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Mark T. Holder, Ph.D. - Publications

Affiliations: 
Evolution, Ecology, and Behavior University of Kansas, Lawrence, KS, United States 
Area:
Phylogenetics

33 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
2015 McTavish EJ, Steel M, Holder MT. Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections. Molecular Phylogenetics and Evolution. 93: 289-95. PMID 26256643 DOI: 10.1016/j.ympev.2015.07.027  1
2015 McTavish EJ, Hinchliff CE, Allman JF, Brown JW, Cranston KA, Holder MT, Rees JA, Smith SA. Phylesystem: a git-based data store for community-curated phylogenetic estimates. Bioinformatics (Oxford, England). PMID 25940563 DOI: 10.1093/bioinformatics/btv276  1
2015 Lewis PO, Holder MT, Swofford DL. Phycas: software for Bayesian phylogenetic analysis. Systematic Biology. 64: 525-31. PMID 25577605 DOI: 10.1093/sysbio/syu132  1
2013 Oaks JR, Sukumaran J, Esselstyn JA, Linkem CW, Siler CD, Holder MT, Brown RM. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution; International Journal of Organic Evolution. 67: 991-1010. PMID 23550751 DOI: 10.1111/j.1558-5646.2012.01840.x  1
2012 Koch JM, Holder MT. An algorithm for calculating the probability of classes of data patterns on a genealogy. Plos Currents. 4: e4fd1286980c08. PMID 23868168 DOI: 10.1371/4fd1286980c08  1
2012 Peterson AT, Holder MT. Phylogenetic assessment of filoviruses: how many lineages of Marburg virus? Ecology and Evolution. 2: 1826-33. PMID 22957185 DOI: 10.1002/ece3.297  1
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/pro.2071  1
2012 Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. 61: 675-89. PMID 22357728 DOI: 10.1093/sysbio/sys025  1
2012 Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology. 61: 90-106. PMID 22139466 DOI: 10.1093/sysbio/syr095  1
2012 Heath TA, Holder MT, Huelsenbeck JP. A dirichlet process prior for estimating lineage-specific substitution rates. Molecular Biology and Evolution. 29: 939-55. PMID 22049064 DOI: 10.1093/molbev/msr255  1
2012 Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology. 61: 170-3. PMID 21963610 DOI: 10.1093/sysbio/syr100  1
2011 Holder MT, Steel M. Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts. Journal of Theoretical Biology. 280: 159-66. PMID 21540039 DOI: 10.1016/j.jtbi.2011.04.005  1
2011 Sukumaran J, Holder MT. Ginkgo: spatially-explicit simulator of complex phylogeographic histories. Molecular Ecology Resources. 11: 364-9. PMID 21429145 DOI: 10.1111/j.1755-0998.2010.02926.x  1
2011 Edgcomb V, Orsi W, Bunge J, Jeon S, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, Varela R, Epstein S. Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. The Isme Journal. 5: 1344-56. PMID 21390079 DOI: 10.1038/ismej.2011.6  1
2011 Lakner C, Holder MT, Goldman N, Naylor GJ. What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood. Systematic Biology. 60: 161-74. PMID 21233085 DOI: 10.1093/sysbio/syq088  1
2010 Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P. The phylogenetic position of Myxozoa: exploring conflicting signals in phylogenomic and ribosomal data sets. Molecular Biology and Evolution. 27: 2733-46. PMID 20576761 DOI: 10.1093/molbev/msq159  1
2010 Holder MT, Lewis PO, Swofford DL. The akaike information criterion will not choose the no common mechanism model. Systematic Biology. 59: 477-85. PMID 20547783 DOI: 10.1093/sysbio/syq028  1
2010 Sukumaran J, Holder MT. DendroPy: a Python library for phylogenetic computing. Bioinformatics (Oxford, England). 26: 1569-71. PMID 20421198 DOI: 10.1093/bioinformatics/btq228  1
2010 Allman ES, Holder MT, Rhodes JA. Estimating trees from filtered data: identifiability of models for morphological phylogenetics. Journal of Theoretical Biology. 263: 108-19. PMID 20004210 DOI: 10.1016/j.jtbi.2009.12.001  1
2010 Peterson AT, Knapp S, Guralnick R, SoberĂ³ N J, Holder MT. The big questions for biodiversity informatics Systematics and Biodiversity. 8: 159-168. DOI: 10.1080/14772001003739369  1
2008 Holder MT, Sukumaran J, Lewis PO. A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology. 57: 814-21. PMID 18853367 DOI: 10.1080/10635150802422308  1
2008 Holder MT, Zwickl DJ, Dessimoz C. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 4013-21. PMID 18852108 DOI: 10.1098/rstb.2008.0162  1
2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BI, Piel WH, Pond SLK, Poon AFY, et al. The 2006 NESCent phyloinformatics hackathon: A field report Evolutionary Bioinformatics. 3: 287-296.  1
2006 Gelfand AE, Silander JA, Wu S, Latimer A, Lewis PO, Rebelo AG, Holder M. Explaining species distribution patterns through hierarchical modeling Bayesian Analysis. 1: 41-92. DOI: 10.1214/06-BA102  1
2006 Alfaro ME, Holder MT. The posterior and the prior in Bayesian phylogenetics Annual Review of Ecology, Evolution, and Systematics. 37: 19-42. DOI: 10.1146/annurev.ecolsys.37.091305.110021  1
2005 Holder MT, Lewis PO, Swofford DL, Larget B. Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics. Systematic Biology. 54: 961-5. PMID 16385776  1
2005 Lewis PO, Holder MT, Holsinger KE. Polytomies and Bayesian phylogenetic inference. Systematic Biology. 54: 241-53. PMID 16012095 DOI: 10.1080/10635150590924208  1
2004 Zwickl DJ, Holder MT. Model parameterization, prior distributions, and the general time-reversible model in bayesian phylogenetics Systematic Biology. 53: 877-888. PMID 15764557 DOI: 10.1080/10635150490522584  1
2003 Holder M, Lewis PO. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics. 4: 275-84. PMID 12671658 DOI: 10.1038/nrg1044  1
2002 Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO, Hillis DM. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Molecular Biology and Evolution. 19: 1717-26. PMID 12270898  1
2001 Holder MT, Anderson JA, Holloway AK. Difficulties in detecting hybridization. Systematic Biology. 50: 978-82. PMID 12116644 DOI: 10.1080/106351501753462911  1
2000 Hillis DM, Holder MT. Reconstructing the tree of life Trends in Ecology and Evolution. 47-50.  1
1999 Holder MT, Erdmann MV, Wilcox TP, Caldwell RL, Hillis DM. Two living species of coelacanths? Proceedings of the National Academy of Sciences of the United States of America. 96: 12616-20. PMID 10535971 DOI: 10.1073/pnas.96.22.12616  1
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