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Journal Article
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.
Grismer LL, Neang T, Chav T, Perry L. Wood J, Oaks JR, Holden J, Grismer JL, Szutz TR, Youmans TM.  2008.  Additional amphibians and reptiles from the Phnom Samkos Wildlife Sanctuary in Northwestern Cardamom Mountains, Cambodia, with comments on their taxonomy and the discovery of four new species. Raffles Bulletin of Zoology. 56:161-175.
Peterson TA, Knapp S, Guralnick R, Soberón J, Holder MT.  2010.  The big questions for biodiversity informatics. Systematics and Biodiversity. 8:159–168.
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.
Pollock DD, Zwickl DJ, McGuire JA, Hillis DM.  2002.  Increased taxon sampling is advantageous for phylogenetic inference. SYSTEMATIC BIOLOGY. 51:664-671.
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.
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.
Peterson TA, Holder MT.  2012.  Phylogenetic Assessment of Filoviruses: How Many Lineages of Marburvirus? Ecology and Evolution. 2(8):1826-1833.
Hillis DM, Pollock DD, McGuire JA, Zwickl DJ.  2003.  Is sparse taxon sampling a problem for phylogenetic inference? SYSTEMATIC BIOLOGY. 52:124-126.
Book Chapter
Holder KK, Holder MT.  2007.  Phylogeography and Population Genetics. Biology and Conservation of {R}idley Sea Turtles. :107–118.