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In Review

Chris Stockmann, Krow Ampofo, Andrew T. Pavia, Anne J. Blaschke, Benjamin Chan, Edwards O. Mason, Larry J. Forney, Carrie L. Byington. 2012. Evidence for Red Queen Dymanics in Invasive Streptococcus pneumonia Serotypes Following the Introduction of a Pneumococcal Conjugate Vaccine.

Tyerman, JG, JM Ponciano, P. Joyce, LJ Forney, and LJ Harmon. 2012. The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms.

In Press

Hickey, Roxana J., Z. Abdo, X. Zhou, K. Nemeth, M. Hansmann, TW Osborn III, F. Wang, L.J. Forney. 2012. Effects of tampons and menses on the temporal dynamics of vaginal microbiota.

Witkin, S.S., X. Zhou, G.E. Reya, W.J. Ledger, L.J. Forney. 2012. Bacterial Characterization of Paired Vaginal and Vestibular Samples From women with Vulvar Vestibulitis Syndrome. American Journal of Obstetrics and Gynecology.

2012

Brotman, RM, LL Jones, J. Sakamoto, P. Gajer, K Ault, L Peralta, LJ Forney, Z. Abdo, and J Ravel. 2012. Association between Trichomonas vaginalis and the vaginal microbiota among asymptomatic reproductive-age women in the United States. Sexually Transmitted Diseases, 39(10), 807-812. PMID: 23007708

Gajer, P., R. M. Brotman, G. Bail, J. Sakamoto, U. M. E. Schütte, X. Zhong, S. S. Koeng, L. Fu, Z. Ma, X. Zhou, Z. Abdo, L. J. Forney and J. Ravel. 2012. Temporal Dynamics of the Human Vaginal Microbiota. Science Translational Medicine, 4(132):132ra52.
PMID: 22553250

Hickey, Roxana J., X. Zhou, J.D. Pierson, J.Ravel, L.J. Forney. 2012. Understanding vaginal microbiome complexity from an ecological perspective. Translational Research, 160(4):267-82. PMID: 22683415

Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome.
Nature, 486(7402), 207–214. PMID: 22699609

Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature, 486(7402), 215–221.
PMID: 22699610

Ma, B., L.J. Forney, J. Ravel. 2012. The Vaginal Microbiome: Rethinking Health and Disease. Annual Review of Microbiology.
PMID: 22746335   doi: 10.1146/annurev-micro-092611-150157

Ma Z., J. Geng, Z. Abdo and L.J. Forney. 2012. “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.

Yuan, S., D. B. Cohen, J. Ravel, Z. Abdo and L. J. Forney. 2012. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One, 7(3):e33865. PMID: 22457796

2011

Copland, W.K., V. Krishnan, D. Beck, M. Settles, J. Foster, KC Cho, M. Day, R. Hickey, U.M.E. Schütte, X. Zhou, C.J. Williams, L.J. Forney and Z. Abdo. 2011. mcaGUI: a graphical user interface (GUI) to facilitate analysis of microbial community data. Bioinformatics, 28(16):2198-9. PMID: 22692220

Eastman, J. M., Harmon, L. J., La, H.-J., Joyce, P. and Forney, L. J. 2011. The onion model, a simple neutral model for the evolution of diversity in bacterial biofilms. Journal of Evolutionary Biology, 24: 2496–2504. PMID: 21929684

Forney, L., Koutchma, T. and Ye, Z. 2011. Characterization and Simulation of Ultraviolet Processing of Liquid Foods Using Computational Fluid Dynamics, in Innovative Food Processing Technologies: Advances in Multiphysics Simulation (eds K. Knoerzer, P. Juliano, P. Roupas and C. Versteeg), Blackwell Publishing Ltd., Oxford, UK. doi: 10.1002/9780470959435.ch14

Hunt, K. M., Foster, J. A., Forney, L. J., Schütte, U. M. E., Beck, D. L., Abdo, Z., Fox, L. K., et al. 2011. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS ONE, 6(6):e21313. PMID: 21695057
doi: 10.1371/journal.pone.0021313.

Ma Z., Z. Abdo and L. J. Forney. 2011. Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. Future Medicine, 8: 681- 688. PMID: 22754581

Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., et al. 2011. Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences, 108 Suppl 1, 4680–4687. PMID: 20534435

2010

Forney, L.J., P. Gajer, C.J.Williams, G.M. Schneider, S.S. Koenig, S. McCulle, S. Karlebach, R.M. Brotman, C. C. Davis, K. Ault, and J. Ravel. 2010. Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis. J. Clin. Microbiol. 2010 May;48(5):1741-8. Epub 2010 Mar 3. PMID: 20200290   doi:10.1128/JCM.01710-09

Lim J.Y., H-J La, H. Sheng, L.J. Forney, C.J. Hovde. 2010. Influence of plasmid pO157 on Escherichia coli O157:H7 Sakai biofilm formation. Appl. Environ. Microbiol. 76(3):963-6. Epub 2009 Dec 4. PMID: 19966025. doi 10.1128/AEM.01068-09

Lyons, R., Settles, M., Iyer, S., Forney, L., & Foster, J. 2010. Initiative for Bioinformatics and Evolutionary Studies Core Laboratories: A Multidisciplinary Resource for High-Throughput Biomedical Studies. Journal of Biomolecular Techniques: JBT, 21(3 Suppl), S75.

Ravel J., P. Gajer, Z. Abdo, G.M. Schneider, S.S. Koenig, S. McCulle, S. Karlebach, R. Gorle, J. Russell, C.O.Tacket, R.M. Brotman, C.C. Davis, K. Ault, L. Peralta, L.J. Forney. 2010. Microbes and Health Sackler Colloquium: Vaginal microbiome of reproductive-age women. [pdf] Proc Natl Acad Sci U S A. 2010 Aug 19. [Epub ahead of print June 3, 2010] PMID: 20534435
doi: 10.1073/pnas.1002611107

Schütte U.M.E., Z. Abdo, J. Foster, J. Ravel, J. Bunge, B. Solheim, L.J. Forney. 2010. Bacterial diversity in a glacier foreland of the high Arctic. [pdf] Molecular Ecology (2010), 19:54–66. doi: 10.1111/j.1365-294X.2009.04479.x

Sota M., H. Yano, J.M. Hughes, G.W. Daughdrill, Z. Abdo, L.J. Forney, and E.M. Top. 2010. Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J. 4:1568-80. Epub 2010 Jun 3. PMID: 20520653   sdoi:10.1038/ismej.2010.72

Zhou X., R.M. Brotman, P. Gajer, Z. Abdo, U. Schüette, S. Ma, J. Ravel, L.J. Forney. 2010. Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth.
Dis Obstet Gynecol. doi:10.1155/2010/737425

Zhou X., M.A. Hansmann, C.C. Davis, H. Suzuki, C.J. Brown, U. Schütte, J.D. Pierson, L.J. Forney. 2010. The vaginal bacterial communities of Japanese women resemble those of women in other racial groups. FEMS Immunol Med. Microbiol. 58:169-181.
Epub 2009 Oct 3. PMID: 19912342. PubMed - indexed for MEDLINE] PMCID: PMC2868947.
doi: 10.1111/j.1574-695X.2009.00618.x

2009

Hu, B., Zhou, X., Forney, L., & Chen, S. 2009. Changes in microbial community composition following treatment of methanogenic granules with chloroform. Environmental progress & sustainable energy, 28(1), 60–71. doi:10.1002/ep.10338

Ponciano, J.M., H.J. La, P. Joyce and L.J. Forney. 2009. Evolution of Diversity in Spatially Structured Escherichia coli Populations. Appl. Environ. Microbiol. 75:6047-6054. doi:10.1128/AEM.00063-09

Schütte, U.M.E., Z. Abdo, S.J. Bent, C.J. Williams, G.M. Schneider, B. Solheim, and L.J. Forney. 2009. Bacterial succession in a glacier foreland of the High Arctic. ISME J. 3:1258–1268. doi:10.1038/ismej.2009.71

Yamamoto, T., X. Zhou, C. Williams, A. Hochwalt, L.J. Forney. 2009. Bacterial populations in the vaginas of healthy adolescent women. [pdf] J. Ped Adol Gynecol. 22:11-18.

Zhou, X, R. Westman, R. Hickey, M.A. Hansmann, C. Kennedy, T.W. Osborn, and L.J. Forney. 2009. Vaginal microbiota of women with frequent vulvovaginal candidiasis. Infect. Immun. 77:4130-4135. doi:10.1128/IAI.00436-09

2008

Bent, S.J. and L.J. Forney. 2008. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. [pdf] ISME J 2: 689-695. mini review, doi:10.1038/ismej.2008.44

Escalante, A.E., L.E. Eguiarte, L. Espinosa-Asuar, L.J. Forney, A.M. Noguez and V. Souza. 2008. Diversity of aquatic prokaryotic communities in the Cuatro Ciénegas basin: evidence of highly structured communities. [pdf] FEMS Microbial Ecol. 65:50-60.
doi:10.1111/j.1574-6941.2008.00496.x

Foster, L., S. Krone, L.J. Forney. 2008. Application of ecological network theory to the human microbiome. [pdf] Interdisc. Perspectives Infect Dis. Vol. 2008, doi:10.1155/2008/839501

Heijs, S.K., A. M. Laverman, L.J. Forney, P.R. Hardoim, and J.D. van Elsas. 2008. Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. [pdf] FEMS Microbiol Ecol 64:362–377. doi:10.1111/j.1574-6941.2008.00463.x

Noguez, A.M., A.E. Escalante, L.J. Forney, M. Nava-Mendoza, I. Rosas, V. Souza, F. García-Oliva. 2008. Soil aggregates in a tropical deciduous forest: effects on C and N dynamics, and microbial communities as determined by t-RFLPs. [pdf] Biogeochemistry 89: 209-220. doi:10.1007/s10533-008-9214-7

Schüette, U.M.E., Z. Abdo, S.J. Bent, C. Shyu, C.J. Williams, J.D. Pierson, 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. [pdf] Appl. Microbiol. Biotechnol. 80: 365-380. doi:10.1007/s00253-008-1565-4

Suzuki, H., C.J. Brown, L.J. Forney, and E.M. Top. 2008. Comparison of correspondence analysis methods for synonymous codon usage in bacteria. [pdf] DNA Research, doi:10.1093/dnares/dsn028

2007

Bent, S.J., J.D. Pierson, L.J. Forney. 2007. Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl. Environ. Microbiol. 73:2399–2401.

Brown, C.J., M. Wong, C. Davis, A. Kanti, X. Zhou, and L.J. Forney. 2007. Preliminary characterization of the normal microbiota of the human vulva using cultivation-independent methods. [pdf] FEMS Medical Microbiol. 56:271-276.

Shyu, C., T. Soule, T., S.J. Bent, J.A. Foster, and L.J. Forney. 2007. MiCA: A web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microbial Ecol. 53:562-570. doi:10.1007/s00248-006-9106-0

Sota, M., M. Tsuda, H. Yano, H. Suzuki, L.J. Forney, and E.M. Top. 2007. Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids.
J. Bacteriol. 189: 3091-3098.

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. ISME J 1: 121-133. doi:10.1038/ismej.2007.12

2006

Forney, L.J., J.A. Foster, W. Ledger. 2006. The vaginal flora of healthy women is not always dominated by Lactobacillus sp.[pdf] J. Infect. Dis. 194:1468-1469. [Correspondence]

Abdo, Z., U.M.E. Schüette, S.J. Bent, C.J. Williams, L.J. Forney, and P. Joyce. 2006. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. [pdf]
Environ. Microbiol. 5: 929–938. doi: 10.1111/j.1462-2920.2005.00959.x

Heijs, S.K., G. Alosi. I. Bouloubassi, R.D. Pancost, C. Pierre, J.S. Sinninghe Damsté, J.C. Gottschal, J.D. van Elsas, and L.J. Forney. 2006. Microbial community structure in three deep-sea carbonate crusts. [pdf] Microbial Ecology 52: 451-462.
doi:10.1007/s00248-006-9099-8

H.-J. Ahn, H.-J.La, and L.J. Forney. 2006. System for determining the relative fitness of multiple bacterial populations without using selective markers. [pdf]. Appl. Environ. Microbiol. 72: 7383–7385. doi:10.1128/AEM.01246-06

Souza, V., L. Espinosa-Asuar, A. Escalante, L. E. Eguiarte, J. Farmer, L. Forney, L. Lloret, J. M. Rodríguez Martínez, X. Soberón, R. Dirzo and J. J. Elser. 2006. Marine Jurassic microbes in a continental karst setting: evolutionary and conservation implications. [pdf] Proc. Natl. Acad. Sci (USA) PNAS 103: 6565–6570. doi:10.1073/pnas.0601434103

Wu, X.-L. L.J. Forney, and P. Joyce. 2006. Comments on ‘Bayesian hierarchical error model for analysis of gene expression data’. [pdf] Bioinformatics 22:2446-2451. doi:10.1093/bioinformatics/btl173

2005

Coolen, M.J., E. Post, C.C. Davis, and L.J. Forney. 2005. Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms (T-RFLPs) of 16S rRNA genes.
Appl. Environ. Microbiol. 71:8729-8737.

Coolen, M.J., E. Post, C.C. Davis, and L.J. Forney. 2005. Heijs S.K., J.S. Damsté, and L.J. Forney. 2005. Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea.
FEMS Microbiol Ecol. 54(1):47-56.

De Gelder, L., F. P. J. Vandecasteele, C. J. Brown, L.J. Forney, and E. M. Top. 2005. Plasmid donor affects host range of the promiscuous IncP-1β plasmid pB10 in a sewage sludge microbial community. [pdf] Appl. Environ. Microbiol. 71.
doi: 10.1128/AEM.71.9.5309-5317.2005

Joyce, P., Z. Abdo, J. Ponciano, L. De Gelder, L. Forney, and E. M. Top. 2005. Modeling the impact of periodic bottlenecks, unidirectional mutation and observational error in experimental evolution. [pdf] J. Math. Biol. 50: 645–662.
doi:10.1007/s00285-004-0300-8

Noguez, A. M., H. T. Arita, A. E. Escalante, L.J. Forney, F. García-Oliva, and V. Souza. 2005. Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest. [pdf] Global Ecology and Biogeography 14:241-248.

Ponciano, J.M., F. P.J. Vandecasteele, T.F. Hess, L.J. Forney, R.L. Crawford, and P. Joyce. 2005. Use of stochastic models to assess the effect of environmental factors on microbial growth. [pdf] Appl. Environ. Microbiol. 71:2355-2364.
doi:10.1128/AEM.71.5.2355–2364.2005

2004

Forney, L.J., X. Zhou, C.J. Brown. 2004. Molecular microbial ecology: land of the one-eyed king. [pdf]
Curr. Opin. Microbiol. 7:210–220. doi:10.1016/j.mib.2004.04.015

De Gelder, L., J. M. Ponciano, Z. Abdo, P. Joyce, L.J. Forney, E. M. 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. [pdf] Genetics 168: 1131-1144. doi:10.1534/genetics.104.033431

Oda, Y. W.G. Meijer, J.L. Gibson, J.C. Gottschal, and L.J. Forney. 2004. Analysis of diversity among 3-chlorobenzoate-degrading strains of Rhodopseudomonas palustris. [pdf] Microbial Ecology 47: 68 - 79.

Werne, J.P., R.R. Haese, T. Zitter, G. Aloisi, I. Bouloubassi, S. Heijs, A.F. Médioni, R.D. Pancost, J.S. Damsté, G. de Lange, L.J. Forney, J.C. Gottschalf, J-P. Foucher, J. Mascle, J. Woodside, the MEDINAUT and MEDINETH Shipboard Scientific Parties. (2004). Life at cold seeps: a synthesis of biogeochemical and ecological data from Kazan mud volcano, eastern Mediterranean Sea. [pdf] Chemical Geology 205:67–390. doi:10.1016/j.chemgeo.2003.12.031

Zhou, X., S.J. Bent, M.G. Schneider, C.C. Davis, M.R. Islam, L.J. Forney. 2004. Characterization of vaginal microbial communities in adult healthy women as determined by sequencing clones and terminal restriction fragment length polymorphism (T-RFLP) analyses. [pdf] Microbiology 150: 2565–2573.

2003

Bent S.J., C.L. Gucker, Y. Oda, L.J. Forney. 2003. Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale. [pdf] Appl. Environ. Microbiol. 69: 5192-5197. doi:10.1128/AEM.69.9.5192–5197.2003

Oda, Y., B. Star, L.A. Huisman, J.C. Gottschal, and L.J. Forney. 2003. Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. [pdf] Appl. Environ. Microbiol. 69: 5186-5191. doi:10.1128/AEM.69.9.5186-5191.2003

Schlüter, A., H. Heuer, R. Szczepanowski, L.J. Forney, C.M. Thomas, A. Pühler and E.M. Top. 2003. The 64,508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a wastewater treatment plant provides evidence for recombination between members of different branches of the IncP-1β group. [pdf] Microbiology 149: 3139-3153. doi:10.1099/mic.0.26570-0

2002

Liu, W-T., T.L. Marsh, L.J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rDNA. [pdf] Appl. Environ. Microbiol. 63:4516-4522.

Nakatsu, C.H., R. Korona, R.E. Lenski, F.J. de Bruijn, T.L. Marsh and L.J. Forney 1998. Genomic rearrangements observed in Ralstonia sp. during experimental evolution. [pdf] J. Bacteriol. 180:4325-4331.

Oda, Y., W. Wanders, L.A. Huisman, W.G. Huisman, W.G. Meijer, J.C. Meijer, J.C. Gottschal, and L.J. Forney. 2002. Genotypic and phenotypic diversity within species of purple nonsulfur bacteria isolated from aquatic sediments. [pdf] Appl. Environ. Microbiol. 68:3467-3477. doi:10.1128/AEM.68.7.3467–3477.2002

Oda, Y., Y.P. de Vries, L.J. Forney, and J.C. Gottschal, 2001. Acquisition of the ability for Rhodopseudomonas palustris to degrade chlorinated benzoic acids as the sole carbon source. [pdf] FEMS Microbiol. Ecol. 38:133-139.

Riley, M.S., V.S. Cooper, R.E. Lenski, L.J. Forney, and T.L. Marsh 2000. Rapid phenotypic radiation of a soil bacterium during experimental evolution for 1000 generations. [pdf] Microbiology 147:995-1006.

Tauch A., S. Schneiker, W. Selbitschka, A. Pühler, L. S. van Overbeek, K. Smalla, C. M. Thomas, M. J. Bailey, L.J. Forney, A. Weightman, P. Ceglowski, T. Pembroke, E. Tietze, G. Schröder, E. Lanka, and J. D. van Elsas. 2002. The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. [pdf] Microbiology 148:1637-1653.


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