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Conference Proceedings

Salter [Kubatko] LA. 2000. Algorithms for phylogenetic tree reconstruction. Proceeding of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences. 2:459-465.

Journal Article

Liu L, Yu L, Kubatko LS, Pearl DK, Edwards SV. 2009. Coalescent methods for estimating multilocus phylogenetic trees. Molecular Phylogenetics and Evolution. 53(1):320-328.D.

Efromovich S, Kubatko LS. 2008. Coalescent time distributions in trees of arbitrary size. Statistical Applications in Genetics and Molecular Biology. Vol 7: Iss. 1, Art. 2

Standberg AKK, Salter [Kubatko] LA. 2004. A comparison of methods for estimating the transition:transversion ratio from DNA sequences. Molecular Phylogenetics and Evolution. 32:495-503.

Boykin LM, Kubatko LS, Lowrey TK. 2010. Comparison of methods for rooting phylogenetic trees: A case study using Orcuttieae (Poacea: Chloridoidea). Molecular Phylogenetics and Evolution. 54:687-700.

Salter [Kubatko] LA. 2001. Complexity of the likelihood surface for a large DNA data set. Systematic Biology. 50:970-978.

Brock G, Pihur V, Kubatko LS. 2009. Detecting gene regulatory networks from microarray data usig fuzzy logic. Fuzzy Systems in Bioinformatics and Computational Biology. pgs:141-164.

Meng C, Kubatko LS. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theoretical Population Biology. 75:35-45.

Shoff ME, Joslin EY, Tu L, Kubatko LS, Fuerst PA. 2008. Efficacy of contact lens systems against recent clinical and tap water Acanthamoeba isolates. Cornea. 27(6):713-719.

Wang Q, Salter [Kubatko] LA, Pearl DK. 2002. Estimation of evolutionary parameters with phylogenetic trees. Journal of Molecular Evolution. 55:684-695.

Brock GN, Beavis WD, Kubatko LS. 2009. Fuzzy logic and related methods as a screening tool for detecting gene regulatory networks. Information Fusion. 10:250-259.

Degnan J, Salter [Kubatko] LA. 2005. Gene tree distributions under the coalescent process. Evolution. 59:24-37.

Kubatko LS. 2009. Identifying hybridization events in the presence of coalescence via model selection. Systematic Biology. 58(5):478-488.

Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology. 56:17-24.

Kubatko LS, Gibbs HL, Bloomquist E. 2010. Inferring Species-Level Phylogenies Using Multi-Locus Data for a Recent Radiation of Sistrurus Rattlesnakes. Systematic Biology, accepted.

Kubatko LS. 2009. Modeling the past: A resource for the future (review of the book Coalescent Theory:An Introduction by John Wakeley). Trends in Ecology and Evolution. 24(3):125-126.

Stone AC, Battistuzzi F, Kubatko LS, Perry GH, Trudeau E, Lin H, Kumar S. 2010. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical Transactions of Royal Society B. 365:inpress.

Frankel W, Tranovich J, Salter [Kubatko] LA, Bumgardner G, Baker P. 2002. The optimal number of biopsies to evaluate for liver transplantation. Liver Transplantation. 8:1044-1050.

Melman SD, Steinauer ML, Cunningham C, Kubatko LS, Mwangi IN, Mutuku MW, Karanja DMS, Colley DG, Black C, Secor WE et al.. 2009. Reduced susceptibility of naturally occurring Schistosoma mansoni to praziquantel following repeated exposures: origin, measurement and likelihood of persistence. PLoS Neglected Tropical Diseases. 3(8)e504. doi:10.1371/journal.ntd.0000504D

Salter [Kubatko] LA. 2004. Review of The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny (Edited by Marco Salemi and Anne-Mieke Vandamme. Cambridge, England: Cambridge University Press). American Journal of Human Biology. 16:354-355.

Huang H, He Q, Kubatko LS, Knowles LL. 2010. Sources of error for species-tree estimation: Impact of mutational and coalescent effects on accuracy and implications for choosing among different methods . Systematic Biology, accepted.

Gilchrist M, Salter [Kubatko] LA, Wagner A. 2004. A statistical framework for interpreting high-throughput proteomic datasets. Bioinformatics. 20(5):689-700.

Kubatko LS, Carstens BC, Knowles LL. 2009. STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence. Bioinformatics. 25(7):971-973.

Salter [Kubatko] LA, Pearl DK. 2001. A stochastic search strategy for estimation of maximum likelihoodphylogenetic trees. Systematic Biology. 50:7-17.

Turner T, Salter [Kubatko] LA, Gold J. 2001. Temporal-method estimation of Ne from highly polymorphic loci. Conservation Genetics. 2:297-308.

Powell A, Jacobson D, Salter [Kubatko] LA, Natvig D. 2003. Variation among natural isolates of Neurospora on small spatial scales. Mycologia. 95:809-819.

Wilbur A, Kubatko LS, Feurstein J, Hurtado A, Hill K, Stone A. 2007. Vitamin D receptor gene polymorphisms and susceptibility to M. tuberculosis in Native Paraguayans. Tuberculosis. 87:329-337.

Special Volume

Pearl DK, Salter [Kubatko] LA. 2002. The analysis of DNA sequences. Biostatistical Genetics and Genetic Epidemiology. :217-227.

Kubatko LS. 2007. Inference of Phylogenetic Trees. Tutorials in Mathematical Biosciences IV: Evolution and Ecology. pgs:1-38.

Harmon M, VanPool T, Leonard R, VanPool C, Salter [Kubatko] LA. 2006. Reconstructing the flow of information across time and space: A phylogenetic analysis of ceramic traditions from Pre-Hispanic West Mexico, North Mexico and the U.S. Southwest. Mapping Our Ancestors: Phylogenetic Methods in Anthropology and Prehistory. pgs:209-229.