Publications
2008
Carlton, J.M., J. Adams, J.C. Silva, S.L. Bidwell, H. Lorenzi, E. Caler, D. LaCount, S.V. Date, J. Crabtree, S.V. Angiuoli, E.F. Merino, P. Amedeo, Q. Cheng, R. Chettier, R.M.R. Coulson, B.S. Crabb, H.A. del Portillo, K. Essien, T.V. Feldblyum, C. Fernandez-Becerra, S. Fields, P.R. Gilson, A.H. Gueye, X. Guo, R. Hughes, S. Kang'a, T.W.A. Kooij, M.l Korsinczky, C. Kurschner, E.V.-S. Meyer, V.Nene, I. Paulsen, O. White, S.A. Ralph, Q. Ren, T.J. Sargeant, S. Sahasrabudhe, S. Salzberg, L.W. Schoenfeld, C.J. Stoeckert, S.A. Sullivan, M. Vignali, M.M. Yamamoto, S.L. Hoffman, J.R. Wortman, M.J. Gardner, M. Galinski, J.W. Barnwell and C.M. Fraser-Liggett.
Comparative genomics of the neglected human parasite Plasmodium vivax illuminates malaria parasite biology. Nature 9 October 2008 455:757-763.
Brotman RM, Klebanoff MA, Nansel TR, Andrews WW, Schwebke JR, Zhang J, Yu KF, Zenilman JM, Scharfstein DO.
A longitudinal study of vaginal douching and bacterial vaginosis -- A marginal structural modeling analysis. Am J Epidemiol. 2008 May 29.
Brotman RM, Ghanem KG, Klebanoff MA, Taha TE, Scharfstein DO, Zenilman JM:
The effect of vaginal douching cessation on bacterial vaginosis: a pilot study. Am J Obstet Gynecol. 2008 Feb 21.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell and Jennifer R Wortman
Automated eukaryotic gene structure annotation using EvidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008 Jan 11;9(1):R7
Guo, X. and J.C. Silva.
2008. Properties of non-coding DNA and identification of putative cis-regulatory regions in Theileria parva. BMC Genomics 9:582 [Epub ahead of print].
Egan, A., A. Mahurkar, J. Crabtree, J.H. Badger, J.M. Carlton, J.C. Silva.
2008. IDEA: Interactive Display for Evolutionary Analyses. BMC Bioinformatics 9:524 [Epub ahead of print].
Fedorova, N. D.N. Khaldi, V.S. Joardar, R. Maiti, P. Amedeo, M.J. Anderson, J. Crabtree, J.C. Silva, J.H. Badger, A. Albarraq, S. Angiuoli, H. Bussey, P. Bowyer, P.J. Cotty, P.S. Dyer, A. Egan, K. Galens, C.M. Fraser-Liggett, B.J. Haas, J.M. Inman, R. Kent, S. Lemieux, I. Malavazi, J. Orvis, T. Roemer, C.M. Ronning, J.P. Sundaram, G. Sutton, G. Turner, J.C. Venter, O.R. White, B.R. Whitty, P. Youngman, K.H. Wolfe, G.H. Goldman, J.R. Wortman, B. Jiang, D.W. Denning, W.C. Nierman.
2008. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genetics 4:e1000046.
Lin, H., S. Ouyang, A. Egan, K. Nobuta, B.J. Haas, W. Zhu, X. Gu, J.C. Silva, B.C. Meyers, and C.R. Buell.
2008. Characterization of paralogous protein families in rice. BMC Plant Biology 8: 18.
Fricke WF, Wright MS, Lindell AH, Harkins DA, Baker-Austin C, Ravel J* and R Stepanauskas.
2008. Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate E. coli SMS-3-5. Journal of Bacteriology. 190(20):6779-94. (*senior and corresponding author)
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sperandio V, Ravel J.
2008. The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology. 190(20):6881-93.
Brotmann, R.M. and J. Ravel.
2008. Ready or not: the molecular diagnosis of bacterial vaginosis. Clinical Infectious Diseases. 47(1):44-6.
Donia MS, Ravel J, Schmidt EW.
A global assembly line for cyanobactins. 2008. Nature Chemical Biology. 4(6):341-3. Epub 2008 Apr 20.
S.E. Schutzer, L.R.K. Schlater, C.M. Ronning, D. DeShazer, B.J. Luft, J.J. Dunn, J. Ravel, C.M. Fraser-Liggett, and W.C. Nierman.
2008. Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from select agent lists. PLoS ONE. 2008; 3(4): e2058.
K.E. Wommack, J. Bahsvar and J. Ravel.
2008. Metagenomics: Read size matters. Applied and Environmental Microbiology. 74(5):1453-1463.
Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, Jones KM, Crabtree J, Forberger H, Nene V.
Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biology 2008, 9(12):R183
Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methé BA.
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics 2008, 9:562.
Bek-Thomsen M., Tettelin H., Hance I., Nelson K.E., and Kilian M.
(2008) Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis and Streptococcus infantis in the upper respiratory tract of adults determined by a non-culture strategy. Infect. Immun..
Jiang S.-M., Ishmael N., Dunning Hotopp J., Puliti M., Tissi 3., Kumar n., Cieslewicz M.J., Tettelin H., and Wessels M.R.
(2008) Variation in the group B Streptococcus CsrRS regulon and effects on pathogenicity. J. Bacteriol. 190, 1956-1965. Epub 2008 Jan. 18. [PubMed]
Laroucau, K., Thierry S., Vorimore F., Blanco K., Kaleta E., Hoop R., Magnino S., Vanrompay D., Sachse K., Myers G. S. A., Bavoil P.M., Vergnaud G., and Pourcel C.
(2008) High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA). Infect Genet Evol 8:171-81. [PubMed]
(2008): Evolution of Diversity in Pathogen Populations. International Journal of Infectious Diseases. Vol. 12, Page e26.: doi:10.1016/j.ijid.2008.05.110
