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Heath TA, Zwickl DJ, Kim J, Hillis DM.  2008.  Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology. 57:160-166.
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Hillis DM, Pollock DD, McGuire JA, Zwickl DJ.  2003.  Is sparse taxon sampling a problem for phylogenetic inference? SYSTEMATIC BIOLOGY. 52:124-126.
Zakon HH, Lu Y, Zwickl DJ, Hillis DM.  2006.  Sodium channel genes and the evolution of diversity in communication signals of electric fishes: Convergent molecular evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 103:3675-3680. Abstract
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Wilcox TP, Zwickl DJ, Heath TA, Hillis DM.  2002.  Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution. 25:361-71.
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Zakon HH, Zwickl DJ, Lu Y, Hillis DM.  2008.  Molecular evolution of communication signals in electric fish. JOURNAL OF EXPERIMENTAL BIOLOGY. 211:1814-1818. Abstract
Zwickl DJ, Holder MT.  2004.  Model Parameterization, Prior Distributions and the General Time-Reversible Model in Bayesian Phylogenetics. Systematic Biology. 53:877-888.
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Pollock DD, Zwickl DJ, McGuire JA, Hillis DM.  2002.  Increased taxon sampling is advantageous for phylogenetic inference. SYSTEMATIC BIOLOGY. 51:664-671.
Zwickl DJ, Hillis DM.  2002.  Increased taxon sampling greatly reduces phylogenetic error. SYSTEMATIC BIOLOGY. 51:588-598. Abstract
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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.
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Holder MT, Zwickl DJ, Dessimoz C.  2008.  Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes. Philosophical Transactions of the Royal Society B: Biological Sciences. 363:4013-4012.
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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.
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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.