Hickey R.J., Z. Abdo, X. Zhou, K. Nemeth, M. Hansmann, T. Osborn, F. Wang, and L.J. Forney. Effects of tampons and menses on the temporal dynamics of vaginal microbiota. British Journal of Obstetrics and Gynecology. In Review.

Copland, W.K., V. Krishnan, D. Beck, M. Settles, J. Foster, KC Cho, M. Day, R. Hickey, U.M.E. Schutte, X. Zhou, C.J. Williams, L.J. Forney and Z. Abdo. mcaGUI: a graphical user interface (GUI) to facilitate analysis of microbial community data. Bioinformatics. In press.

Brotman, R.M., L.L. Jones, J. Sakamoto, P. Gajer, K Ault, L. Peralta, L.J. Forney, Z. Abdo, and J. Ravel. Association between Trichomonas vaginalis and the vaginal microbiota among asymptomatic reproductive-age women in the United States. Sexually Transmitted Diseases. In press.

Hughes, J. M., B. K. Lohman, G. E. Deckert, E. P. Nichols, M. Settles, Z. Abdo and E. M. Top. The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation. MBio. In press.

Gajer, P., R. M. Brotman, G. Bail, J. Sakamoto, U. M. E. Shutte, X. Zhong, S. S. Koeng, L. Fu, Z. Ma, X. Zhou, Z. Abdo, L. J. Forney and J. Ravel. Temporal Dynamics of the Human Vaginal Microbiota. Science Translational Medicine, 4(132):132ra52.

Sanapareddy, N., R. Legge, B. Jovov, A. McCoy, L. Burcal, F. Araujo-Perez, T. Randall, J. Galanko, A. Benson, R. Sandler, J. Rawls, Z. Abdo, A. A. Fodor and T. O. Keku. Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans. The International Society of Microbial Ecology (ISME) Journal. doi:10.1038/ismej.2012.43

Yuan, S., D. B. Cohen, J. Ravel, Z. Abdo and L. J. Forney. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One, 7(3): e33865.

Ma Z., J. Geng, Z. Abdo and L. J. Forney. A bird’s eye view of microbial community dynamics. Book chapter in Microbial Ecological Theory: Current Perspectives. Editors: Lesley A. Ogilvie and Penny R. Hirsch. ISBN: 978-1-908230-09-6.

Peever, T. L., W. Chen, Z. Abdo and W.J. Kaiser. Genetics of virulence in Ascochyta rabiei. Plant Pathology, doi: 10.111/j.1365-3059.2011.02566.x.

Stewart, J.E., Z. Abdo, R. K. Dumroese, N. B. Klopfenstein and M.-S. Kim. Virulence of Fusarium oxysporum and F. commune to Douglas-fir (Pseudotsuga menziesii) seedlings. Forest Pathology, doi: 10.111/j.1439-0329.2011.00746.x.



Ma Z., Z. Abdo and L. J. Forney. Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. Future Medicine, 8: 681-688.

Hunt K.M., J.A. Foster, L.J. Forney, U.M.E. Schütte, D.L. Beck, Z. Abdo, L.K. Fox, J.E. Williams, M.K. McGuire and M.A. McGuire. The vast richness and personalization of human milk bacterial communities. PLoS One. 6(6), e21313. doi:10.1371/journal.pone.0021313.

Stewart, J.E., M. Kawabe, Z. Abdo, T. Arie and T. L. Peever. 2011. Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species. PLoS One. 6(5): e20083. doi:10.1371/journal.pone.0020083.

Ravel, J., P. Gajer, Z. Abdo, G. M. Schneider, S. McCulle, S. Koenig, S. Karlebach, R. Gorle, J. Russell, C. O. Tacket, R. Brotman, C. C. Davis, K. Ault, L. Perralta and L. J. Forney. The vaginal microbiome of reproductive age women. Proceedings of the National Academy of Science, 108, supl. 1: 4680-4687.



Zhou, X., R. Brotman, P. Gajer, Z. Abdo, U.M.E. Schuette, S. Ma, J. Ravel and L.J. Forney. Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. Infectious Diseases of Obstetrics and Gynecology, doi:10.1155/2010/737425.

Sota M. H. Yano, J. Hughes, G.W. Daughdrill, Z. Abdo, L.J. Forney and E.M. Top. Shifts in Host Range of a Promiscuous Plasmid through Parallel Evolution of its Replication Initiation Protein. The International Society of Microbial Ecology (ISME) Journal, 4(12): 1568-1580.

Ripplinger, J., Z. Abdo, and J. Sullivan. Effects of parameter estimation on maximum likelihood bootstrap analysis. Molecular Phylogenetics and Evolution, 56: 642–648.

Shen , X.J., J. F. Rawls, T. Randall, L. Burcal, C.N. Mpande, N. Jenkins, B. Jovov, Z. Abdo, R.S. Sandler,  T.O. Keku. Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes, 1: 138-147.

Schütte, U.M.E., Z. Abdo, J. Foster, J. Ravel, J. Bunge, B. Solheim and L. Forney. 2010. Bacterial diversity in a glacier foreland of the High Arctic. Molecular Ecology, 19: 54-66.



Buzbas, E. O., P. Joyce and Z. Abdo. Estimation of selection intensity under overdominance by Baysian methods. Statistical Applications in Genetics and Molecular Biology, 8(1):Article 32.

Schütte, U.M.E., Z. Abdo, S.J. Bent, C.J. Williams, G.M. Schneider, B. Solheim, and L.J. Forney. Microbial succession along a glacial foreland chronological sequence in the High Arctic, Spitsbergen, Norway. The International Society of Microbial Ecology (ISME) Journal, 3: 1258-1268.

Rokyta, D., Z. Abdo and H. Wichman. Submitted. Viral Domestication: The Genetics of Adaptation for Eight Microvirid Bacteriophages. Journal of Molecular Evolution, 69:229–239.



Heuer, H., Z. Abdo and K. Smalla. 2008. Patchydistribution of£exible genetic elements in bacterial populations mediates robustness to environmental uncertainty. FEMS Microbiology and Ecology, 65: 361-371.

Schütte, U. M. E., Z. Abdo, S. J. Bent, C. Shyu, C. J. Williams, J. D. Pierson and L. J. Forney. 2008. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Applied Microbiology and Biotechnology, 80(3): 365-380.



Zhou, X., C. J. Brown, Z. Abdo, C. C. Davis, M. A. Hansmann, P. Joyce, J. A. Foster, and L. J. Forney. 2007. Differences in the composition of vaginal microbial communities found in healthy Caucasian and Black women. International Society for Microbial Ecology Journal, 1: 121-133.

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.



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.



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.

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.

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.



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.

Abdo, Z., K. A. Crandall, and P. Joyce. 2004.  Evaluating the performance of likelihood methods for detecting population structure and migration.  Molecular Ecology, 13: 837-851.



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