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2012
Koch JM, Holder MT.  2012.  An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy. PLOS Currents Tree of Life.
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.
2010
Peterson TA, Knapp S, Guralnick R, Soberón J, Holder MT.  2010.  The big questions for biodiversity informatics. Systematics and Biodiversity. 8:159–168.
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.
2008
Heath TA, Zwickl DJ, Kim J, Hillis DM.  2008.  Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology. 57:160-166.
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.
1999
Kichler KL, Holder MT, Davis SK, Marquez R, Owens D.  1999.  Detection of multiple paternity in the Kemp's ridley sea turtle with limited sampling. Molecular Ecology. 8:819-830.