| Year |
Citation |
Score |
| 2021 |
Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. Plos Computational Biology. 17: e1008924. PMID 33983918 DOI: 10.1371/journal.pcbi.1008924 |
0.723 |
|
| 2021 |
McTavish EJ, Sanchez Reyes LL, Holder MT. OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life. Systematic Biology. PMID 33970279 DOI: 10.1093/sysbio/syab033 |
0.798 |
|
| 2020 |
Gibson MJS, Crawford DJ, Holder MT, Mort ME, Kerbs B, de Sequeira MM, Kelly JK. Genome-wide genotyping estimates mating system parameters and paternity in the island species Tolpis succulenta. American Journal of Botany. 107: 1189-1197. PMID 32864742 DOI: 10.1002/Ajb2.1515 |
0.537 |
|
| 2018 |
McTavish EJ, Holder M, Cranston K. Nurturing a sustainable Open Tree of Life Biodiversity Information Science and Standards. 2: e25727. DOI: 10.3897/biss.2.25727 |
0.789 |
|
| 2017 |
Redelings BD, Holder MT. A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species. Peerj. 5: e3058. PMID 28265520 DOI: 10.7717/Peerj.3058 |
0.399 |
|
| 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 |
0.789 |
|
| 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 |
0.793 |
|
| 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 |
0.807 |
|
| 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 |
0.784 |
|
| 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 |
0.358 |
|
| 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 |
0.3 |
|
| 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 |
0.687 |
|
| 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 |
0.794 |
|
| 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 |
0.803 |
|
| 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 |
0.774 |
|
| 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 |
0.756 |
|
| 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 |
0.417 |
|
| 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 |
0.687 |
|
| 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 |
0.399 |
|
| 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 |
0.38 |
|
| 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 |
0.41 |
|
| 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 |
0.758 |
|
| 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 |
0.729 |
|
| 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 |
0.403 |
|
| 2010 |
Peterson AT, Knapp S, Guralnick R, Soberó N J, Holder MT. The big questions for biodiversity informatics Systematics and Biodiversity. 8: 159-168. DOI: 10.1080/14772001003739369 |
0.349 |
|
| 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 |
0.787 |
|
| 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 |
0.801 |
|
| 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. DOI: 10.4137/Ebo.S0 |
0.749 |
|
| 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 |
0.71 |
|
| 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 |
0.352 |
|
| 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 DOI: 10.1080/10635150500354670 |
0.758 |
|
| 2005 |
Lewis PO, Holder MT, Holsinger KE. Polytomies and Bayesian phylogenetic inference. Systematic Biology. 54: 241-53. PMID 16012095 DOI: 10.1080/10635150590924208 |
0.741 |
|
| 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 |
0.789 |
|
| 2003 |
Holder M, Lewis PO. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics. 4: 275-84. PMID 12671658 DOI: 10.1038/Nrg1044 |
0.731 |
|
| 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 DOI: 10.1093/Oxfordjournals.Molbev.A003994 |
0.709 |
|
| 2001 |
Holder MT, Anderson JA, Holloway AK. Difficulties in detecting hybridization. Systematic Biology. 50: 978-82. PMID 12116644 DOI: 10.1080/106351501753462911 |
0.661 |
|
| 2000 |
Hillis DM, Holder MT. Reconstructing the tree of life Trends in Ecology and Evolution. 47-50. |
0.618 |
|
| 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 |
0.765 |
|
| 1999 |
Kichler K, Holder MT, Davis SK, Márquez-M R, Owens DW. Detection of multiple paternity in the Kemp's ridley sea turtle with limited sampling Molecular Ecology. 8: 819-830. DOI: 10.1046/j.1365-294X.1999.00635.x |
0.731 |
|
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