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2002
Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO, Hillis DM.  2002.  Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference. Molecular Biology and Evolution. 19:1717-1726.
2006
Brown RM, Richards S, Sukumaran J, Fougopoulos J.  2006.  A new morphologically cryptic species of forest frog (genus Platymantis) from New Britain Island, Bismarck Archipelago. Zootaxa. 1334:45–68.
2007
Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder MT, Holland R, Holloway A, Katayama T, Lewis PO et al..  2007.  The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics. 3:357–366.
2009
Wiens J, Sukumaran J, Pyron A, Brown RM.  2009.  Evolutionary and biogeographic origins of high tropical diversity in Old World frogs (Ranidae). Evolution. 63:1217–1231.
2010
Holder MT, Sukumaran J, Brown RM.  2010.  Recent Developments in Bayesian Phylogenetics. Bayesian Modeling in Bioinformatics. :inpress.
Matsui M, Tominaga A, Liu W, Khonsue W, Grismer LL, Diesmos AC, Das I, Sudin A, Yambun P, Yong H et al..  2010.  Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetics and Evolution. 54:561-570.
Siler CD, Oaks JR, Esselstyn JA, Diesmos AC, Brown RM.  2010.  Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution. ::inpress.
Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P.  2010.  The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets. Molecular Biology and Evolution. 27:2733–2746.
2011
Edgcomb V, Orsi W, Bunge J, Jeon SO, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, Varela R et al..  2011.  Protistan Microbial Observatory in the Cariaco Basin, Caribbean. I. Species richness and endemicity. ISME Journal. 5(8):1344-1356.
2012
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning JAP, Dokholyan NV, Echave J et al..  2012.  The interface of protein structure, protein biophysics, and molecular evolution. Protein Science. 21:769-785.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic Biology. 61(1):170-173.
Vos RA, Balhoff JP, Caravas J, Holder MT, Lapp H, Maddison WP, Midford P, Priyam A, Sukumaran J, Xia X et al..  2012.  NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. 61(4):675-689.