João Setubal - Publications

Affiliations: 
Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 

84 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Lima-Junior JD, Viana-Niero C, Conde Oliveira DV, Machado GE, Rabello MC, Martins-Junior J, Martins LF, Digiampietri LA, da Silva AM, Setubal JC, Russell DA, Jacobs-Sera D, Pope WH, Hatfull GF, Leão SC. Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U. Bmc Microbiology. 16: 111. PMID 27316672 DOI: 10.1186/S12866-016-0734-3  1
2016 Guarischi-Sousa R, Puigvert M, Coll NS, Siri MI, Pianzzola MJ, Valls M, Setubal JC. Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031. Standards in Genomic Sciences. 11: 7. PMID 26779304 DOI: 10.1186/S40793-016-0131-4  1
2015 Setubal JC, Almeida N. TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 499. PMID 26605385 DOI: 10.1109/TCBB.2015.2410352  1
2015 Schwartz AR, Potnis N, Timilsina S, Wilson M, Patané J, Martins J, Minsavage GV, Dahlbeck D, Akhunova A, Almeida N, Vallad GE, Barak JD, White FF, Miller SA, Ritchie D, ... ... Setubal JC, et al. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Frontiers in Microbiology. 6: 535. PMID 26089818 DOI: 10.3389/Fmicb.2015.00535  1
2014 Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Frontiers in Microbiology. 5: 634. PMID 25520705 DOI: 10.3389/Fmicb.2014.00634  1
2014 Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM. Genetic resources for advanced biofuel production described with the Gene Ontology. Frontiers in Microbiology. 5: 528. PMID 25346727 DOI: 10.3389/Fmicb.2014.00528  1
2014 Thomas AM, Gleber-Netto FO, Fernandes GR, Amorim M, Barbosa LF, Francisco AL, de Andrade AG, Setubal JC, Kowalski LP, Nunes DN, Dias-Neto E. Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms. Bmc Microbiology. 14: 250. PMID 25278091 DOI: 10.1186/S12866-014-0250-2  1
2014 Ferreira AJ, Siam R, Setubal JC, Moustafa A, Sayed A, Chambergo FS, Dawe AS, Ghazy MA, Sharaf H, Ouf A, Alam I, Abdel-Haleem AM, Lehvaslaiho H, Ramadan E, Antunes A, et al. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses. Plos One. 9: e97338. PMID 24921648 DOI: 10.1371/Journal.Pone.0097338  1
2014 Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB, Siam R, El-Dorry H. A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. The Journal of Biological Chemistry. 289: 1675-87. PMID 24280218 DOI: 10.1074/Jbc.M113.493429  1
2014 Wulff NA, Zhang S, Setubal JC, Almeida NF, Martins EC, Harakava R, Kumar D, Rangel LT, Foissac X, Bové JM, Gabriel DW. The complete genome sequence of 'Candidatus Liberibacter americanus', associated with Citrus huanglongbing. Molecular Plant-Microbe Interactions : Mpmi. 27: 163-76. PMID 24200077 DOI: 10.1094/Mpmi-09-13-0292-R  1
2013 Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N. Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. Bmc Genomics. 14: 551. PMID 23941402 DOI: 10.1186/1471-2164-14-551  1
2013 Martins LF, Antunes LP, Pascon RC, de Oliveira JC, Digiampietri LA, Barbosa D, Peixoto BM, Vallim MA, Viana-Niero C, Ostroski EH, Telles GP, Dias Z, da Cruz JB, Juliano L, Verjovski-Almeida S, ... ... Setubal JC, et al. Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms. Plos One. 8: e61928. PMID 23637931 DOI: 10.1371/Journal.Pone.0061928  1
2013 Rajasekaran P, Alexander JC, Seleem MN, Jain N, Sriranganathan N, Wattam AR, Setubal JC, Boyle SM. Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages. International Journal of Antimicrobial Agents. 41: 358-62. PMID 23305655 DOI: 10.1016/J.Ijantimicag.2012.11.017  1
2013 Slater S, Setubal JC, Goodner B, Houmiel K, Sun J, Kaul R, Goldman BS, Farrand SK, Almeida N, Burr T, Nester E, Rhoads DM, Kadoi R, Ostheimer T, Pride N, et al. Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium. Applied and Environmental Microbiology. 79: 1414-7. PMID 23241979 DOI: 10.1128/Aem.03192-12  1
2013 Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, Setubal JC, Tyler BM, Peccoud J. Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic Acids Research. 41: e25. PMID 23042248 DOI: 10.1093/Nar/Gks908  1
2013 Martins LF, Antunes LP, Pascon RC, De Oliveira JCF, Digiampietri LA, Barbosa D, Peixoto BM, Vallim MA, Viana-Niero C, Ostroski EH, Telles GP, Dias Z, Da Cruz JB, Juliano L, Verjovski-Almeida S, ... ... Setubal JC, et al. Correction: Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms (PLoS ONE) Plos One. 8. DOI: 10.1371/annotation/2cca811e-d45b-4854-a420-d0405309ef43  1
2013 Setubal JC, Almeida NF. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8213: VI.  1
2012 Yang K, Heath LS, Setubal JC. REGEN: Ancestral Genome Reconstruction for Bacteria. Genes. 3: 423-43. PMID 24704978 DOI: 10.3390/Genes3030423  1
2012 Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, ... ... Setubal JC, et al. Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. Mbio. 3: e00246-11. PMID 23131829 DOI: 10.1128/mBio.00388-12  1
2012 Wattam AR, Inzana TJ, Williams KP, Mane SP, Shukla M, Almeida NF, Dickerman AW, Mason S, Moriyón I, O'Callaghan D, Whatmore AM, Sobral BW, Tiller RV, Hoffmaster AR, Frace MA, ... ... Setubal JC, et al. Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. Mbio. 3: e00246-12. PMID 22930339 DOI: 10.1128/Mbio.00246-12  1
2012 Dias Z, Dias U, Setubal JC. SIS: a program to generate draft genome sequence scaffolds for prokaryotes. Bmc Bioinformatics. 13: 96. PMID 22583530 DOI: 10.1186/1471-2105-13-96  1
2012 Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. Bmc Genomics. 13: 162. PMID 22554235 DOI: 10.1186/1471-2164-13-162  1
2012 Paschoal AR, Maracaja-Coutinho V, Setubal JC, Simões ZL, Verjovski-Almeida S, Durham AM. Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases. Rna Biology. 9: 274-82. PMID 22336709 DOI: 10.4161/rna.19352  1
2012 Dias Z, Dias U, Heath LS, Setubal JC. Sorting genomes using almost-symmetric inversions Proceedings of the Acm Symposium On Applied Computing. 1368-1374. DOI: 10.1145/2245276.2231993  1
2012 Collén PN, Collén J, da Reis MS, Pedersén M, Setubal JC, Varani AM, Colepicolo P, Oliveira MC. Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta) Journal of Applied Phycology. 24: 641-647. DOI: 10.1007/s10811-011-9681-4  1
2011 Staquicini FI, Cardó-Vila M, Kolonin MG, Trepel M, Edwards JK, Nunes DN, Sergeeva A, Efstathiou E, Sun J, Almeida NF, Tu SM, Botz GH, Wallace MJ, O'Connell DJ, Krajewski S, ... ... Setubal JC, et al. Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients. Proceedings of the National Academy of Sciences of the United States of America. 108: 18637-42. PMID 22049339 DOI: 10.1073/Pnas.1114503108  1
2011 Jalan N, Aritua V, Kumar D, Yu F, Jones JB, Graham JH, Setubal JC, Wang N. Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity. Journal of Bacteriology. 193: 6342-57. PMID 21908674 DOI: 10.1128/Jb.05777-11  1
2011 Cai R, Lewis J, Yan S, Liu H, Clarke CR, Campanile F, Almeida NF, Studholme DJ, Lindeberg M, Schneider D, Zaccardelli M, Setubal JC, Morales-Lizcano NP, Bernal A, Coaker G, et al. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. Plos Pathogens. 7: e1002130. PMID 21901088 DOI: 10.1371/Journal.Ppat.1002130  1
2011 Hamilton TL, Ludwig M, Dixon R, Boyd ES, Dos Santos PC, Setubal JC, Bryant DA, Dean DR, Peters JW. Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii. Journal of Bacteriology. 193: 4477-86. PMID 21724999 DOI: 10.1128/Jb.05099-11  1
2011 Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB, Ryan RP, Sharlach M, Behlau F, Dow JM, Momol M, White FF, Preston JF, Vinatzer BA, Koebnik R, Setubal JC, et al. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. Bmc Genomics. 12: 146. PMID 21396108 DOI: 10.1186/1471-2164-12-146  1
2011 Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Pühler A, Schlüter A. 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. 155: 50-62. PMID 21329740 DOI: 10.1016/j.jbiotec.2011.01.010  1
2011 Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, ... ... Setubal JC, et al. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 43: 109-16. PMID 21186353 DOI: 10.1038/Ng.740  1
2011 Zhang H, Setubal JC, Zhan X, Zheng Z, Yu L, Wu J, Chen D. 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. Journal of Industrial Microbiology & Biotechnology. 38: 667-77. PMID 20730594 DOI: 10.1007/s10295-010-0810-x  1
2011 Yang K, Setubal JC. A whole genome simulator of prokaryote genome evolution 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 508-510. DOI: 10.1145/2147805.2147885  1
2011 Dias Z, Dias U, Setubal JC. Using inversion signatures to generate draft genome sequence scaffolds 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 39-48. DOI: 10.1145/2147805.2147810  1
2011 Saldanha H, Ribeiro E, Holanda M, Araujo A, Rodrigues G, Walter ME, Setubal JC, Dávila A. A cloud architecture for bioinformatics workflows Closer 2011 - Proceedings of the 1st International Conference On Cloud Computing and Services Science. 477-483.  1
2010 Torto-Alalibo T, Collmer CW, Gwinn-Giglio M, Lindeberg M, Meng S, Chibucos MC, Tseng TT, Lomax J, Biehl B, Ireland A, Bird D, Dean RA, Glasner JD, Perna N, Setubal JC, et al. Unifying themes in microbial associations with animal and plant hosts described using the gene ontology. Microbiology and Molecular Biology Reviews : Mmbr. 74: 479-503. PMID 21119014 DOI: 10.1128/Mmbr.00017-10  1
2010 Tiller RV, Gee JE, Frace MA, Taylor TK, Setubal JC, Hoffmaster AR, De BK. Characterization of novel Brucella strains originating from wild native rodent species in North Queensland, Australia. Applied and Environmental Microbiology. 76: 5837-45. PMID 20639360 DOI: 10.1128/AEM.00620-10  1
2010 Moreira LM, Almeida NF, Potnis N, Digiampietri LA, Adi SS, Bortolossi JC, da Silva AC, da Silva AM, de Moraes FE, de Oliveira JC, de Souza RF, Facincani AP, Ferraz AL, Ferro MI, Furlan LR, ... ... Setubal JC, 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. 11: 238. PMID 20388224 DOI: 10.1186/1471-2164-11-238  1
2010 Warren AS, Archuleta J, Feng WC, Setubal JC. Missing genes in the annotation of prokaryotic genomes. Bmc Bioinformatics. 11: 131. PMID 20230630 DOI: 10.1186/1471-2105-11-131  1
2010 Almeida NF, Yan S, Cai R, Clarke CR, Morris CE, Schaad NW, Schuenzel EL, Lacy GH, Sun X, Jones JB, Castillo JA, Bull CT, Leman S, Guttman DS, Setubal JC, et al. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology. 100: 208-15. PMID 20128693 DOI: 10.1094/Phyto-100-3-0208  1
2010 Yang K, Setubal JC. Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 230-236. DOI: 10.1145/1854776.1854810  1
2010 Dias U, Dias Z, Setubal JC. A simulation tool for the study of symmetric inversions in bacterial genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6398: 240-251. DOI: 10.1007/978-3-642-16181-0_20  1
2010 Myers E, Fisher PS, Irwin K, Baek J, Setubal J. The complexity and application of syntactic pattern recognition using finite inductive strings Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6282: 125-136. DOI: 10.1007/978-3-642-16001-1_11  1
2010 Fisher PS, Baek J, Adeyeye JO, Setubal J. Finite inductive sequences, kolmogorov complexity with application to genome sequences International Conference On Bioinformatics, Computational Biology, Genomics and Chemoinformatics 2010, Bcbgc 2010. 78-83.  1
2009 Dias-Neto E, Nunes DN, Giordano RJ, Sun J, Botz GH, Yang K, Setubal JC, Pasqualini R, Arap W. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. Plos One. 4: e8338. PMID 20020040 DOI: 10.1371/Journal.Pone.0008338  1
2009 Chibucos MC, Tseng TT, Setubal JC. Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology. 17: 312-9. PMID 19576779 DOI: 10.1016/j.tim.2009.05.001  1
2009 Setubal JC, dos Santos P, Goldman BS, Ertesvåg H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D, Cromes L, Curatti L, Du Z, Godsy E, Goodner B, Hellner-Burris K, et al. Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. Journal of Bacteriology. 191: 4534-45. PMID 19429624 DOI: 10.1128/Jb.00504-09  1
2009 Wattam AR, Williams KP, Snyder EE, Almeida NF, Shukla M, Dickerman AW, Crasta OR, Kenyon R, Lu J, Shallom JM, Yoo H, Ficht TA, Tsolis RM, Munk C, Tapia R, ... ... Setubal JC, et al. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. Journal of Bacteriology. 191: 3569-79. PMID 19346311 DOI: 10.1128/Jb.01767-08  1
2009 Gillespie JJ, Ammerman NC, Dreher-Lesnick SM, Rahman MS, Worley MJ, Setubal JC, Sobral BS, Azad AF. An anomalous type IV secretion system in Rickettsia is evolutionarily conserved. Plos One. 4: e4833. PMID 19279686 DOI: 10.1371/Journal.Pone.0004833  1
2009 Tseng TT, Tyler BM, Setubal JC. Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. Bmc Microbiology. 9: S2. PMID 19278550 DOI: 10.1186/1471-2180-9-S1-S2  1
2009 Slater SC, Goldman BS, Goodner B, Setubal JC, Farrand SK, Nester EW, Burr TJ, Banta L, Dickerman AW, Paulsen I, Otten L, Suen G, Welch R, Almeida NF, Arnold F, et al. Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. Journal of Bacteriology. 191: 2501-11. PMID 19251847 DOI: 10.1128/Jb.01779-08  1
2009 Warren AS, Setubal JC. The Genome Reverse Compiler: an explorative annotation tool. Bmc Bioinformatics. 10: 35. PMID 19173744 DOI: 10.1186/1471-2105-10-35  1
2009 Almeida NF, Yan S, Lindeberg M, Studholme DJ, Schneider DJ, Condon B, Liu H, Viana CJ, Warren A, Evans C, Kemen E, Maclean D, Angot A, Martin GB, Jones JD, ... ... Setubal JC, 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 : Mpmi. 22: 52-62. PMID 19061402 DOI: 10.1094/Mpmi-22-1-0052  1
2008 Gillespie JJ, Williams K, Shukla M, Snyder EE, Nordberg EK, Ceraul SM, Dharmanolla C, Rainey D, Soneja J, Shallom JM, Vishnubhat ND, Wattam R, Purkayastha A, Czar M, Crasta O, ... Setubal JC, et al. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. Plos One. 3: e2018. PMID 19194535 DOI: 10.1371/Journal.Pone.0002018  1
2008 Yan S, Liu H, Mohr TJ, Jenrette J, Chiodini R, Zaccardelli M, Setubal JC, Vinatzer BA. 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. 74: 3171-81. PMID 18378665 DOI: 10.1128/AEM.00180-08  1
2008 Slater SC, Goodner BW, Setubal JC, Goldman BS, Wood DW, Nester EW. The agrobacterium tumefaciens C58 genome Agrobacterium: From Biology to Biotechnology. 149-181. DOI: 10.1007/978-0-387-72290-0_4  1
2007 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. 8: 407. PMID 17996068 DOI: 10.1186/1471-2164-8-407  1
2007 Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC. A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. Nucleic Acids Research. 35: 3953-62. PMID 17553834 DOI: 10.1093/nar/gkm377  1
2007 Snyder EE, Kampanya N, Lu J, Nordberg EK, Karur HR, Shukla M, Soneja J, Tian Y, Xue T, Yoo H, Zhang F, Dharmanolla C, Dongre NV, Gillespie JJ, Hamelius J, ... ... Setubal JC, et al. PATRIC: the VBI PathoSystems Resource Integration Center. Nucleic Acids Research. 35: D401-6. PMID 17142235 DOI: 10.1093/Nar/Gkl858  1
2007 Setubal JC, Verjovski-Almeida S. Brazilian Symposium on Bioinformatics Computers in Biology and Medicine. 37: 113-114. DOI: 10.1016/j.compbiomed.2006.03.001  1
2007 Digiampietri LA, Setubal JC, Medeiros CB, Barga RS. Traceability mechanisms for bioinformatics scientific workflows Aaai Workshop - Technical Report. 26-33.  1
2006 Baker SC, Jukneliene D, Purkayastha A, Snyder EE, Crasta OR, Czar MJ, Setubal JC, Sobral BW. Developing bioinformatic resources for coronaviruses. Advances in Experimental Medicine and Biology. 581: 395-8. PMID 17037566 DOI: 10.1007/978-0-387-33012-9_70  1
2006 Lorenzini DM, da Silva PI, Soares MB, Arruda P, Setubal J, Daffre S. Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana. Developmental and Comparative Immunology. 30: 545-56. PMID 16386302 DOI: 10.1016/J.Dci.2005.09.001  1
2006 Setubal JC, Reis M, Matsunaga J, Haake DA. Lipoprotein computational prediction in spirochaetal genomes. Microbiology (Reading, England). 152: 113-21. PMID 16385121 DOI: 10.1099/mic.0.28317-0  1
2005 Hance ME, Czar MJ, Azad A, Purkayastha A, Snyder EE, Crasta OR, Setubal JC, Sobral BW. The pathogen resource integration center: implications for Rickettsial research. Annals of the New York Academy of Sciences. 1063: 459-65. PMID 16481560 DOI: 10.1196/Annals.1355.066  1
2005 Digiampietri LA, Medeiros CB, Setubal JC. A framework based on Web service orchestration for bioinformatics workflow management. Genetics and Molecular Research : Gmr. 4: 535-42. PMID 16342038  1
2005 Setubal JC, Moreira LM, da Silva AC. Bacterial phytopathogens and genome science. Current Opinion in Microbiology. 8: 595-600. PMID 16125997 DOI: 10.1016/j.mib.2005.08.015  1
2005 Moreira LM, De Souza RF, Digiampietri LA, Da Silva AC, Setubal JC. Comparative analyses of Xanthomonas and Xylella complete genomes. Omics : a Journal of Integrative Biology. 9: 43-76. PMID 15805778 DOI: 10.1089/omi.2005.9.43  1
2005 Setubal JC, Verjovski-Almeida S. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Compuer Seience): Preface Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3594: i.  1
2005 Agarwal PK, Akutsu T, Amihood A, Apostolico A, Benham C, Benson G, Blanchette M, El-Mabrouk N, Gascuel O, Giancarlo R, Guigo R, Hallet M, Huson D, Kucherov G, Lacey M, ... ... Setubal JC, et al. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3692: V-VI.  1
2005 Setubal JC, Verjovski-Almeida S. Advances in Bioinformatics and Computational Biology - Brazilian Symposium on Bioinformatics, BSB 2005, Proceedings: Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3594: v.  1
2004 Monteiro-Vitorello CB, Camargo LE, Van Sluys MA, Kitajima JP, Truffi D, do Amaral AM, Harakava R, de Oliveira JC, Wood D, de Oliveira MC, Miyaki C, Takita MA, da Silva AC, Furlan LR, Carraro DM, et al. The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Molecular Plant-Microbe Interactions : Mpmi. 17: 827-36. PMID 15305603 DOI: 10.1094/Mpmi.2004.17.8.827  1
2004 Moreira LM, de Souza RF, Almeida NF, Setubal JC, Oliveira JC, Furlan LR, Ferro JA, da Silva AC. Comparative genomics analyses of citrus-associated bacteria. Annual Review of Phytopathology. 42: 163-84. PMID 15283664 DOI: 10.1146/annurev.phyto.42.040803.140310  1
2004 Nascimento AL, Verjovski-Almeida S, Van Sluys MA, Monteiro-Vitorello CB, Camargo LE, Digiampietri LA, Harstkeerl RA, Ho PL, Marques MV, Oliveira MC, Setubal JC, Haake DA, Martins EA. Genome features of Leptospira interrogans serovar Copenhageni. Brazilian Journal of Medical and Biological Research = Revista Brasileira De Pesquisas MéDicas E BiolóGicas / Sociedade Brasileira De BiofíSica ... [Et Al.]. 37: 459-77. PMID 15064809  1
2004 Nascimento AL, Ko AI, Martins EA, Monteiro-Vitorello CB, Ho PL, Haake DA, Verjovski-Almeida S, Hartskeerl RA, Marques MV, Oliveira MC, Menck CF, Leite LC, Carrer H, Coutinho LL, Degrave WM, ... ... Setubal JC, et al. Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. Journal of Bacteriology. 186: 2164-72. PMID 15028702 DOI: 10.1128/Jb.186.7.2164-2172.2004  1
2004 DeMarco R, Kowaltowski AT, Machado AA, Soares MB, Gargioni C, Kawano T, Rodrigues V, Madeira AM, Wilson RA, Menck CF, Setubal JC, Dias-Neto E, Leite LC, Verjovski-Almeida S. Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. Journal of Virology. 78: 2967-78. PMID 14990715 DOI: 10.1128/Jvi.78.6.2967-2978.2004  1
2003 Verjovski-Almeida S, DeMarco R, Martins EA, Guimarães PE, Ojopi EP, Paquola AC, Piazza JP, Nishiyama MY, Kitajima JP, Adamson RE, Ashton PD, Bonaldo MF, Coulson PS, Dillon GP, Farias LP, ... ... Setubal JC, et al. Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genetics. 35: 148-57. PMID 12973350 DOI: 10.1038/Ng1237  1
2003 Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LE, da Silva AC, Moon DH, Takita MA, Lemos EG, Machado MA, Ferro MI, da Silva FR, Goldman MH, Goldman GH, ... ... Setubal JC, et al. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. Journal of Bacteriology. 185: 1018-26. PMID 12533478 DOI: 10.1128/Jb.185.3.1018-1026.2003  1
2002 Van Sluys MA, Monteiro-Vitorello CB, Camargo LE, Menck CF, Da Silva AC, Ferro JA, Oliveira MC, Setubal JC, Kitajima JP, Simpson AJ. Comparative genomic analysis of plant-associated bacteria. Annual Review of Phytopathology. 40: 169-89. PMID 12147758 DOI: 10.1146/Annurev.Phyto.40.030402.090559  1
2002 da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM, do Amaral AM, Bertolini MC, Camargo LE, Camarotte G, Cannavan F, ... ... Setubal JC, et al. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature. 417: 459-63. PMID 12024217 DOI: 10.1038/417459a  1
2001 Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, et al. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science (New York, N.Y.). 294: 2317-23. PMID 11743193 DOI: 10.1126/Science.1066804  1
1999 Werneck RFF, Setubal JC, Da Conceicao AF. Finding minimum congestion spanning trees Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1668: 60. DOI: 10.1145/351827.384253  1
1995 Meidanis J, Setubal JC. Multiple alignment of biological sequences with gap flexibility Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 911: 411-426.  1
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