Software

Barcoding of Life

Abdo, Z. and G.B. Golding. 2007. A step toward barcoding life: A model based, decision theoretic method to assign genes to pre-existing species groups. Systematic Biology. 56: 44-56.

Microbial Ecology

Abdo, Z., U. Schuette, S. Bent, C. Williams, L. J. Forney, and P. Joyce. 2006. Statistical methods for characterizing diversity of microbial communities. Environmental Microbiology, 8:929–938. (pdf file)

Experimental Evolution

Joyce, P., Z. Abdo, J. M. Ponciano, L. De Gelder, L. J. Forney, and E. Top. 2005. Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution. Journal of Mathematical Biology, 50: 645–662. (pdf file)

De Gelder, L., J. M. Ponciano, Z. Abdo, P. Joyce, L. Forney, and E. Top. 2004. Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic sensitive mutants in a population of resistant bacteria during experimental evolution. Genetics, 168: 1131-1144. (pdf file)

Phylogenetic Analysis

Sullivan, J., Z. Abdo, P. Joyce, and D. L. Swofford. 2005. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution, 22: 1386-1392. (pdf file)

Abdo, Z., V. Minin, P. Joyce and J. Sullivan. 2005. Accounting for uncertainty in the tree topology has little effect on the decision theoretic approach to model selection in phylogeny estimation. Molecular Biology and Evolution, 22: 691-703. (pdf file)

Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology, 52:674-683. (pdf file)