samplers: windows into population history.
Kuhner MK. Kuhner MK. Trends Ecol Evol. 2009 Feb;24(2):86-93. doi: 10.1016/j.tree.2008.09.007. Epub 2008 Dec 26. Trends Ecol Evol. 2009. PMID: 19101058 Free PMC article. Review.
Assessing Differences Between Ancestral Recombination Graphs.
Kuhner MK, Yamato J. Kuhner MK, et al. J Mol Evol. 2015 Jun;80(5-6):258-64. doi: 10.1007/s00239-015-9676-x. Epub 2015 Apr 5. J Mol Evol. 2015. PMID: 25841763
A Consensus Method for Ancestral Recombination Graphs.
Kuhner MK, Yamato J. Kuhner MK, et al. J Mol Evol. 2017 Mar;84(2-3):129-138. doi: 10.1007/s00239-017-9786-8. Epub 2017 Mar 11. J Mol Evol. 2017. PMID: 28285392
Correcting for sequencing error in maximum likelihood phylogeny inference.
Kuhner MK, McGill J. Kuhner MK, et al. G3 (Bethesda). 2014 Nov 4;4(12):2545-52. doi: 10.1534/g3.114.014365. G3 (Bethesda). 2014. PMID: 25378476 Free PMC article.
Bayesian inference of local trees along chromosomes by the sequential Markov coalescent.
Zheng C, Kuhner MK, Thompson EA. Zheng C, et al. Among authors: kuhner mk. J Mol Evol. 2014 May;78(5):279-92. doi: 10.1007/s00239-014-9620-5. Epub 2014 May 11. J Mol Evol. 2014. PMID: 24817610 Free PMC article.
However, in a small trial on simulated data, recovery of local trees was similar to that of LAMARC (Kuhner et al. Genetics 156:1393-1401, 2000a), a sampler which uses the full model....
However, in a small trial on simulated data, recovery of local trees was similar to that of LAMARC (Kuhner et al. Genetics 156:1393-1 …
Joint inference of identity by descent along multiple chromosomes from population samples.
Zheng C, Kuhner MK, Thompson EA. Zheng C, et al. Among authors: kuhner mk. J Comput Biol. 2014 Mar;21(3):185-200. doi: 10.1089/cmb.2013.0140. J Comput Biol. 2014. PMID: 24606562 Free PMC article.
Correcting coalescent analyses for panel-based SNP ascertainment.
McGill JR, Walkup EA, Kuhner MK. McGill JR, et al. Among authors: kuhner mk. Genetics. 2013 Apr;193(4):1185-96. doi: 10.1534/genetics.112.146738. Epub 2013 Jan 18. Genetics. 2013. PMID: 23335334 Free PMC article.
The limits of fine-scale mapping.
Smith LP, Kuhner MK. Smith LP, et al. Among authors: kuhner mk. Genet Epidemiol. 2009 May;33(4):344-56. doi: 10.1002/gepi.20387. Genet Epidemiol. 2009. PMID: 19048633 Free PMC article.
Robustness of coalescent estimators to between-lineage mutation rate variation.
Kuhner MK. Kuhner MK. Mol Biol Evol. 2006 Dec;23(12):2355-60. doi: 10.1093/molbev/msl106. Epub 2006 Sep 6. Mol Biol Evol. 2006. PMID: 16956973
Theor Popul Biol. 7:256-276) and the coalescent maximum likelihood algorithm LAMARC (Kuhner MK. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. ...
Theor Popul Biol. 7:256-276) and the coalescent maximum likelihood algorithm LAMARC (Kuhner MK. 2006. LAMARC 2.0: maximum like …
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters.
Kuhner MK. Kuhner MK. Bioinformatics. 2006 Mar 15;22(6):768-70. doi: 10.1093/bioinformatics/btk051. Epub 2006 Jan 12. Bioinformatics. 2006. PMID: 16410317
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