Biblio

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2012
Yang, K., L. S. Heath, and J. C. Setubal, "REGEN: Ancestral Genome Reconstruction for Bacteria", Genes, vol. 3, issue 4, pp. 423 - 443, 12/2012.
2011
Potnis, N., K. Krasileva, V. Chow, N. F. Almeida, P. B. Patil, R. P. Ryan, M. Sharlach, F. Behlau, M. J. Dow, M. T. Momol, et al., "Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper", BMC Genomics, vol. 12, issue 1, pp. 146, 2011.
Dias, Z., U. Dias, and J. C. Setubal, "Using inversion signatures to generate draft genome scaffolds", ACM International Conference on Bioinformatics and Computational Biology 2011, Chicago, IL, 08/2011.
Collen, P. N., J. Collen, M. S. Reis, M. Pedersen, J. C. Setubal, A. M. Varani, P. Colepicolo, and M. C. Oliveira, "Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta)", Journal of Applied Phycology, 05/2011. Abstract
Saldanha, H. V., E. Ribeiro, M. Holanda, A. Araujo, G. Rodrigues, M. E. Walter, J. C. Setubal, and A. Davila, "A cloud architecture for bioinformatics workflows", First International Conference on Cloud Computing and Services Science, 05/2011.
2010
Warren, A. S., J. Archuleta, W. - C. Feng, and J. C. Setubal, "Missing genes in the annotation of prokaryotic genomes", BMC Bioinformatics, vol. 11, issue 1, pp. 131, 2010.
Myers, E., P. S. Fisher, K. Irwin, J. Baek, and J. C. Setubal, "The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings", Pattern Recognition in Bioinformatics 2010, Nijmegen, The Netherlands, Springer, 10/2010.
Yang, K., and J. C. Setubal, "Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes", ACM International Conference on Bioinformatics and Computational Biology 2010, Niagara Falls, NY, ACM Digital Libraries, 08/2010.
Almeida, N. F., S. Yan, R. Cai, C. R. Clarke, C. E. Morris, N. W. Schaad, E. L. Schuenzel, G. H. Lacy, X. Sun, J. B. Jones, et al., "PAMDB, A Multilocus Sequence Typing and Analysis Database and Website for Plant-Associated Microbes", Phytopathology, vol. 100, issue 3, pp. 208 - 215, 03/2010.
2009
Gillespie, J. J., N. C. Ammerman, S. M. Dreher-Lesnick, S. M. Rahman, M. J. Worley, J. C. Setubal, B. S. Sobral, and A. F. Azad, "An Anomalous Type IV Secretion System in Rickettsia Is Evolutionarily Conserved", PLoS ONE, vol. 4, issue 3, pp. e4833, 3/2009.
Warren, A. S., and J. C. Setubal, "The Genome Reverse Compiler: an explorative annotation tool", BMC Bioinformatics, vol. 10, issue 1, pp. 35, 2009.
Tseng, T. - T., B. M. Tyler, and J. C. Setubal, "Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology", BMC Microbiology, vol. 9, issue Suppl 1, pp. S2, 2009.
Dias-Neto, E., D. N. Nunes, R. J. Giordano, J. Sun, G. H. Botz, K. Yang, J. C. Setubal, R. Pasqualini, and W. Arap, "Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis", PLoS ONE, vol. 4, issue 12, pp. e8338, 12/2009.
Chibucos, M. C., T. - T. Tseng, and J. C. Setubal, "Describing commonalities in microbial effector delivery using the Gene Ontology", Trends in Microbiology, vol. 17, issue 7, pp. 312 - 319, 07/2009.
Setubal, J. C., P. dos Santos, B. S. Goldman, H. Ertesvag, G. Espin, L. M. Rubio, S. Valla, N. F. Almeida, D. Balasubramanian, L. Cromes, et al., "Genome Sequence of Azotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes", Journal of Bacteriology, vol. 191, issue 14, pp. 4534 - 4545, 07/2009.
Wattam, A. R., K. P. Williams, E. E. Snyder, N. F. Almeida, M. Shukla, A. W. Dickerman, O. R. Crasta, R. Kenyon, J. Lu, J. M. Shallom, et al., "Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle", Journal of Bacteriology, vol. 191, issue 11, pp. 3569 - 3579, 06/2009.
Slater, S. C., B. S. Goldman, B. Goodner, J. C. Setubal, S. K. Farrand, E. W. Nester, T. J. Burr, L. Banta, A. W. Dickerman, I. Paulsen, et al., "Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria", Journal of Bacteriology, vol. 191, issue 8, pp. 2501 - 2511, 04/2009.
Almeida, N. F., S. Yan, M. Lindeberg, D. J. Studholme, D. J. Schneider, B. Condon, H. Liu, C. J. Viana, A. Warren, C. Evans, et al., "A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000", Molecular Plant-Microbe Interactions, vol. 22, issue 1, pp. 52 - 62, 01/2009.
2008
Gillespie, J. J., K. Williams, M. Shukla, E. E. Snyder, E. K. Nordberg, S. M. Ceraul, C. Dharmanolla, D. Rainey, J. Soneja, J. M. Shallom, et al., "Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life", PLoS ONE, vol. 3, issue 4, pp. e2018, 4/2008.
Yan, S., H. Liu, T. J. Mohr, J. Jenrette, R. Chiodini, M. Zaccardelli, J. C. Setubal, and B. A. Vinatzer, "Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain", Applied and Environmental Microbiology, vol. 74, issue 10, pp. 3171 - 3181, 05/2008.
2007
Venancio, T. M., R. DeMarco, G. T. Almeida, K. C. Oliveira, J. C. Setubal, and S. Verjovski-Almeida, "Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions", BMC Genomics, vol. 8, issue 1, pp. 407, 2007.
Yu, G. X., E. E. Snyder, S. M. Boyle, O. R. Crasta, M. Czar, S. P. Mane, A. Purkayastha, B. Sobral, and J. C. Setubal, "A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case", Nucleic Acids Research, vol. 35, issue 12, pp. 3953 - 3962, 06/2007.
Snyder, E. E., N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, et al., "PATRIC: The VBI PathoSystems Resource Integration Center", Nucleic Acids Research, vol. 35, issue Database, pp. D401 - D406, 01/2007.
2006
LORENZINI, D., P. SILVAJR, M. SOARES, P. Arruda, J. C. Setubal, and S. DAFFRE, "Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana", Developmental & Comparative Immunology, vol. 30, issue 6, pp. 545 - 556, 2006.
Setubal, J. C., M. Reis, J. Matsunaga, and D. A. Haake, "Lipoprotein computational prediction in spirochaetal genomes", Microbiology, vol. 152, issue 1, pp. 113 - 121, 01/2006.