Publications
2012
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 Review.
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.
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.
Accepted.
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.
Accepted.
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. The mucosal microbial signature of colorectal adenomas and associations
with obesity. The
International Society of Microbial Ecology (ISME) Journal. In Press.
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.
2011
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.
2010
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.
2009
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.
2008
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.
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.