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Paul O. Lewis, Ph.D. - Publications

Affiliations: 
Ecology and Evolutionary Biology University of Connecticut, Storrs, CT, United States 
Area:
Phylogenetics
Website:
http://www.eeb.uconn.edu/people/plewis/
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49 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
2020 Wang YB, Chen MH, Shi W, Lewis P, Kuo L. Inflated Density Ratio and Its Variation and Generalization for Computing Marginal Likelihoods. Journal of the Korean Statistical Society. 49: 244-263. PMID 33071541 DOI: 10.1007/S42952-019-00013-Z  0.354
2019 Wang YB, Chen MH, Kuo L, Lewis PO. Partition Weighted Approach for Estimating the Marginal Posterior Density with Applications. Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America. 28: 334-349. PMID 31263347 DOI: 10.1080/10618600.2018.1529600  0.323
2019 Fučíková K, Lewis PO, Neupane S, Karol KG, Lewis LA. Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae. Peerj. 7: e6899. PMID 31143537 DOI: 10.7717/Peerj.6899  0.584
2019 Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics. Systematic Biology. PMID 31034053 DOI: 10.1093/Sysbio/Syz020  0.781
2019 Neupane S, Fucíková K, Lewis LA, Kuo L, Chen MH, Lewis PO. Assessing Combinability of Phylogenomic Data using Bayes Factors. Systematic Biology. PMID 30726954 DOI: 10.1093/Sysbio/Syz007  0.643
2018 Wang YB, Chen MH, Kuo L, Lewis PO. A New Monte Carlo Method for Estimating Marginal Likelihoods. Bayesian Analysis. 13: 311-333. PMID 29805725 DOI: 10.1214/17-Ba1049  0.342
2018 McManus HA, Fučíková K, Lewis PO, Lewis LA, Karol KG. Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life. American Journal of Botany. PMID 29722901 DOI: 10.1002/Ajb2.1066  0.314
2017 Neupane S, Lewis PO, Dessein S, Shanks H, Paudyal S, Lens F. Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae). American Journal of Botany. PMID 28274947 DOI: 10.3732/Ajb.1600248  0.565
2017 Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE. Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. American Journal of Botany. PMID 28104589 DOI: 10.3732/Ajb.1600227  0.364
2016 Watanabe S, Fučíková K, Lewis LA, Lewis PO. Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza. American Journal of Botany. 103: 865-75. PMID 27208355 DOI: 10.3732/Ajb.1500481  0.306
2016 Lewis PO, Chen MH, Kuo L, Lewis LA, Fučíková K, Neupane S, Wang YB, Shi D. Estimating Bayesian Phylogenetic Information Content. Systematic Biology. PMID 27155008 DOI: 10.1093/Sysbio/Syw042  0.599
2016 Fučíková K, Lewis LA, Lewis PO. Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta). Data in Brief. 7: 558-70. PMID 27054159 DOI: 10.1016/J.Dib.2016.03.014  0.36
2016 Fučíková K, Lewis PO, Lewis LA. Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution. Molecular Phylogenetics and Evolution. PMID 26903036 DOI: 10.1016/J.Ympev.2016.01.022  0.359
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  0.768
2015 Neupane S, Dessein S, Wikström N, Lewis PO, Long C, Bremer B, Motley TJ. The Hedyotis-Oldenlandia complex (Rubiaceae: Spermacoceae) in Asia and the Pacific: Phylogeny revisited with new generic delimitations Taxon. 64: 299-322. DOI: 10.12705/642.8  0.59
2014 Fučíková K, Lewis PO, Lewis LA. Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta). Journal of Phycology. 50: 14-25. PMID 26988005 DOI: 10.1111/Jpy.12118  0.334
2014 Fučíková K, Lewis PO, González-Halphen D, Lewis LA. Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta). Genome Biology and Evolution. 6: 2170-80. PMID 25106621 DOI: 10.1093/Gbe/Evu172  0.305
2014 Lewis PO, Xie W, Chen MH, Fan Y, Kuo L. Posterior predictive Bayesian phylogenetic model selection. Systematic Biology. 63: 309-21. PMID 24193892 DOI: 10.1093/Sysbio/Syt068  0.494
2014 Fučíková K, Leliaert F, Cooper ED, Å kaloud P, D'Hondt S, De Clerck O, Gurgel CFD, Lewis LA, Lewis PO, Lopez-Bautista JM, Delwiche CF, Verbruggen H. New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data Frontiers in Ecology and Evolution. 2. DOI: 10.3389/Fevo.2014.00063  0.36
2014 Fu?íková K, Lewis PO, Lewis LA. Widespread desert affiliation of trebouxiophycean algae (Trebouxiophyceae, Chlorophyta) including discovery of three new desert genera Phycological Research. DOI: 10.1111/Pre.12062  0.335
2013 Fan Y, Wu R, Chen MH, Kuo L, Lewis PO. A Conditional Autoregressive Model for Detecting Natural Selection in Protein-Coding DNA Sequences Springer Proceedings in Mathematics and Statistics. 55: 203-212. DOI: 10.1007/978-1-4614-7846-1_17  0.308
2012 Tippery NP, Fučíková K, Lewis PO, Lewis LA. Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes. Journal of Phycology. 48: 1482-1493. PMID 27009998 DOI: 10.1111/Jpy.12003  0.364
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  0.729
2011 Xie W, Lewis PO, Fan Y, Kuo L, Chen MH. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic Biology. 60: 150-60. PMID 21187451 DOI: 10.1093/Sysbio/Syq085  0.5
2011 Fan Y, Wu R, Chen MH, Kuo L, Lewis PO. Choosing among partition models in Bayesian phylogenetics. Molecular Biology and Evolution. 28: 523-32. PMID 20801907 DOI: 10.1093/Molbev/Msq224  0.503
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  0.739
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  0.769
2008 Wickett NJ, Fan Y, Lewis PO, Goffinet B. Distribution and evolution of pseudogenes, gene losses, and a gene rearrangement in the plastid genome of the nonphotosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida). Journal of Molecular Evolution. 67: 111-22. PMID 18594897 DOI: 10.1007/S00239-008-9133-1  0.395
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  0.745
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  0.767
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  0.742
2005 Lewis LA, Lewis PO. Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta). Systematic Biology. 54: 936-47. PMID 16338765 DOI: 10.1080/10635150500354852  0.338
2005 Lewis PO, Holder MT, Holsinger KE. Polytomies and Bayesian phylogenetic inference. Systematic Biology. 54: 241-53. PMID 16012095 DOI: 10.1080/10635150590924208  0.784
2003 Lewis PO. NCL: a C++ class library for interpreting data files in NEXUS format. Bioinformatics (Oxford, England). 19: 2330-1. PMID 14630669 DOI: 10.1093/Bioinformatics/Btg319  0.343
2003 Holder M, Lewis PO. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics. 4: 275-84. PMID 12671658 DOI: 10.1038/Nrg1044  0.784
2003 Lewis LA, Lewis PO. 98 Phylodiversity of green algae (chlorophyta) from desert microbiotic crusts Journal of Phycology. 39: 34-34. DOI: 10.1111/J.0022-3646.2003.03906001_98.X  0.357
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  0.734
2002 Holsinger KE, Lewis PO, Dey DK. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology. 11: 1157-64. PMID 12074723 DOI: 10.1046/J.1365-294X.2002.01512.X  0.325
2001 Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology. 50: 525-39. PMID 12116651 DOI: 10.1080/10635150117959  0.736
2001 Lewis PO. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology. 50: 913-25. PMID 12116640 DOI: 10.1080/106351501753462876  0.434
2001 Conant GC, Lewis PO. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Molecular Biology and Evolution. 18: 1024-33. PMID 11371591 DOI: 10.1093/Oxfordjournals.Molbev.A003874  0.639
2001 Lewis PO. Phylogenetic systematics turns over a new leaf. Trends in Ecology & Evolution. 16: 30-37. PMID 11146142 DOI: 10.1016/S0169-5347(00)02025-5  0.422
2001 Lewis PO, Swofford DL. Back to the future: Bayesian inference arrives in phylogenetics Trends in Ecology and Evolution. 16: 600-601. DOI: 10.1016/S0169-5347(01)02322-9  0.783
1998 Lewis PO. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Molecular Biology and Evolution. 15: 277-83. PMID 9501494 DOI: 10.1093/Oxfordjournals.Molbev.A025924  0.406
1995 Williams CG, Hamrick JL, Lewis PO. Multiple-population versus hierarchical conifer breeding programs: a comparison of genetic diversity levels. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 90: 584-94. PMID 24173955 DOI: 10.1007/Bf00222007  0.302
1995 Gaut BS, Lewis PO. Success of maximum likelihood phylogeny inference in the four-taxon case. Molecular Biology and Evolution. 12: 152-62. PMID 7877489 DOI: 10.1093/Oxfordjournals.Molbev.A040183  0.359
1995 Lewis PO, Crawford DJ. Pleistocene refugium endemics exhibit greater allozymic diversity than widespread congeners in the genus Polygonella (Polygonaceae) American Journal of Botany. 82: 141-149. DOI: 10.1002/J.1537-2197.1995.Tb11483.X  0.527
1994 Kaplan NL, Lewis PO, Weir BS. Age of the delta F508 cystic fibrosis mutation. Nature Genetics. 8: 216-8. PMID 7533028 DOI: 10.1038/Ng1194-216A  0.365
1992 Govindaraju D, Lewis P, Cullis C. Phylogenetic analysis of pines using ribosomal DNA restriction fragment length polymorphisms Plant Systematics and Evolution. 179: 141-153. DOI: 10.1007/Bf00937592  0.393
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