2012


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.  

2011


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.  

Hamilton TL, Ludwig M, Dixon R, et al. Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii. J Bacteriol. 2011;193:4477–4486.  http://www.ncbi.nlm.nih.gov/pubmed/21724999

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.  

Shulaev V, Sargent DJ, Crowhurst RN, et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet. 2011;43:109–116.  http://www.ncbi.nlm.nih.gov/pubmed/21186353

2010


Almeida NF, Yan S, Cai R, et al. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology. 2010;100:208–215.  http://www.ncbi.nlm.nih.gov/pubmed/20128693

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.  

Warren AS, Archuleta J, Feng WC, Setubal JC. Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics. 2010;11:131.  http://www.ncbi.nlm.nih.gov/pubmed/20230630

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

2009


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

Chibucos MC, Tseng TT, Setubal JC. Describing commonalities in microbial effector delivery using the Gene Ontology. Trends Microbiol. 2009;17:312–319.  http://www.ncbi.nlm.nih.gov/pubmed/19576779

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

Gillespie JJ, Ammerman NC, Dreher-Lesnick SM, et al. An anomalous type IV secretion system in Rickettsia is evolutionarily conserved. PLoS One. 2009;4:e4833.  http://www.ncbi.nlm.nih.gov/pubmed/19279686

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

Tseng TT, Tyler BM, Setubal JC. Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol. 2009;9 Suppl 1:S2.  http://www.ncbi.nlm.nih.gov/pubmed/19278550

Warren AS, Setubal JC. The Genome Reverse Compiler: an explorative annotation tool. BMC Bioinformatics. 2009;10:35.  http://www.ncbi.nlm.nih.gov/pubmed/19173744

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

2008


Gillespie JJ, Williams K, Shukla M, et al. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One. 2008;3:e2018.  http://www.ncbi.nlm.nih.gov/pubmed/19194535

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

Setubal JC, Braeuning R. Simularity Search. In: Gruber A, Durham AM, Huynh C, del Portillo HA, eds. Bioinformatics in Tropical Disease Research: A Practical and Case-Study Approach. Bethesda, MD: National Center for Biotechnology Information (US); 2008.  http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=bioinfo.TOC&depth=2

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

2007


Setubal JC, Verjovski-Almeida S. Brazilian symposium on bioinformatics. Computers in Biology and Medicine. 2007;37:113–114.  

Snyder EE, Kampanya N, Lu J, et al. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Res. 2007;35:D401–6.  http://www.ncbi.nlm.nih.gov/pubmed/17142235

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

2006


Baker SC, Jukneliene D, Purkayastha A, et al. Developing bioinformatic resources for coronaviruses. Adv Exp Med Biol. 2006;581:395–398.  http://www.ncbi.nlm.nih.gov/pubmed/17037566

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

Setubal JC, Reis M, Matsunaga J, Haake DA. Lipoprotein computational prediction in spirochaetal genomes. Microbiology. 2006;152:113–121.  http://www.ncbi.nlm.nih.gov/pubmed/16385121

Shallom JM, Dongre N, Dharmanolla C, et al. The pathosystems resource integration center: implications for viral pathogens. Journal of Clinical Virology. 2006;36:S205.  

2005


Digiampietri LA, Medeiros CB, Setubal JC. A framework based on Web service orchestration for bioinformatics workflow management. Genet Mol Res. 2005;4:535–542.  http://www.ncbi.nlm.nih.gov/pubmed/16342038

Hance ME, Czar MJ, Azad A, et al. The pathogen resource integration center: implications for Rickettsial research. Ann N Y Acad Sci. 2005;1063:459–465.  http://www.ncbi.nlm.nih.gov/pubmed/16481560

Moreira LM, De Souza RF, Digiampietri LA, Da Silva AC, Setubal JC. Comparative analyses of Xanthomonas and Xylella complete genomes. Omics. 2005;9:43–76.  http://www.ncbi.nlm.nih.gov/pubmed/15805778

Setubal JC, Moreira LM, da Silva AC. Bacterial phytopathogens and genome science. Curr Opin Microbiol. 2005;8:595–600.  http://www.ncbi.nlm.nih.gov/pubmed/16125997

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.  

2004


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

Moreira LM, de Souza RF, Almeida NF Jr., et al. Comparative genomics analyses of citrus-associated bacteria. Annu Rev Phytopathol. 2004;42:163–184.  http://www.ncbi.nlm.nih.gov/pubmed/15283664

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

Nascimento AL, Verjovski-Almeida S, Van Sluys MA, et al. Genome features of Leptospira interrogans serovar Copenhageni. Braz J Med Biol Res. 2004;37:459–477.  http://www.ncbi.nlm.nih.gov/pubmed/15064809

Setubal JC. Bioinformatics. In: Mir L, ed. Genomics. Editora Atheneu; 2004:105–118.  

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