J. C. Setubal: List of Publications

(reverse chronological order)

Books/Edited Books

  1. J. C. Setubal and S. Verjovski-Almeida (Eds.). Advances in Bioinformatics and Computational Biology. Proceedings of the Brazilian Symposium on Bioinformatics, BSB 2005. Lecture Notes in Bioinformatics, v. 3594. Berlin: Springer-Verlag, 2005.
  2. J. C. Setubal and J. Meidanis. Introduction to Computational Molecular Biology, Boston: PWS Publishing Company, 296pp., 1997. This book has been translated to Japanese.
  3. J. Meidanis and J. C. Setubal. An Introduction to Computational Biology, IX Escola de Computação, 1994 (in Portuguese).

Journal papers and book chapters

  1. N. F. Almeida, S. Yan, M. Lindeberg, D. Studholme, D. Schneider, B. Condon, H. Liu, C. Viana, A. Warren, C. Evans, E. Kemen, D. MacLean, A. Angot, G. Martin, J. Jones, A. Collmer, J. C. Setubal, B. Vinatzer. A draft genome sequence of Pseudomonas syringae pv. tomato strain T1 reveals a repertoire of type III related genes significantly divergent from that of Pseudomonas syringae pv tomato strain DC3000. MPMI, accepted for publication.
  2. J. J. Gillespie, K. Williams, E. E. Snyder, E. Nordberg, S. M. Ceraul, C. Dharmanolla, D. Rainey, J. Soneja, J. M. Shallom, M. Shukla, N. D. Vishnubhat, R. Wattam, A. Purkayastha, M. Czar, O. Crasta, J.C. Setubal, A. F. Azad, B. S. Sobral. Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life. PLoS ONE, 3(4): e2018 doi:10.1371/journal.pone.0002018 (2008)
  3. Yan S, Liu H, Mohr TJ, Jenrette J, Chiodini R, Zaccardelli M, Setubal JC, Vinatzer B. The 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.
  4. J.C. Setubal, D. Wood, T. Burr, S. Farrand, B. Goldman, B. Goodner, L. Otten, and S. Slater. The Genomics of Agrobacterium: Insights into Pathogenicity, Biocontrol, and Evolution. In R. Jackson (ed.), Plant Pathogenic Bacteria: Genomics and Molecular Biology, pp. 91-112. Horizon Press, 2009.
  5. J.C. Setubal. Similarity Search (theory), chapter A05. In A. Gruber, A. M. Durham, C. Huynhtop, and H. del Portillo (Eds.) Bioinformatics in Tropical Disease Research: A Practical and Case-Study Approach. Bethesda (MD): National Library of Medicine (US), NCBI; 2008.
  6. Slater, S., Goodner, B., Setubal, J., Goldman, B., Wood, D., Nester, E. The Agrobacterium tumefaciens C58 genome. In Tzfira, T. and Citovsky, V. (eds). Agrobacterium. Springer:New York, 2008.
  7. T. M. Venancio, 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, 8:407, 2007.
  8. G. Yu, E. Snyder, S. Boyle, O. Crasta, M. Czar, S. Mane, A. Purkayastha, B. Sobral, J. C. Setubal. A Versatile Computational Pipeline for Bacterial Genome Annotation Improvement and Comparative Analysis, with Brucella as a Use Case. Nucleic Acids Research, 2007, 35:3953-62.
  9. E. Snyder,..., J. C. Setubal and B. Sobral (43 authors). PATRIC: The VBI PathoSystems Resource Integration Center. Nucleic Acids Research 2007, 35:D401-D406.
  10. 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. 2006; 581:395-8.
  11. J. C. Setubal and S. Verjovski-Almeida. Brazilian Symposium on Bioinformatics, BSB 2005. Guest editorial for a special issue of Computers in Biology and Medicine, 2007, 37(2):113-4.
  12. J. C. Setubal, M. Reis, J. Matsunaga, and D. Haake. Lipoprotein Computational Prediction in Spirochetal Genomes. Microbiology, 152:113--121, 2006.
  13. D. M. Lorenzini, P. I. da Silva Jr, M. B. Soares, P. Arruda, J. C. Setubal, and S. Daffre. Discovery of immune related genes expressed on hemocytes of the tarantula spider Acanthoscurria gomesiana. Developmental and Comparative Immunology, 30:6, 2006, pp. 545-556.
  14. Purkayastha A, Crasta OR, Eckart JD, Czar M, Meng XJ, Setubal JC, Sobral BW. Bioinformatics resources for the study of viruses at the Virginia Bioinformatics Institute. In: R. Holland Cheng (ed.), Structure-based Study of Virus Infection. World Scientific Publishing Company, Stockholm, Sweden. (in press) (ISBN 981-270-405-1)
  15. M. E. Hance, M. J. Czar, A. Azad, A. Purkayastha, E. E. Snyder, O. R. Crasta, J. C. Setubal, B. W. Sobral. The pathogen resource integration center: implications for rickettsial research. Ann N Y Acad Sci. 2005 Dec;1063:459-65.
  16. L. A. Digiampietri, C. B. Medeiros, and J. C. Setubal. A framework based on Web service orchestration for bioinformatics workflow management. Genet Mol Res. 2005 Sep 30;4(3):535-42.
  17. J. C. Setubal, L. M. Moreira, and A. C. Rasera da Silva. Bacterial phytopathogens and genome science. Current Opinion in Microbiology, 2005, 8(5) 595-600.
  18. L. M. Moreira, R. F. de Souza, L. Digiampietri, A. C. Rasera da Silva, and J. C. Setubal. Comparative analyses of Xanthomonas and Xylella complete genomes. OMICS 9(1), pp. 43-76, 2005.
  19. C. B. Monteiro-Vitorello, L. E. A. Camargo, ..., J. C. Setubal (44 authors). The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli. Molecular Plant-Microbe Interactions, 17:8, pp. 827--836, 2004.
  20. L. M. Moreira, R. F. de Souza, N. F. Almeida Jr., J. C. Setubal, J. C. F. Oliveira, L. R. Furlan, J. A. Ferro, A. C. R. da Silva. Comparative genomics analyses of citrus-associated bacteria. Annual Review of Phytopathology, 42: 163-84, 2004.
  21. Nascimento, A. L. T. O., Verjovski-Almeida, S., Van Sluys, M. A., Monteiro-Vitorello, C. B., Camargo, L. E. A., Digiampietri, L. A., Harstkeerl, R. A., Ho, P. L., Marques, M. V., Oliveira, M. C., Setubal, J. C., Haake D. A. and Martins, E. A. L. Genome features of Leptospira interrogans serovar Copenhageni. Brazilian Journal of Medical and Biological Research, 37(2) [serial on the Internet], 2004.
  22. A.L.T.O. Nascimento,..., J.C. Setubal, M.A. van Sluys (47 authors). Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. Journal of Bacteriology, 186(7):2164-2172, 2004.
  23. D. W. Wood, J. C. Setubal, and E. W. Nester. Genome sequence analysis of prokaryotic plant pathogens. In M. Gillings and A. Holmes (eds.), Plant microbiology, pp. 223-241, BIOS Scientific Publishers (Oxford, UK) in cooperation with Marcel Dekker, 2004.
  24. J. C. Setubal. Bioinformatics. In L. Mir (ed), Genomics, Editora Atheneu, (this is an introductory book chapter, in Portuguese), pp. 105-118, 2004.
  25. J. C. Setubal and A. C. R. da Silva. Genomic approaches to the study of plant pathogenic bacteria. In Robert M. Goodman (ed), Encyclopedia of Plant and Crop Science, Marcel Dekker, pp. 524-526, 2004.
  26. R. DeMarco, A. Kowaltowski, A. Machado, M. Bento Soares, C. Gargioni, T. Kawano, V. Rodrigues, A. Madeira, R. A. Wilson, C. Menck, J. C. Setubal, E. Dias-Netto, L. Leite, S. Verjovski-Almeida. Saci-1, -2, and-3 and Perere, Four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. Journal of Virology, 78:6, 2967-2978, 2004.
  27. L. A. Digiampietri, C. B. Medeiros, J. C. Setubal. A data model for comparative genomics. Revista Tecnologia da Informação, 3(2), pp. 35-40, 2003 (preliminary version in Proceedings of the II Brazilian Workshop on Bioinformatics, see below).
  28. J. P. Piazza and J. C. Setubal. New ways for automatic detection of contaminants in EST projects. Revista Tecnologia da Informação, 3(2), pp. ?, 2003 (preliminary version in Proceedings of the II Brazilian Workshop in Bioinformatics, see below).
  29. S. Verjovski-Almeida,..., J. C. Setubal, L. C. C. Leite, E. Dias-Neto (37 authors). Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genetics, 35:2, October 2003.
  30. M.A. Van Sluys,..., J. C. Setubal, J.P. Kitajima (58 authors). Comparative analyses of the complete genome sequences of Pierce's Disease and Citrus Variagated Chlorosis strains of Xylella fastidiosa. Journal of Bacteriology, 185 (3), 2003.
  31. M. A. van Sluys, C. B. Monteiro-Vitorello, L. E. A. Camargo, C. F. M. Menck, A. C. R. da Silva, J. A. Ferro, M. C. Oliveira, J. C. Setubal, J. P. Kitajima, and A. J. G. Simpson. Comparative genomic analysis of plant-associated bacteria. Annual Review of Phytopathology, 40, 169-189, 2002.
  32. A. C. Rasera da Silva, J. Ferro, F. Reinach, ..., J. C. Setubal, J. P. Kitajima (65 authors). Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature, 417(6887):459-463, 2002.
  33. D. W. Wood, J. C. Setubal, et al. (51 authors). The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science, 294:2317-2323, 2001.
  34. R. Werneck and J. C. Setubal. Finding Minimum Congestion Spanning Trees. ACM Journal of Experimental Algorithmics, volume 5, 2000. Preliminary version: R. Werneck, J. C. Setubal, and A. F. da Conceição. Finding Minimum Congestion Spanning Trees. In Proceedings of the Third Workshop on Algorithm Engineering, King's College, London, volume 1668 of Lecture Notes in Computer Science, pp. 60--71, Springer-Verlag, 1999.
  35. A. J. G. Simpson,..., J. C. Setubal (116 authors). The genome sequence of the plant pathogen Xylella fastidiosa. Nature, v. 406, pp. 151-157, 2000.
  36. B. V. Cherkassky, A. V. Goldberg, P. Martin, J. C. Setubal, and J. Stolfi. Augment or Push? A computational study of Bipartite Matching and Unit Capacity Maximum Flow Algorithms. ACM Journal of Experimental Algorithmics, Volume 3, Article 8, 1998. Preliminary version: B. V. Cherkassky, A. V. Goldberg, P. Martin, and J. C. Setubal. Augment or Push? A computational study of Bipartite Matching and Unit Capacity Maximum Flow Algorithms. In I Workshop on Algorithm Engineering, Venice, 1997.
  37. R. J. Anderson and J. C. Setubal. A parallel implementation of the push-relabel algorithm for the maximum flow problem. Journal of Parallel and Distributed Computing, 29(1):17-26, 1995. Preliminary version: R. J. Anderson and J. C. Setubal. On the parallel implementation of Goldberg's maximum flow algorithm. In Proceedings of the 4th Annual ACM Symposium on Parallel Algorithms and Architectures, pp. 168--177, 1992.
  38. R. J. Anderson and J. C. Setubal. Goldberg's algorithm for maximum flow in perspective: a computational study. In David S. Johnson and Catherine C. McGeoch, editors, First DIMACS Implementation Challenge -- Network Flows and Matching, DIMACS Series in Mathematics and Theoretical Computer Science, volume 12, pp. 1-18, American Mathematical Society, 1993.

Conference papers and technical reports not otherwise published, abstracts, etc

  1. P. Balaji, W. Feng, H. Lin, J. Archuleta, S. Matsuoka, A. Warren, J. Setubal, E. Lusk, R. Thakur, I. Foster, D. Katz, S. Jha, K. Shinpaugh, S. Coghlan, and D. Reed. Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer. International Supercomputing Conference, 2008.
  2. L. Digiampietri, C. B. Medeiros, J. C. Setubal and R. Barga. Traceability Mechanisms for Bioinformatics Scientific Workflows. Workshop on Semantic e-Science, AAAI, Vancouver, Canada, 2007.
  3. G. G. L. Costa, L. A. Digiampietri, E. H. Ostroski, J.C. Setubal. Evaluation of Graph-Based Protein Clustering Methods. In Proceedings of the 2005 International Symposium on Mathematical and Computational Biology (BIOMAT 2005), Editora E-papers, 2006.
  4. J. P. Piazza and J. C. Setubal. DNA sequence organism determination by sequence composition analysis. Poster at the Intelligent Systems for Molecular Biology 2005.
  5. P. Carriao, M. Perez, and J. C. Setubal. Parsing BLAST results to find pseudogenes in bacterial genomes. Proceedings of the III Brazilian Workshop on Bioinformatics (poster), Brasilia, 2004.
  6. N. Almeida Jr, J. C. Setubal, M. de Carvalho, and C. Viana. A method to determine homologous protein families based on graph cliques and profiles. Proceedings of the III Brazilian Workshop on Bioinformatics (poster), Brasilia, 2004.
  7. L. Digiampietri, C. M. B. Medeiros, J. C. Setubal. A data model for comparative genomics. Proceedings of the II Brazilian Workshop on Bioinformatics (full paper), Macaé, RJ, December 2003.
  8. J. P. Piazza and J. C. Setubal. New ways for automatic detection of contaminants in EST projects. Proceedings of the II Brazilian Workshop in Bioinformatics (full paper), Macaé, RJ, December 2003.
  9. M. Perez, P. Carriao, and J. C. Setubal. A relational database for COG data. Proceedings of the II Brazilian Workshop in Bioinformatics (poster), Macaé, RJ, December 2003.
  10. J. C. Setubal. Bioinformatics challenges for the 21st century. Proceedings of the 20th Meeting on Genetics and Crop Improvement, ESALQ-USP, 2003 (in Portuguese).
  11. J. C. Setubal and R. Werneck. A program for building contig scaffolds in double-barrelled shotgun genome sequencing. Institute of Computing Technical report IC--01--05, Unicamp, 2001.
  12. J. C. Setubal and N. F. Almeida Jr. Detection of related genes in prokaryotes using syntenic regions. DIMACS Workshop on whole genome comparison, Rutgers University, New Jersey, 2001 (extended abstract).
  13. J. C. Setubal. Syllabus proposal for Theoretical Computer Science. Proceedings of the 2000 Computer Science Teaching Workshop (WEI), Curitiba (Brazil), 2000 (in Portuguese).
  14. N. Franco de Almeida Jr., J. C. Setubal and M. Tompa. On the use of don't care regions in the alignment of protein sequences. Institute of Computing Technical Report IC--99--07, 1999.
  15. J. C. Setubal and J. Meidanis. The bioinformatics of the Xylella fastidiosa genome project. Abstract book of II Annual Conference on Computational Genomics, Reston, VA, USA, november 1998.
  16. N. Franco de Almeida Jr. and J. C. Setubal. A hidden Markov model for finding promoters in prokariotic DNA. Technical report IC--98--37, Instituto de Computação, Unicamp, 1998 (in Portuguese).
  17. J. C. Setubal, P. Macedo, E. Cáceres. Solving the maximum flow problem in parallel, with distributed memory, and asynchronously. In Caderno de resumos do Workshop de Paralelismo e Otimização Combinatória, Buzios, RJ, Brazil, September, 1998.
  18. J. C. Setubal e J. R. Suarez de Oliveira. A uniform approach for seven problems in sequence comparison. Technical Report IC--97--16, Instituto de Computação, Unicamp, 1997 (in Portuguese).
  19. J. C. Setubal. Sequential and Parallel Experimental Results with Bipartite Matching Algorithms. Technical Report IC--96--09, Instituto de Computação, Unicamp, 1996.
  20. J. Meidanis and J. C. Setubal. Multiple alignment of biological sequences with gap flexibility. In Proceedings of the II Latin American Theoretical Informatics, Valparaiso, Chile, volume 911 of Lecture Notes in Computer Science, pp. 411--426, Springer-Verlag, 1995.
  21. C. F. Bella Cruz and J. C. Setubal. An adaptation of Edmonds's Graph Matching Algorithm for parallel execution (in Portuguese). In Anais da II Oficina Nacional em Problemas Combinatórios, pages 39-49. Departamento de Ciência da Computação, IMECC, Unicamp (Technical report DCC-95-17), 1995.
  22. Ronaldo Parente de Menezes and Joao Carlos Setubal. Models of Parallel Computation and their relation to Algorithm Design (in Portuguese), Technical report DCC-95-13, Departamento de Ciencia da Computacao, IMECC, Unicamp, 1995.
  23. J. C. Setubal. New experimental results for bipartite matching. In Proceedings of NETFLOW93, TR-21/93, Dipartimento di Informatica, Universitá di Pisa, pp. 211-216, 1993.
  24. J. C. Setubal e T. Kowaltowski. FIG: a picture specification language. In XV Seminario Integrado de Software e Hardware (VIII Congresso da Sociedade Brasileira de Computação), pp. 67--77, 1988.

Articles in nontechnical publications

  1. J. C. Setubal. The Origin and Meaning of Bioinformatics, Revista ComCiencia, 46, 2003 (In Portuguese).
  2. J. C. Setubal. Genetic Science and Digital Structure. Pesquisa FAPESP (special issue on 50 years of the DNA Double Helix), p. 37, April 2003 (in Portuguese).