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Adjunct Faculty, Virginia Bioinformatics Institute
Associate Professor, Department of Computer Science, Virginia Tech
Phone: (540) 231-9464
Email:setubal@vbi.vt.edu
Fax: 540-231-2606
Administrative Specialist: Maureen Lawrence-Kuether
Phone: (540) 231-3669
Email: mlawre04@vbi.vt.edu
Fax:540-231-2606
Personal_Page
| Setubal Research Group
| website | JCS's main home page
Publications:
Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simoes ZL, Verjovski-Almeida S, Durham AM. Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA Biol. 2012;9:3.
Cai RM, Lewis J, Yan SC, et al. The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity. Plos Pathogens. 2011;7.
D. Wibberg JB A. Goesmann F. Kollin B. Scharf S. Schneiker-Bekel R. Sczcepanowski J.C. Setubal R. Schmitt A. P. Complete Genome Sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, Reveals a Tripartite Genome Consisting of a Circular and a Linear Chromosome and an Accessory Plasmid but Lacking a Tumor-Inducing Ti-Plasmid. Journal of Biotechnology. 2011;155:50–62.
F. I. Staquicini MC-V M. G. Kolonin M. Trepel J. K. Edwards D. N. Nunes A. Sergeevad E. Efstathiou J. Sun N. F. Almeida S. Tub G. H. Botz M. J. Wallace D. J. O'Connell S. Krajewski J. E. Gershenwald J. J. Molldrem A. L. Flamm E. Koivunen R. D. Pentz E. Dias-Neto J.C. Setubal D. J. Cahill P. Troncoso K. Don C. J. Logothetis R. L. Sidman R. Pasqualini and W. Arap. Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients. Proceedings of the National Academy of Sciences. 2011;108.
Hongtao Zhang JCS Xiaobei Zhan Zhiyong Zheng Dingqiang Chen Jianrong Wu Hongtao. Component identification of Electron Transport Chains in Agrobacterium sp. ATCC 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis. Journal of Industrial Microbiology and Biotechnology. 2011;38:667–677.
Jones JB, Potnis N, Krasileva K, et al. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. Bmc Genomics. 2011;12.
N. Jalan VA D. Kumar F. Yu J. Jones J. Graham J.C. Setubal and N. Wang. Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo FL-1195 causing citrus bacterial spot and related strains provides insights into virulence and host-specificity. Journal of Bacteriology. 2011;193:6342–6357.
P.N. Collen JC 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. 2011.
Balaji P, Feng W, Lin H, et al. Global-scale distributed I/O with ParaMEDIC. Concurrency and Computation: Practice and Experience. 2010:n/a-n/a. http://dx.doi.org/10.1002%2Fcpe.1590
Dias U, Dias Z, Setubal JC. A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes. Ottawa: Springer; 2010. RECOMB Comparative Genomics Lecture Notes in Bioinformatics.
Moreira LM, Almeida NF Jr., Potnis N, et al. Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. BMC Genomics. 2010;11:238. http://www.ncbi.nlm.nih.gov/pubmed/20388224
Setubal JC, Moreira LM, Almeida NF, et al. Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp aurantifolii. Bmc Genomics. 2010;11.
Tiller RV, Gee JE, Frace MA, et al. Characterization of novel Brucella strains originating from wild native rodent species in North Queensland, Australia. Appl Environ Microbiol. 2010;76:5837–5845. http://www.ncbi.nlm.nih.gov/pubmed/20639360
Torto-Alalibo T, Collmer C, Gwinn-Giglio M, et al. Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology. Microbiology and Molecular Biology Reviews; 2010.
Tyler BM, Torto-Alalibo T, Collmer CW, et al. Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology. Microbiology and Molecular Biology Reviews. 2010;74:479–503.
Yang K, Setubal JC. Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes. Niagara Falls: ACM Digital Libraries; 2010. ACM International Conference on Bioinformatics and Computational Biology 2010.
Zhang H, Setubal JC, Zhan X, et al. Component identification of electron transport chains in curdlan-producing Agrobacterium sp. ATCC 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis. J Ind Microbiol Biotechnol. 2010. http://www.ncbi.nlm.nih.gov/pubmed/20730594
Almeida NF, Yan S, Lindeberg M, 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. Mol Plant Microbe Interact. 2009;22:52–62. http://www.ncbi.nlm.nih.gov/pubmed/19061402
Dias-Neto E, Nunes DN, Giordano RJ, et al. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS One. 2009;4:e8338. http://www.ncbi.nlm.nih.gov/pubmed/20020040
Setubal JC, dos Santos P, Goldman BS, et al. Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J Bacteriol. 2009;191:4534–4545. http://www.ncbi.nlm.nih.gov/pubmed/19429624
Setubal JC, Wood D, Burr T, et al. The Genomics of Agrobacterium: Insights into Pathogenicity, Biocontrol, and Evolution. In: Jackson RW, ed. Plant Pathogenic Bacteria: Genomics and Molecular Biology. Horizon Press; 2009:91–112. http://www.horizonpress.com/ppb
Slater SC, Goldman BS, Goodner B, et al. Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol. 2009;191:2501–2511. http://www.ncbi.nlm.nih.gov/pubmed/19251847
Wattam AR, Williams KP, Snyder EE, et al. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 2009;191:3569–3579. http://www.ncbi.nlm.nih.gov/pubmed/19346311
Purkayastha A, Crasta OR, Eckart JD, et al. Bioinformatics resources for the study of viruses at the Virginia Bioinformatics Institute. In: Cheng RH, Miyamura T, eds. Structure-based Study of Virus Infection. Stockholm, Sweden: World Scientific Publishing Company; 2008.
http://isbn.nu/981-270-405-1
Slater S, Goodner B, Setubal J, Goldman B, Wood D, Nester E. The Agrobacterium tumefaciens C58 genome. In: Tzfira T, Citovsky V, eds. Agrobacterium. New York: Springer; 2008.
Yan S, Liu H, Mohr TJ, et al. Role of recombination in the evolution of the model plant pathogen Pseudomonas syringae pv. tomato DC3000, a very atypical tomato strain. Appl Environ Microbiol. 2008;74:3171–3181. http://www.ncbi.nlm.nih.gov/pubmed/18378665
Setubal JC, Verjovski-Almeida S. Brazilian symposium on bioinformatics. Computers in Biology and Medicine. 2007;37:113–114.
Venancio TM, DeMarco R, Almeida GT, Oliveira KC, Setubal JC, Verjovski-Almeida S. Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions. BMC Genomics. 2007;8:407. http://www.ncbi.nlm.nih.gov/pubmed/17996068
Yu GX, Snyder EE, Boyle SM, et al. A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. Nucleic Acids Res. 2007;35:3953–3962. http://www.ncbi.nlm.nih.gov/pubmed/17553834
Lorenzini DM, da Silva PI Jr., Soares MB, Arruda P, Setubal J, Daffre S. Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana. Dev Comp Immunol. 2006;30:545–556. http://www.ncbi.nlm.nih.gov/pubmed/16386302
Shallom JM, Dongre N, Dharmanolla C, et al. The pathosystems resource integration center: implications for viral pathogens. Journal of Clinical Virology. 2006;36:S205.
Setubal JC, Verjovski-Almeida S. Advances in Bioinformatics and Computational Biology. Proceedings of the Brazilian Symposium on Bioinformatics, BSB 2005. Berlin: Springer-Verlag; 2005. Lecture Notes in Bioinformatics 3594.
DeMarco R, Kowaltowski AT, Machado AA, et al. Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. J Virol. 2004;78:2967–2978. http://www.ncbi.nlm.nih.gov/pubmed/14990715
Monteiro-Vitorello CB, Camargo LE, Van Sluys MA, et al. The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Mol Plant Microbe Interact. 2004;17:827–836. http://www.ncbi.nlm.nih.gov/pubmed/15305603
Nascimento AL, Ko AI, Martins EA, et al. Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. J Bacteriol. 2004;186:2164–2172. http://www.ncbi.nlm.nih.gov/pubmed/15028702
Setubal JC. Bioinformatics. In: Mir L, ed. Genomics. Editora Atheneu; 2004:105–118.
Setubal JC, da Silva ACR. Genomic approaches to the study of plant pathogenic bacteria. In: Goodman RM, ed. Encyclopedia of Plant and Crop Science.; 2004:524–526.
Wood DW, Setubal JC, Nester EW. Genome sequence analysis of prokaryotic plant pathogens. In: Gillings M, Holmes A, eds. Plant microbiology. Oxford, UK: BIOS Scientific Publishers; 2004:223–241.
Digiampietri LA, Medeiros CB, Setubal JC. A data model for comparative genomics. Revista Tecnologia da Informa. 2003;3(2).
Piazza JP, Setubal JC. New ways for automatic detection of contaminants in EST projects. Revista Tecnologia da Informa. 2003;3(2).
Setubal JC. Genetic Science and Digital Structure. Pesquisa FAPESP. 2003:37.
Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, et al. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol. 2003;185:1018–1026. http://www.ncbi.nlm.nih.gov/pubmed/12533478
Simpson AJ, Reinach FC, Arruda P, et al. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature. 2000;406:151–159. http://www.ncbi.nlm.nih.gov/pubmed/10910347
Werneck RFF, Setubal JC, da Conceicao AF. Finding minimum congestion spanning trees.; 1999. Algorithm Engineering 1668.
Werneck RFF, Setubal JC, da Conceicao AF. Finding minimum congestion spanning trees. Algorithm Engineering. 1999;1668:60–71.
Cherkassky BV, Goldberg AV, Martin P, Setubal JC, Stolfi J. Augment or Push? A computational study of Bipartite Matching and Unit Capacity Maximum Flow Algorithms. ACM Journal of Experimental Algorithmics. 1998;3.
Setubal JC, Meidanis J. Introduction to Computational Molecular Biology. Boston: PWS Publishing Company; 1997.
Anderson R, Setubal JC. A Parallel Implementation of the Push-Relabel Algorithm for the Maximum Flow Problem. Journal of Parallel and Distributed Computing. 1995;29:17–26.
Meidanis J, Setubal JC. Multiple Alignment of Biological Sequences with Gap Flexibility.; 1995. Latin '95: Theoretical Informatics 911.
Meidanis J, Setubal JC. Multiple Alignment of Biological Sequences with Gap Flexibility. Latin '95: Theoretical Informatics. 1995;911:411–426.
Meidanis J, Setubal JC. An Introduction to Computational Biology.; 1994. IX Escola de Computacao.
Anderson RJ, Setubal JC. Goldberg's algorithm for maximum flow in perspective: a computational study. In: Johnson DS, McGeoch CC, eds. First DIMACS Implementation Challenge -- Network Flows and Matching. American Mathematical Society; 1993:1–18. DIMACS Series in Mathematics and Theoretical Computer Science 12.
Simpson AJ, Reinach FC, Arruda P, et al.
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