João Carlos Setubal: List of Publications

PubMed bibliography

Scopus Profile

Google Scholar profile

ResearcherID profile (Web of Science)

Lattes CV

In the lists below, reverse chronological order is adopted

Books/Edited Books

Editorials

Journal Papers and Book Chapters

Genome Announcements

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

Articles in nontechnical publications

Books/Edited Books

• J.C. Setubal and Waldeyr Mendes da Silva (Eds.). Advances in Bioinformatics and Computational Biology. Proceedings of the Brazilian Symposium on Bioinformatics, BSB 2020. Lecture Notes in Bioinformatics, v. 12558. Berlin: Springer-Verlag, 2020.
• J.C. Setubal, Jens Stoye, and Peter F. Stadler (Eds.). Comparative Genomics. Methods in Molecular Biology, vol. 1704. New York : Springer, 2018.
• J.C. Setubal and Nalvo F. de Almeida (Eds.). Advances in Bioinformatics and Computational Biology. Proceedings of the Brazilian Symposium on Bioinformatics, BSB 2013. Lecture Notes in Bioinformatics, v. 8213. Berlin: Springer-Verlag, 2013.
• 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.
• J.C. Setubal and J. Meidanis. Introduction to Computational Molecular Biology, Boston: PWS Publishing Company, 296pp., 1997. This book has been translated to Japanese.
• J. Meidanis and J.C. Setubal. An Introduction to Computational Biology, IX Escola de Computacao, 1994 (in Portuguese).

Editorials

• Setubal JC, Stoye J, Dutilh BE. Editorial: Computational Methods for Microbiome Analysis. Front Genet. 11:623897. doi: 10.3389/fgene.2020.623897, 2020.
• J.C. Setubal and Nalvo Almeida. TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013. Guest editorial for a special section of ACM/IEEE Transactions on Computational Biology and Bioinformatics, 2015.
• 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, 7(2):113-4, 2007.

Journal papers and book chapters

• 2024

  • V.S. Flores, D.E. Amgarten, B.K.V. Iha, K.A. Ryon, D. Danko, B.T. Tierney, C. Mason, A.M. da Silva, J.C. Setubal. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Scientific Reports, accepted.

  • D. Carhuaricra-Huaman, I.H.L. Gonzalez, P.L. Ramos, A.M. da Silva, J.C. Setubal. Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host. PeerJ, accepted.

  • Nascimento Filho EG, Vieira ML, Dias M, Mendes MA, Sanchez FB, Setubal JC, Heinemann MB, Souza GO, Pimenta DC, Nascimento ALTO. Global proteome of the saprophytic strain Leptospira biflexa and comparative analysis with pathogenic strain Leptospira interrogans uncover new pathogenesis mechanisms. J. Proteomics. 2024;297:105125. doi:10.1016/j.jprot.2024.105125. PMID: 38364905.

• 2023

  Boettger, B.C., Piroupo, C.M., Setubal, J.C., Girardello, R. and Pignatari, A.C. Co-carriage of Plasmid NDM and Chromosomal KPC in Klebsiella pneumoniae ST255 Human Wound Isolate in Brazil. Current Microbiology 80, 394 (2023). https://doi.org/10.1007/s00284-023-03509-4

  N.S. Xavier Costa; G. Ribeiro Júnior; E.C.T. do Nascimento; J.M. de Brito; L. Antonangelo; C.S. Faria; J.S. Monteiro; J.C. Setubal; J.R.R. Pinho; R.V. Pereira; M. Seelaender; G.S. de Castro; J.D.C.C. Lima; R.A.A. Monteiro; A.N. Duarte-Neto; P.H.N. Saldiva; L.F.F. da Silva; M. Dolhnikoff; T. Mauad. COVID-19 induces more pronounced extracellular matrix deposition than other causes of ARDS. Respiratory Research, accepted.

  • M. Laux, C. Piroupo, J.C. Setubal, A. Giani. The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: two new Metagenome-Assembled Genomes from the South American clade. Harmful Algae, Volume 129, number 102518, 2023.

  • Singh, Nitin K.; Wood, Jason M.; Patane, Jose; Moura, L.M.S.; Lombardino, Jonathan; Setubal, João Carlos; Venkateswaran, Kasthuri. Characterization of metagenome-assembled genomes from the International Space Station. Microbiome, 11, article 125, 2023.

  • Carrau A., Tano J., Moyano L., Ripa M.B., Petrocelli S., Piskulic L., Moreira L.M., Patané J.S.L., Setubal J.C., Orellano E.G. A novel BLUF photoreceptor modulates the Xanthomonas citri subsp. citri host plant interaction. Photochemical and Photobiological Sciences, 2023. DOI: 10.1007/s43630-023-00420-6

  • Inague A., Alecrim L.C., Monteiro J.S., Yoshinaga M.Y., Setubal J.C., Miyamoto S., Giordano R.J. Oxygen-induced pathological angiogenesis promotes intense lipid synthesis and remodeling in the retina. iScience, 26 (6), art. no. 106777, 2023. DOI: 10.1016/j.isci.2023.106777.

  • L.A.R. Carnero, A. Kuramoto, L.C. de Oliveira, J.S. Monteiro, J.C. Setubal, E. Cunha-Neto, E.C. Sabino, R. J. Giordano. Anti-Trypanosoma cruzi antibody profiling in patients with Chagas disease treated with benznidazole assessed by genome phage display. PLoS Neglected Tropical Diseases, 17(1), 2023.

• 2022

  • J.C. Setubal and Emmanuel Dias-Neto. Microbiomes. Reference Module in Life Sciences, 2022.

  • V.M. Oliveira, F.D. Andreote, P.C. Cortelo, I. Castro-Gamboa, L.V. Costa-Lotufo. M.L.T.M. Polizeli, O.H. Thiemann, J.C. Setubal. Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology. Biota Neotropica 22 (spe), 2022.

  • Carhuaricra Huaman DE, Luna Espinoza LR, Rodríguez Cueva CL, Duran Gonzales CG, Rosadio Alcántara RH, Setubal JC, Maturrano Hernández L. Genomic Characterization of Salmonella Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru. Microorganisms. 2022 Aug 27;10(9). doi: 10.3390/microorganisms10091726.

  • de Menezes TA, de Freitas MAM, Lima MS, Soares AC, Leal C, Busch MS, Tschoeke DA, de O Vidal L, Atella GC, Kruger RH, Setubal J, Vasconcelos AA, de Mahiques MM, Siegle E, Asp NE, Cosenza C, Hajdu E, de Rezende CE, Thompson CC, Thompson FL. Fluxes of the Amazon River plume nutrients and microbes into marine sponges. Science of the Total Environment. 2022 Nov 15;847:157474. doi: 10.1016/j.scitotenv.2022.157474.

  • J.S. Erjefält, N.S.X. Costa, J. Jönsson, O. Cozzolino, K.C. Dantas, C. Clausson, P. Siddhuraj, C. Lindö, M. Alyamani, S. Lombardi, A. Mendroni Jr, L. Antonangelo, C. Silvério Faria, A.N. Duarte-Neto, R.A.A. Monteiro, J.R.R. Pinho, M.S. Gomes-Gouvêa, R.V. Pereira, J.S. Monteiro, J.C. Setubal, E.P. de Oliveira, J. Theodoro Filho, C. Sanden, J.M. Orengo, M.A. Sleeman, L.F.F. da Silva, P.H.N. Saldiva, M. Dolhnikoff, T. Mauad. Diffuse alveolar damage patterns reflect the immunological and molecular heterogeneity in fatal COVID-19. eBioMedicine, Volume 83, 104229, 2022.

  • V.M Balcão, A. Basu, B. Cieza, F.N. Rossi, C. Pereira, M. Vila, J.C. Setubal, T. Ha, A.M. da Silva. Pseudomonas tailed lytic phages: genome mechanical analysis and putative correlation with virion morphogenesis yield. Future Microbiology, 17(13):1009-1026, 2022.

  • D. Amgarten, B. Iha, C.M. Piroupo, A.M. da Silva, J.C. Setubal. vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and neural networks. Phage, 3(4):204-212, 2022.

  • S.J. Arévalo, D.Z. Sifuentes, A.C. Portocarrero, M.B. Reategui, C.M. Pimentel, L.F. Martins, P.M. Pierry, C.M. Piroupo, A.G. Santa Cruz, M.Q. Aguilar, C. Farah, J.C. Setubal, and A.M. da Silva. Genomic characterization of Bacillus strains capable to degrade cyanide isolated from mine tailings in Peru, with emphasis on Bacillus safensis and its cyanide-degrading enzyme CynD. Applied and Environmental Microbiology, 10(9):1726, 2022.

  • A.C.A. Butarelli; L.S.S. Ferreira; R. Riyuzo; H.M.B. DallAgnol; C.M. Piroupo; A.M. da Silva; J.C. Setubal; L.T. DallAgnol. Cyanobacterial diversity through culture-dependent and independent approaches in Chapada das Mesas National Park, Maranhão, Brazil. Environmental Science and Pollution Research,29:77359-77374, 2022.

  • V.F. Paixão, O.J. Sosa, D.V. Pellegrina, B. Dazzani, T.B. Corrêa, E.R. Bertoldi, L.B. Alves-de-Moraes, D.O. Pessoa, V.P. Oliveira, R.A.C. Zevallos, L.C. Russo, F.L. Forti, J.E. Ferreira, H.C. Freitas, J. Jukemura, M.C.C. Machado, M.D. Begnami, J.C. Setubal, D.S. Bassères, E.M. Reis. Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma, Cellular Oncology, 45(3):479-504. doi: 10.1007/s13402-022-00678-5. 2022.

  • Guillermo Uceda-Campos, Oseias R. Feitosa-Junior, Caio R. N. Santiago, Paulo M. Pierry, Paulo A. Zaini, Wesley O. de Santana, Joaquim Martins-Junior, Deibs Barbosa, Luciano A. Digiampietri, João C. Setubal, and Aline M. da Silva. Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems. Microorganisms, 10(5), 2022.

  • V. Marquioni, F.P.N. Rossi, D.C. Mendonça, L.F. Martins, F. Behlau, J.C. Setubal, A.M. da Silva, M.T.M. Novo-Mansur. Isolation and characterization of vB_XciM_LucasX, a new jumbo phage that infects Xanthomonas citri and Xanthomonas fuscans. PLoS ONE 17(4): e0266891, 2022.

  • Patané JSL, Moreira LM, de Melo Teixeira M, Martins J Jr, Setubal JC, Varani AM. New insights into plant natriuretic peptide evolution: From the lysogenic conversion in Xanthomonas to the lateral transfer to the whitefly Bemisia tabaci. Gene, 821:146326. doi: 10.1016/j.gene.2022.146326, 2022.

  • Antunes KH, Stein RT, Franceschina C, da Silva EF, de Freitas DN, Silveira J, Mocellin M, Leitão L, Fachi JL, Pral LP, Gonzalez A, Oliveira S, Duarte L, Cassão G, Gonçalves JIB, Reis TM, Abbadi BL, Dornelles M, Sperotto NDM, Rigo M, Rodrigues H, Jones M, Epifanio M, Guima S, Setubal JC, Jorge TR, Mansur DS, Mayer FQ, Varela APM, Bizarro CV, Machado P, Basso LA, Polack FP, Custovic A, Vinolo MAR, de Souza APD. Short-chain fatty acid acetate triggers antiviral response mediated by RIG-I in cells from infants with respiratory syncytial virus bronchiolitis. EBioMedicine, 77:103891. doi: 10.1016/j.ebiom.2022.103891, 2022.

  • Nakamura Gouvea N, Alves Lima C, Benites LF, Iha C, Maracaja Coutinho V, Aliaga Tobar V, Amaral M, Yokoya NS, Marinho Soriano E, Graminha MAS, Collén J, Cabral Oliveira M, Setubal JC, Colepicolo P. Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta: Gracilariales). Journal of Phycology, doi: 10.1111/jpy.13238, 2022.

  • O. Palmeira, L. Matos, M.S. Naslavsky, H.M.S. Bueno, J.P. Soler, J.C. Setubal, M. Zatz. Longitudinal 16S rRNA gut microbiota data of infant triplets show partial susceptibility to host genetics. iScience, 25(3):103861. doi: 10.1016/j.isci.2022.103861, 2022.

  • L.K. Harada; E.C. Silva; T.J. Oliveira; F.C. Moreli; B.B. Silva; G. Tomazetto; C. Pereira; F.N. Rossi; F.M. Squina; M.M.D.C. Vila; J.C. Setubal; A.M. da Silva; V.M. Balcão. Characterization and in vitro testing of newly isolated lytic bacteriophages for biocontrol of Pseudomonas aeruginosa. Future Microbiology, 17:111-141. doi: 10.2217/fmb-2021-0027, 2022.

• 2021

  • J.C. Setubal. Metagenome-assembled genomes: concepts, analogies, and challenges. Biophysical Reviews, 13(6), article 27, 2021.

  • L.A. Rodriguez-Carnero, A.A.R. Teixeira, F.H.F Tang, A. Kuramoto, M.J.M. Alves, W. Colli, J.C. Setubal, E. Cunha-Neto, R. Pasqualini, W. Arap, R.J. Giordano. Protocol for design, construction, and selection of genome phage (gPhage) display libraries. STAR Protocols Volume 2, Issue 4, 100936, 2021.

  • I.O. Prata, E.F.G. Cubillosa, D. Barbosa, J. Martins Jr., J.C. Setubal, G. Wunderlich. Plasmodium falciparum Acetyl-CoA Synthetase is essential for parasite intraerythrocytic development and chromatin modification, ACS Infectious Diseases, 7(12):3224-3240, 2021.

  • C. Lemes, M. Villa, E. Felestrino, L. Perucci, R. Assis, I. Cordeiro, N. Fonseca, L. Guerra, F. do Carmo, W. Caneschi, L. Moraes, L. Kamino, P. Vale, S. Guima, J.C. Setubal, A. Salgado, L. Moreira. 16S rRNA gene amplicon sequencing data of the Iron Quadrangle ferruginous caves (Brazil) shows the importance of conserving this singular and threatened geosystem. Diversity, 13 (10), 494, 2021.

  • L. Braga, R.V. Pereira, L.F. Martins, L. Moura, F.B. Sanchez, J.S.P. Patané, A.M. da Silva, J.C. Setubal. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics, 22:652, 2021.

  • L.T. Rangel, S.M. Soucy, J.C. Setubal, J.P. Gogarten, G.P. Fournier. An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets. Genome Biology and Evolution, 13(9), 2021.

  • A.A. Teixeira, L.R. Carnero, A. Kuramoto, F.H.F. Tang, C.H. Gomes, N.B. Pereira, L.C. de Oliveira, R. Garrini, J.S. Monteiro, J.C. Setubal, E.C. Sabino, R. Pasqualini, W. Colli, W. Arap, M.J.M. Alves, E. Cunha-Neto, R.J. Giordano. A refined genome phage display methodology delineates the human antibody response in Chagas disease patients. iScience, 24 (102540), 2021.

  • L.S.S. Ferreira, A.C.A. Butarelli, R.C. Sousa, M.A. de Oliveira, P.H.G. Moraes, I.S. Ribeiro, P.F.R. Sousa, H.M.B. Dall'Agnol, A.R.J. Lima, E.C. Gonçalves, K. Sivonen, D. Fewer, R.R. Franco, C.M. Piroupo, A.M. da Silva, J.C. Setubal, L.T. Dall'Agnol. High-quality draft genome sequence of Pantanalinema sp. GBBB05, a cyanobacterium from Cerrado biome. Frontiers in Ecology and Evolution, section Phylogenetics, Phylogenomics, and Systematics. v9, 336, 2021.

  • R.A.B. Assis, A.M. Varani, C.H.D. Sagawa, J.S.L. Patané, J.C. Setubal, G. Uceda-Campos, A.M. da Silva, P.A. Zaini, N.F. Almeida, L.M. Moreira, and A.M. Dandekar. Comparative genomic analysis of Xanthomonas arboricola pv. juglandis population reveals the role of mobile genetic elements associated with adaptation and evolution of virulence. Genomics, Volume 113, Issue 4, Pages 2513-2525, 2021.

  • R. Girardello, C.M. Piroupo, J. Martins Jr, M.H. Maffucci, A.P. Cury, M.R.G. Franco, F.M. Malta, N.C. Rocha, J.R.R. Pinho, F. Rossi, A.J.S. Duarte, J.C. Setubal. Genomic characterization of mcr-1.1-producing Escherichia coli recovered from human infections in São Paulo, Brazil. Frontiers in Microbiology, Section Antimicrobials, Resistance and Chemotherapy, v12, 663414, 2021.

  • A.T. Fabro, J. Machado-Rugolo, C.M. Baldavira, T. Prieto, C. Farhat, F. Mangone, S. Batah, H. Cruvinel, M. Alda, J.S. Monteiro, A. Padua, S. Morais, R. Oliveira, M. Santos, J. Baddini, J.C. Setubal, C. Rainho, H.H.B. Yoo, P.L. Silva, M. A. Nagai, V.L. Capelozzi. Circulating plasma miRNA and clinical/hemodynamic characteristics provide additional predictive information about acute pulmonary thromboembolism, chronic thromboembolic pulmonary hypertension and idiopathic pulmonary hypertension. Frontiers in Pharmacology, Section Respiratory Pharmacology, 12(1287), 2021.

  • L.M. Vieira, N.A.N. Jorge, J.B. de Sousa, J.C. Setubal, P.F. Stadler, M.E.T. Walter. Competing Endogenous RNA in Colorectal Cancer: an analysis for colon, rectum and rectosigmoid junction. Frontiers in Oncology, section Molecular and Cellular Oncology. v11, 681579, 2021.

  • M.B. Casaro; A.M. Thomas; E. Mendes; C. Fukumori; W.R. Ribeiro; F.A. de Oliveira; A.R. Crisma; G.M. Murata; B. Bizzarro; A. Sá-Nunes; J.C. Setubal; M.P.A. Mayer; F.S. Martins; A.T. Vieira; A.T.F.B. Antiorio; W. Tavares de-Lima; N.O.S. Camara; R. Curi; E. Dias-Neto; C.M. Ferreira. A probiotic has differential effects on allergic airway inflammation in A/J and C57BL/6 mice and is correlated correlated with the gut microbiome. Microbiome, 9(1):134, 2021.

  • L. Braga, F.H. Coutinho, D.E. Amgarten, W. Kot, L. Hansen, J.C. Setubal, L. Philippot. Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis. Environmental Microbiology Reports, 13(3):348-354, 2021

  • D.O. Pessoa, F.E. Rius, D. Papaiz, A.L.P. Ayub, A.S. Morais, C.F. de Souza, V.F. da Paixão, J.C. Setubal, J. Newton-Bishop, J. Nsengimana, H. Azevedo, E.M. Reis, and M.G. Jasiulionis. Transcriptional signatures underlying dynamic phenotypic switching and malignancy in a linear cellular model of melanoma progression. Neoplasia, 23(4): 439-455, 2021.

  • R. de Pedro-Jové, M. Puigvert, P. Sebastià, A. P. Macho, J. S. Monteiro, N. S. Coll, J. C. Setubal, and M. Valls. Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection. BMC Genomics, 12 (170), 2021.

  • Ladin ZS, Ferrell B, Dums JT, Moore RM, Levia DF, Shriver WG, DAmico V, Trammell TLE, Setubal JC, Wommack KE. Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Scientific Reports 15;11(1):1629. doi: 10.1038/s41598-020-80602-9, 2021.

• 2020

  • Sato FT, Yap YA, Crisma AR, Portovedo M, Murata GM, Hirabara SM, Ribeiro WR, Marcantonio Ferreira C, Cruz MM, Pereira JNB, Payolla TB, Guima SES, Thomas AM, Setubal JC, Alonso-Vale MIC, Santos MF, Curi R, Marino E, Vinolo MAR. Tributyrin Attenuates Metabolic and Inflammatory Changes Associated with Obesity through a GPR109A-Dependent Mechanism. Cells. 2020; 9(9):2007. https://doi.org/10.3390/cells9092007

  • E.B. Felestrino, A.B. Sanchez, W.L. Caneschi, C.G.C. Lemes, R.A.B. Assis, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.H.Y. Kamino, F.F. do Carmo, A.M. da Silva, A.M. Thomas, J.S.L. Patané, F.C. Ferreira, L.G. de Freitas, A.M. Varani, J.A. Ferro, R.S. Silva, N.F. Almeida, C.C.M. Garcia, J.C. Setubal, L.M. Moreira. Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant. PLoS ONE, 10.1371/JOURNAL.PONE.0241546, 2020.

  • F.S. do Nascimento et al. Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol. PLoS ONE, 10.1371/JOURNAL.PONE.0242553, 2020.

  • C.K. Zimpel, J.S. Patané, A.C.P. Guedes, R.F. de Souza, T.T. Pereira, N.C.S. Camargo, A.F. de Souza Filho, C.Y. Ikuta, J.S. Ferreira Neto, J.C. Setubal, M.B. Heinemann, A.M.S. Guimaraes. Global distribution and evolution of Mycobacterium bovis lineages. Frontiers in Microbiology - Evolutionary and Genomic Microbiology, 11(843), 2020.

  • Braga LPP, Spor A, Kot W, Breuil MC, Hansen LH, Setubal JC, Philippot L. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Microbiome, 6;8(1):52, 2020.

  • Al Assal, K.; Prifti, E.; Belda, E.; Sala, P.; Clément, K.; Dao, M.-C.; Doré, J.; Levenez, F.; Taddei, C.R.; Fonseca, D.C.; Rocha, I.M.; Balmant, B.D.; Thomas, A.M.; Santo, M.A.; Dias-Neto, E.; Setubal, J.C.; Zucker, J.-D.; Belarmino, G.; Torrinhas, R.S.; Waitzberg, D.L. Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission. Nutrients, 12(2):278, 10.3390/nu12020278, 2020.

• 2019

  • R. Guarischi-Sousa, J.S. Monteiro, L.C. Alecrim, J.S. Michalolski, L.B. Cardeal, E.N. Ferreira, D.M. Carraro, D.N. Nunes, E. Dias-Neto, J. Reimand, P.C. Boutros, J.C. Setubal, and R.J. Giordano. A transcriptomic signature of pathological angiogenesis predicts breast cancer patient survival. PLoS Genetics, 15 (12): e1008482, 2019.

  • W.L. Caneschi, A.B. Sanchez, E.B. Felestrino, C.G.C. Lemes, I.F. Cordeiro, N.P. Fonseca, M.M. Villa, I.T. Vieira, L.A.G. de Moraes, R.A.B. Assis, F.F. do Carmo, L.H.Y. Kamino, R.S. Silva, J.A. Ferro, M.I.T. Ferro, R.M. Ferreira, V.L. Santos, U.C.M. Silva, N.F. Almeida, A.M. Varani, C.C.M. Garcia, J.C. Setubal, L.M. Moreira. Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments. Scientific Reports, 9, Article number: 18006, 2019.

  • N.P. Fonseca, J.S.L. Patané, A.M. Varani, E.B. Felestrino, W.L. Caneschi, A.B. Sanchez, I.F. Cordeiro, C.C. Lemes, R.B. Assis, C.C. Garcia, J. Belasque Jr., J. Martins Jr., A.P. Facincani, R.M. Ferreira, F.J. Jaciani, N.F. Almeida, J.A. Ferro, L.M. Moreira, J.C. Setubal. Analyses of seven new genomes of Xanthomonas citri pv. aurantifolii strains, causative agents of citrus canker B and C, show a reduced repertoire of pathogenicity-related genes. Frontiers in Microbiology, section Plant Microbe Interactions, 2019.

  • S. Ha, E. Dimitrova, S. Hoops, D. Altarawy, M. Ansariola, D. Deb, J. Glazebrook, R. Hillmer, H. Hosamadine, F. Katagiri, J. McDowell, M. McGraw, J.C. Setubal, B.M. Tyler, R. Laubenbacher. PlantSimLab - A Modeling and Simulation Web Tool for Plant Biologists. BMC Bioinformatics, 2019.

  • N.P. Fonseca, E.B. Felestrino, W.L. Caneschi, A.B. Sanchez, I.F. Cordeiro, C.G.C. Lemes, R.A.B. Assis, F.M.S. Carvalho, J.A. Ferro, A.M. Varani, J. Belasque, J.C. Setubal, G.P. Telles, D.S. Aguena, N.F. Almeida, L.M. Moreira. Comparative genomics and multiplex PCR for detection and identification of Xanthomonas pathotypes associated with citrus diseases. PeerJ:e7676, https://doi.org/10.7717/peerj.7676, 2019.

  • M. Baptista et al. Where We Aspire to Publish: A Position Paper on Scientific Communication in Biochemistry and Molecular Biology. Brazilian Journal of Medical and Biological Research, 52(9), 2019.

  • C. Fukumori, M.B. Casaroa, A.M. Thomas, E. Mendes, W.R. Ribeiro, A.R. Crisma, G.M. Murata, B. Bizzarro, E. Dias-Neto, J.C. Setubal, M.A. Oliveira, W. Tavares-de-Lima, R. Curi, S. Bordin, P. Sartorelli, C.M. Ferreira. Maternal supplementation with a synbiotic has distinct outcomes on offspring gut microbiota formation in A/J and C57BL/6 mice, differentially affecting airway inflammatory cell infiltration and mucus production. Journal of Functional Foods, 61(103496), 2019.

  • S.P. Braga, A.P. dos Santos, T. Paganini, D. Barbosa, G.W. Condomitti, C. Morais, L.F. Martins, A.M. da Silva, J.C. Setubal, M.A. Vallim, R.C. Pascon. First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans, Brazilian Journal of Microbiology, 50, pp. 1051–1062, 2019.

  • J.S.L. Patané, J. Martins Jr., L.T. Rangel, J. Belasque, L.A. Digiampietri, A.P. Facincani, F.J. Jaciani, R.M. Ferreira, Y. Zhang, A.M. Varani, N.F. Almeida, N. Wang, J.A. Ferro, L.M. Moreira, J.C. Setubal. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics, 20 (700), 2019.

  • L. T. Rangel, J. Marden, S. Colston, J. C. Setubal, J. Graf, J. P. Gogarten. Identification and characterization of putative Aeromonas spp. T3SS effectors. PLoS ONE, journal.pone.0214035, June, 2019.

  • N. M. Silva, A. M. S. A. de Oliveira, S. Pegorin, C. E. Giustia, V. B. Ferraric, D. Barbosa, L. F. Martins, C. Morais, J. C. Setubal, S. P. Vasconcellos, A. M. da Silva, J. C. F. de Oliveira, R. C. Pascon, C. Viana-Niero. Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting. PLoS ONE, journal.pone.0215396, April, 2019.

  • Fachi, J.L., Felipe, J.S., Pral, L.P., Da Silva, B.K., Corrê,a, R.O., Andrade, M.C., Fonseca, D.M., Basso, P.J., Câ,mara, N.O.S., Souza, E.L.S., Martins, F.S., Guima, S.E., Thomas, A.M., Setubal, J.C., Magalhã,es, Y.T., Forti, F.L., Candreva, T., Rodrigues, H.G., de Jesus, M.B., Consonni, S.R., Farias, A.S., Varga-Weisz, P.D., Vinolo, M.A.R. Butyrate protects mice from Clostridium difficile-induced colitis through a HIF-1 dependent mechanism. Cell Reports, Volume 27, Issue 3, 16 April 2019, Pages 750-761.e7

  • A.M. Thomas, P. Manghi, F. Asnicar, E. Pasolli, F. Armanini, M. Zolfo, F. Beghini, C. Pozzi, S. Gandini, D. Serrano, S. Tarallo, A. Francavilla, G. Gallo, M. Trompetto, F. Cordero, E. Dias-Neto, J. C. Setubal, B. Pardini, M. Rescigno, L. Waldron, A. Naccarati, N. Segata. Combined metagenomic analysis of colorectal cancer datasets defines cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine, 25:667-678, 2019.

  • R.I. Amman et al. Towards unrestricted usage of public genomic data. Science, 363(6425):350-352, 2019.

  • Fenny H.F. Tang, Fernanda I Staquicini, André, A. R. Teixeira, Jussara S Michaloski, Gislene M Namiyama, Noemi N Taniwaki, João C Setubal, Aline M da Silva, Richard L. Sidman, Renata Pasqualini, Wadih Arap, Ricardo J Giordano. A ligand motif enables differential vascular targeting of endothelial junctions between brain and retina. PNAS, 116(6):2300-2305, 2019.

  • E. Ramadan, M. Maged, A. El Hosseiny, F. Chambergo, J.C. Setubal, and Hamza El Dorry. Molecular adaptations of bacterial mercuric reductase to the hypersaline Kebrit Deep in the Red Sea. Applied and Environmental Microbiology, 85(4):e01431-18, 2019.

  • P.L. Ramos, S. Santos, S. Vasconcellos, R. Rocha, J.B. Cruz, P. Eugenio, M. Kondo, H. Cabral, M. Juliano, L. Juliano, J.C. Setubal, A.M. da Silva, L. Cappelini. A tropical composting operation unit at São Paulo Zoo as a source of bacterial proteolytic enzymes. Applied Biochemistry and Biotechnology, 187(1), pp. 282-297, 2019.

• 2018

  • Pereira ASA, Amaral MS, Vasconcelos EJR, Pires DS, Asif H, daSilva LF, Morales-Vicente DA, Carneiro VC, Angeli CB, Palmisano G, Fantappie MR, Pierce RJ, Setubal JC, Verjovski-Almeida S. Inhibition of histone methyltransferase EZH2 in Schistosoma mansoni in vitro by GSK343 reduces egg laying and decreases the expression of genes implicated in DNA replication and noncoding RNA metabolism. PLoS neglected tropical diseases. 2018; 12(10):e0006873.

  • K.P. de Souza, J.C. Setubal, A.C.P.L.F. de Carvalho, G. Oliveira, A. Chateau, R.C.O. Alves. Machine Learning Meets Genome Assembly. Briefings in Bioinformatics, 20(6):2116-2129, 2019.

  • D. Amgarten, L.P.P. Braga, A.M. da Silva, J.C. Setubal. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. Frontiers in Genetics, section Bioinformatics and Computational Biology, 304, 2018

  • L.F. da Silva, F. Beckedorff, A.C. Ayupe, M.S. Amaral, V. Mesel, A. Videira, E.M. Reis, J.C.Setubal, S. Verjovski-Almeida. Chromatin landscape distinguishes the genomic loci of hundreds of androgen-receptor-associated lincRNAs from the loci of non-associated lincRNAs. Frontiers in Genetics, section RNA, 9(132), 2018.

  • L.P.P. Braga, S.M. Soucy, D. Amgarten, A.M. Da Silva, J.C. Setubal. Bacterial diversification in the light of the interactions with phages: the genetic symbionts and their role in ecological speciation. Frontiers in Ecology and Evolution, section Population and Evolutionary Dynamics. doi.org/10.3389/fevo.2018.00006, 2018.

  • J.C. Setubal, N.F. Almeida, A.R. Wattam. Comparative Genomics for Prokaryotes. Methods in Molecular Biology, v. 1704, pp. 55-78. Springer New York, 2018.

  • A.M. Thomas, F.P. Lima, L.M.S. Moura, A.M. da Silva; E. Dias-Neto, J.C. Setubal. Comparative Metagenomics. Methods in Molecular Biology, v. 1704, pp. 243-260. Springer New York, 2018.

  • J.C. Setubal and P.F. Stadler. Gene Phylogenies and Orthologous Groups. Methods in Molecular Biology, v. 1704, pp. 1-28. Springer New York, 2018.

  • J.S.L. Patané, J. Martins Jr, J.C. Setubal. Phylogenomics. Methods in Molecular Biology, v. 1704, pp. 103-187. Springer New York, 2018.

  • L.A.G de Moraes, E.B. Felestrino, R.A.B Assis, D. Matos, J.C. Lima, L.A. Lima, N.F. Almeida, J.C. Setubal, C.C.M. Garcia, and L.M. Moreira. TabPath: interactive Tables for Metabolic Pathway analysis, Bioinformatics, 34(6):1040-1042, 2018.

• 2017

  • R.A.B. Assis, L.C. Polloni, J.S.L. Patané, S. Thakur, E.B. Felestrino, J. Diaz-Caballero, R. Nascimento, P.A. Zaini, L.R. Goulart, L.A. Digiampietri, J.C. Setubal, N.F. Almeida, A.M. Dandekar, D.S. Guttman, and L.M. Moreira. Comparative analysis of 69 complete Xanthomonadaceae genomes reveals seven effector protein families with diverse adaptive and evolutionary histories. Scientific Reports, 7(1):16133, 2017.

  • E. Mendez, B.G. Acetturi, A.M. Thomas, F. Martins, A. Crisma, G. Massa, T. Braga, N. Câmara, A. Franco, J.C. Setubal, W. Ribeiro, C. Valduga, R. Curi, E. Dias Neto, W.T. de Lima, C. M. Ferreira. Prophylactic supplementation of Bifidobacterium longum 51A protects mice from ovariectomy-induced exacerbated allergic airway inflammation and airway hyperresponsiveness. Frontiers in Microbiology, section Microbial Immunology, 8:1732, 2017.

  • N. Wang, E.A. Pierson, J.C. Setubal, J. Xu, J.G. Levy, Y. Zhang, L.T. Rangel, and J. Martins. The Candidatus Liberibacter-Host Interface: Insights into Pathogenesis Mechanisms and Disease Control. Annual Review of Phytopathology, 55, September, 2017.

  • L.M. Moreira, M.R. Soares, A.P. Facincani, C.B. Ferreira, R.M. Ferreira, M.I.T. Ferro, F.C. Gozzo, E.B. Felestrino, R.A.B. Assis, C.C.M. Garcia, J.C. Setubal, J.A. Ferro, J.C.F. de Oliveira. Proteomic analysis reveals adaptation mechanisms of Xanthomonas citri subsp. citri during initial stages of Citrus sinensis infection. BMC Microbiology, 17:155, 2017.

  • D. Amgarten, L.F. Martins, K.C. Lombardi, L.P. Antunes, A.P.S. de Souza, G.G. Nicastro, E.W. Kitajima, R.B. Quaggio, C. Upton, J.C. Setubal, A.M. da Silva. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, 18 (346), 2017.

  • L.N. Lemos, R.V. Pereira, R.B. Quaggio, L.F. Martins, L.M.S. Moura, A.R. da Silva, L.P. Antunes, A.M. da Silva, J.C. Setubal. Genome-centric analysis of a thermophilic and cellulolytic bacterial consortium derived from composting. Frontiers in Microbiology, 8 (644), 2017.

  • I. Erill, M. Puigvert, L. Legrand, R. Guarischi-Sousa, J.C. Setubal, S. Genin, A. Guidot, Marc Valls. Comparative analysis of Ralstonia solanacearum methylomes. Frontiers in Plant Science, 8 (504), 2017.

  • M. Puigvert, R. Guarischi-Sousa, P. Zuluaga, N. Sanchez Coll, A.P. Macho, J.C. Setubal and Marc Valls. Transcriptomes of Ralstonia solanacearum during root colonization of Solanum commersonii. Frontiers in Plant Science, 8 (370), 2017.

  • J.S.L. Patané, J. Martins Jr., A.B. Castelão, C. Nishibe, L. Montera, F. Bigi, M.J. Zumárraga, A.A. Cataldi, A. Fonseca Junior, E. Roxo, A.L.A.R. Osório, K.S. Jorge, T.C. Thacker, N.F. de Almeida Jr., F.R. Araújo, J.C. Setubal. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses. Genome Biology and Evolution, 9(3):521-535, 2017.

  • D. Paez-Espino, I-Min Chen, K. Palaniappan, A. Ratner, K. Chu, E. Szeto, M. Pillay, J. Huang, V. Markowitz, T. Nielsen, M. Huntemann, T. Reddy, G. Pavlopoulos, M. Sullivan, B. Campbell, F. Chen, K. McMahon, S. Hallam, V. Denef, R. Cavicchioli, S. Caffrey, W. Streit, J. Webster, K. Handley, G. Salekdeh, N. Tsesmetzis, J.C. Setubal, P. Pope, W. Liu, A. Rivers, N. Ivanova, N. Kyrpides. IMG/VR: A database of cultured and uncultured DNA Viruses and Retroviruses. Nucleic Acids Research, 45 (D1), D457-D465 (database issue), 2017.

  • F. Rossi, R. Girardello, C. Morais, A. Cury, L. Martins, A.M. da Silva, E. Abdala, P. Hoff, T. Di Gioia, J. de Almeida Júnior, J.C. Setubal, and A. Duarte. Plasmid-mediated mcr-1 in a carbapenem-susceptible Escherichia coli causing blood infection in Brazil: an unnoticeable spread of colistin resistance? Clinics, 2017.

• 2016

  • L.P. Antunes, L.F. Martins, R.V. Pereira, A.M. Thomas, D. Barbosa, L.N. Lemos, G.M.M. Silva, L.M.S. Moura, G.W.C. Epamino, L.A. Digiampietri, K.C. Lombardi, P.L. Ramos, R.B. Quaggio, J.C.F. de Oliveira, R.C. Pascon, J.B. da Cruz, A.M. da Silva, J.C. Setubal. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Scientific Reports, 6:38915, 2016.

  • A.M. Thomas, E.C. de Jesus, A. Lopes, S. Aguiar Junior, M.D. Begnami, R.M. Rocha, P.A. Carpinetti, A.C. Aranha, C. Hoffmann, H.C. Freitas, I.T. da Silva, D.N. Nunes, J.C. Setubal, E. Dias-Neto. Tissue-associated bacterial alterations in rectal carcinoma patients revealed by 16S rRNA community profiling. Frontiers in Cellular and Infection Microbiology, 6:179. doi: 10.3389/fcimb.2016.00179, 2016

  • J. D. Lima-Junior, C. Viana-Niero, D. V. C. Oliveira, G. E. Machado, M. C. S. Rabello, J. Martins-Junior, L. F. Martins, L. A. Digiampietri, A. M. da Silva, J. C. Setubal, D. A. Russell, D. Jacobs-Sera, W. H. Pope, G. F. Hatfull, S. C. Leao. 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, 16:11, 2016.

  • R. Guarischi-Sousa; M. Puigvert; N.S. Coll; M.I. Siri; M.J. Pianzzola; M. Valls; J.C. Setubal. Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031. Standards in Genomic Sciences, 11:7, 2016.

• 2015
  • L. Anderson, M.S. Amaral, F. Beckedorff, L.F. Silva, B. Dazzani, K.C. Oliveira, G.T. Almeida, M.R. Gomes, D.S. Pires, J.C. Setubal, R. DeMarco, S. Verjovski-Almeida. Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. PLoS Neglected Tropical Diseases. 9(12):e0004334, 2015
  • AR Schwartz, N Potnis, S Timilsina, M Wilson, J Patane, J Martins, GV Minsavage, D Dahlbeck, A Akhunova, N Almeida, GE Vallad, JD Barak, FF White, SA Miller, D Ritchie, E Goss, RS Bart, JC Setubal, JB Jones, BJ Staskawicz. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity. Frontiers in Microbiology, 6(00535), 2015.
  • Y. Zhang, N. Jalan, E. Goss, J.B. Jones, J.C. Setubal, X. Deng, N. Wang. Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas. ISME Journal, 9:2128-2138, 2015.
  • Neha Potnis, J.C. Setubal, Rebecca Bart, Deepak Shantharaj and Jeffrey B Jones. High-throughput DNA sequencing technology as a tool in understanding plant-pathogenic bacteria. In Nian Wang et al. (Eds.) Virulence mechanisms of plant-pathogenic bacteria, pp. 183-196. St. Paul, MN: APS Press, 2015.
  • J.C. Setubal and N.F. Almeida. The Azotobacter vinelandii genome: an update. In Frans J. de Bruijn (Ed.) Biological Nitrogen Fixation. Volume 1, Chapter 22, pp. 225-234, Wiley-Blackwell, 2015.
  • A. Durham, J. Barrera, e J.C. Setubal. Interdisciplinaridade em Ação na Pesquisa e Pós-Graduação em Bioinformática. In Arlindo Philippi Jr e Valdir Fernandes (Eds.) Práticas da Interdisciplinaridade no Ensino e na Pesquisa. Editora Manole, 2015.
• 2014
  • E. Purwantini, T. Torto-Alalibo, J. Lomax, J.C. Setubal, B. Tyler, B. Mukhopadhyay. Genetic resources for methane production from biomass described with gene ontology. Frontiers in Microbiology, 5:634, 2014.
  • T. Torto-Alalibo, E. Purwantini, J. Lomax, J.C. Setubal, B. Mukhopadhyay, B.M. Tyler. Genetic Resources for Advanced Biofuel Production Described with the Gene Ontology. Frontiers in Microbiology, 5:528. doi: 10.3389/fmicb.2014.00528, 2014.
  • Andrew M Thomas, Frederico OG Netto, Gustavo Ribeiro Fernandes, Maria Galli de Amorim, Luisa B. Gomez, Ana Lúcia Noronha Francisco, J.C. Setubal, Luiz Paulo Kowalski, Diana Noronha Nunes, Emmanuel Dias-Neto. Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms. BMC Microbiology, 14(1):250, 2014.
  • A.J.S. Ferreira, R. Siam, J.C. Setubal, A. Moustafa, A. Sayed, F.S. Chambergo, A.S. Dawe, M.A. Ghazy, H. Sharaf, A. Ouf, I. Alam, A.M. Abdel-Haleem, H. Lehvaslaiho, E. Ramadan, A. Antunes, U. Stingl, J.A.C. Archer, B.R. Jankovic, M. Sogin, V.B. Bajic, H. El-Dorry. Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. PLoS ONE, 9(6):e97338, 2014.
  • A. Sayed, M. Ghazy, A.J.S. Ferreira, J.C. Setubal, F.S. Chambergo, A. Ouf, M. Adel, A.S. Dawe, J.A.C. Archer, V.B. Bajic, R. Siam, H. El-Dorry. A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. Journal of Biological Chemistry, 289(3):1675-1687, 2014.
  • N.A. Wulff, S. Zhang, J.C. Setubal, N.F. Almeida, E.C. Martins, R. Harakava, D. Kumar, L.T. Rangel, X. Foissac, J.M. Bové, D.W. Gabriel. The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing. Microbe Plant Molecular Interactions, 27(2):163-176, 2014.
• 2013
  • N. Jalan, D. Kumar, M., Fahong Yu, J. Jones, J. Graham, F. White, J. Setubal, N. Wang. Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. BMC Genomics, 2013, 14:551.
  • L.F. Martins, L. P. Antunes, R.C. Pascon, J.C. Franco de Oliveira, L.A. Digiampietri, D. Barbosa, B.M. Peixoto, M.A. Vallim, C. Viana-Niero, E.H. Ostroski, G.P. Telles, Z. Dias, J.B. da Cruz, L. Juliano, S. Verjovski-Almeida, A.M. da Silva, J.C. Setubal. Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms. PLoS ONE, 8(4):e61928, 2013.
  • S.C. Slater, J.C. Setubal, et al. The Genome of Agrobacterium tumefaciens C58: Reconciliation of sequence data, updated annotation, and distribution of linear chromosome in genus Agrobacterium. Applied and Environmental Microbiology, 79(4):1414-1417, 2013.
  • P. Rajasekaran, J.C. Alexander, M.N. Seleem, N. Jain, N. Sriranganathan, A.R. Wattam, J.C. Setubal, S.M. Boyle. Peptide nucleic acids inhibit the growth of Brucella suis in pure culture and infected murine macrophages. International Journal of Antimicrobial Agents, 41(4):358--62, 2013.
  • M.L. Wilson, Y. Cai, R. Hanlon, S. Taylor, B. Chevreux, J.C. Setubal, B.M. Tyler, J. Peccoud. Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic Acids Research 41(1):e25, 2013.
• 2012
  • A. Wattam, T. Inzana, K. Williams, S. Mane, M. Shukla, N. Almeida, A. Dickerman, S. Mason, I. Moriyon, D. O'Callaghan, A. Whatmore, B. Sobral, R. Tiller, A. Hoffmaster, M. Frace, C. De Castro, A. Molinaro, S. Boyle, B. De, and J. C. Setubal. Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway. mBio, 3(5): e00246-12, 2012.
  • H. Saldanha, E. Ribeiro, C. Borges, A. Araujo, R. Gallon, M. Holanda, M. E. Walter, R. Togawa, and J.C. Setubal. Towards a hybrid federated cloud platform to efficiently execute bioinformatics workflows. In Bioinformatics, InTech Publishers, 2012.
  • K. Yang, L. Heath, and J. C. Setubal. REGEN: Ancestral Genome Reconstruction for Bacteria. Genes, 3(3), 423-443, 2012.
  • Z. Dias, U. Dias, J.C. Setubal. SIS: a program to generate draft genome sequence scaffolds for prokaryotes. BMC Bioinformatics, 13(1):96, 2012. Web server and software download available here.
  • Patricia C. Dos Santos, Zhong Fang, Steven W. Mason, J.C. Setubal and Ray Dixon. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genomics, 13(1):162, 2012.
  • A.R. Paschoal, V. Maracaja-Coutinho, J.C. Setubal, Z.L. Paulino Simões, S. Verjovski-Almeida and A.M. Durham. Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases. RNA Biology, 9(3), 2012.
  • P.N. Collen, 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, 24(4):641-647, 2012.
• 2011
  • F. I. Staquicini, M. Cardó-Vila, 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, 108, 2011.
  • N. Jalan, V. Aritua, D. Kumar, F. Yu, J. Jones, J. Graham, J.C. Setubal and N. Wang. 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. J. of Bacteriology, 193:6342-6357, 2011.
  • T. L. Hamilton, M. Ludwig, R. Dixon, E. S. Boyd, P. dos Santos, J. C. Setubal, D. A. Bryant, D. R. Dean, and J. W. Peters. Transcriptional profiling of Nitrogen Fixation in Azotobacter vinelandii. J. of Bacteriology, 193:4477-4486, 2011.
  • R. Cai, J. Lewis, S. Yan, H. Liu, C. R. Clarke, F. Campanile, N. F. Almeida, D. J. Studholme, M. Lindeberg, D. Schneider, M. Zaccardelli, J. C. Setubal, N. P. Morales-Lizcano, A. Bernal, G. Coaker, C. Baker, C. L. Bender, S. Leman, B. A. Vinatzer. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathogens, 7(8), 2011.
  • N. Potnis, K. Krasileva, V. Chow, N. F. Almeida, P. B. Patil, R. P. Ryan, M. Sharlach, F. Behlau, J. Max Dow, F. F. White, J. F. Preston, B. A. Vinatzer, R. Koebnik, João C. Setubal, D. J. Norman, B. Staskawicz and J. B. Jones. Comparative Genomics Reveals Diversity among Xanthomonads Infecting Tomato and Pepper. BMC Genomics 2011, 12:146.
  • D. Wibberg, J. Blom, A. Goesmann, F. Kollin, B. Scharf, S. Schneiker-Bekel, R. Sczcepanowski, J.C. Setubal, R. Schmitt, A. Pühler and Andreas Schlüter. 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, 2011.
  • Hongtao Zhang, Joao C. Setubal, 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. J. of Industrial Microbiology and Biotechnology, 38:667-677, 2011.
  • V. Shulaev, D. Sargent, R. Crowhurst, T. Mockler, et al. The genome of woodland strawberry ( Fragaria vesca). Nature Genetics, 43:109-116, 2011. doi:10.1038/ng.740
• 2010
  • Trudy Torto-Alalibo, Candace Collmer, Michelle Gwinn-Giglio, Magdalen Lindeberg, Shaowu Meng, Marcus C. Chibucos, Tsai-Tien Tseng, Jane Lomax, Bryan Biehl, Amelia Ireland, David Bird, Ralph A. Dean, Jeremy D. Glasner, Nicole Perna, Joao C. Setubal, Alan Collmer and Brett M. Tyler. Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology. Microbiology and Molecular Biology Reviews, 74(4):479-503, 2010.
  • R. Tiller, J. Gee, M. Frace, T. Taylor, J.C. Setubal, A. Hoffmaster and B. De. Characterization of novel Brucella strains originating from wild native rodent species in North Queensland, Australia. Applied and Environmental Microbiology, 76(17):5837-45, 2010.
  • L.M. Moreira, N.F. Almeida Jr, N. Potnis, L.A. Digiampietri,..., J.A. Ferro, B.A. Vinatzer and J.C. Setubal (31 authors). 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), 2010.
  • A.N. Warren, J. Archuleta, W. Feng, J.C. Setubal. Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics, 11(131), 2010.
  • 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. Journal of Concurrency and Computation: Practice and Experience , doi:10.1002/cpe.1590, 2010.
  • N. Almeida, S. Yan, R. Cai, C. R. Clarke, C. E. Morris, N. W. Schaad, E. L. Schuenzel, G. H. Lacy, X. Sun, J. B. Jones, J. A. Castillo, C. T. Bull, S. Leman, D. S. Guttman, J. C. Setubal, and B. A. Vinatzer. PAMDB, a Multilocus Sequence Typing and Analysis Database and Website for Plant-Associated Microbes. Phytopathology, 100(3), pp. 208-215, 2010.
• 2009
  • Emmanuel Dias-Neto, Diana N. Nunes, Ricardo J. Giordano, Jessica Sun, Gregory H. Botz, Kuan Yang, Joao C. Setubal, Renata Pasqualini, Wadih Arap. Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis. PLoS ONE, 4(12):e8338, 2009.
  • M. Chibucos, T. T. Tseng, and J.C. Setubal. Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology, 17(7), pp. 312-319, 2009.
  • J.C. Setubal, P.C. dos Santos, B. Goldman, et al. (44 authors). The genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J. of Bacteriology, 191(14):4534-45, 2009.
  • A.R. Wattam, K.P. Williams, E.S. Snyder, N.F.Almeida, M. Shukla,..., S.M. Boyle, J.C. Setubal (22 authors). Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. Journal of Bacteriology, 191(11):3569-79, 2009.
  • J.J. Gillespie, N.C. Ammerman, S.M. Dreher-Lesnick, M.S. 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, 4(3): e4833. doi:10.1371/journal.pone.0004833, 2009.
  • S. Slater, B. Goldman, B. Goodner, J.C. Setubal, ..., and D. Wood (36 authors). Genome sequences of three Agrobacterium biovars help elucidate the evolution of multi-chromosome genomes in bacteria. J. of Bacteriology, 191 (8), 2501-2511, 2009.
  • T.-T. Tseng , B.M. Tyler, and J.C. Setubal. Protein Secretion Systems in Bacterial-Host Associations, and their Description in the Gene Ontology. BMC Microbiology, 2009, 9(Suppl 1):S2.
  • A.N. Warren and J.C. Setubal. The Genome Reverse Compiler: an explorative annotation tool. BMC Bioinformatics, 10:35, 2009. GRC is available here
  • 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. Molecular Microbe-Plant Interactions, 22:52-62, 2009.
  • 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.
• 2008
  • 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)
  • 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. 74(10):3171-81, 2008.
  • 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.
  • 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.
  • 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 and Tatsuo Miyamura (eds.), Structure-based Study of Virus Infection. World Scientific Publishing Company, Stockholm, Sweden, 2008 (ISBN 981-270-405-1)
• 2007
  • 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.
  • 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.
  • E. Snyder,..., J. C. Setubal and B. Sobral (43 authors). PATRIC: The VBI PathoSystems Resource Integration Center. Nucleic Acids Research 2007, 35:D401-D406.
• 2006
  • J. C. Setubal, M. Reis, J. Matsunaga, and D. Haake. Lipoprotein Computational Prediction in Spirochetal Genomes. Microbiology, 152:113--121, 2006.
  • 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.
• 2005
  • 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.
  • 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.
  • 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.
  • 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.
• 2004
  • 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.
  • 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.
  • 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):459-77, 2004.
  • 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.
  • 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.
  • J. C. Setubal. Bioinformatics. In L. Mir (ed), Genomics, Editora Atheneu, (this is an introductory book chapter, in Portuguese), pp. 105-118, 2004.
  • 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.
  • 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.
  • 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).
• 2003
  • 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).
  • 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.
  • 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.
• 2002
  • 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.
  • 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.
• 2001 and before
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Genome and Resource Announcements

• D.M. Soares, S.V. Atum, E.J. Bechara, J.C. Setubal, C.V. Stevani and Renato S. Freire. Exploring the Microbiota of the Guarapiranga Water Reservoir with Long-Read Sequencing Technology. Frontiers in Marine Science, 791101, 2021.

• M. Rossmann, A.M. Thomas, S.S. Guima, L.F. Martins, P. Inderbitzin, V. Knight-Connoni, A.M. da Silva, J.C. Setubal. Microbiomes of field-grown maize and soybean in Southeastern and Central Brazil inferred by high-throughput 16S and ITS amplicon sequencing. Microbiology Resource Announcements, 10 (31): e00528-21, 2021.

• Paulo Marques Pierry, Wesley Oliveira de Santana, João Paulo Kitajima, Joaquim Martins-Junior, Paulo Adriano Zaini, Guillermo Uceda-Campos, Oseias R. Feitosa-Junior, Patrícia Isabela Silva Pessoa, Helvécio Della Coletta-Filho, Alessandra Alves de Souza, Marcos Antonio Machado, Abelmon da Silva Gesteira, Layla Farage Martins, Murilo Sena Amaral, Felipe Cesar Beckedorff, Luiz Gonzaga Paula de Almeida, Ana Tereza Ribeiro de Vasconcelos, Sergio Verjovski-Almeida, João Carlos Setubal, and Aline Maria da Silva. High-Quality Draft Genome Sequence Resources of Eight Xylella fastidiosa Strains Isolated from Citrus, Coffee, Plum, and Hibiscus in South America. Phytopathology 110 (11), 1751-1755, 2020.

• D.D. Almeida, J.P. Kitajima, M.Y. Nishiyama Jr, G.W. Condomitti, U.C. de Oliveira, J.C. Setubal & I.L.M. Junqueira-de-Azevedo. The complete mitochondrial genome of Bothrops jararaca (Reptilia, Serpentes, Viperidae), Mitochondrial DNA Part B, 1:1, 907-908, 2016.

• Raiol T, De-Souza MT, Oliveira JV, Silva HS, Orem JC, Cavalcante DA, Almeida NF, Telles GP, Setubal JC, Brigido MM, Torres FA, Stadler PS, Walter ME, Moraes LM. Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring. Genome Announcements, 2(5), 2014.

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

• Wang N, Jin T, Trivedi P, Setubal JC, Tang J, Machado MA, Triplett E, Coletta-Filho HD, Cubero J, Deng X, et al. 2015. Announcement of the International Citrus Microbiome (Phytobiome) Consortium. J Cit Pathol. iocv_journalcitruspathology_27940.
• A. Warren and J.C. Setubal. Using Entropy Estimates for DAG-Based Ontologies. In Proceedings of the 15th Bio-Ontologies Special Interest Group Meeting of ISMB 2012.
• Z. Dias, U. Dias, L. Heath, and J.C. Setubal. Sorting Genomes Using Almost-Symmetric Inversions. In Proceedings of the 27th Symposium on Applied Computing, March 26-30, 2012, Riva del Garda, Italy.
• Zanoni Dias, Ulisses Dias, and Joao C. Setubal. Using Inversion Signatures to Generate Draft Genome Sequence Scaffolds. Proceedings of ACM International Conference on Bioinformatics, Computational Biology and Biomedicine 2011, (regular paper).
• U. Dias, Z. Dias, and J.C. Setubal. A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes. Proceedings of RECOMB Comparative Genomics 2010. Lecture Notes in Computer Science Volume 6398, 2011, DOI: 10.1007/978-3-642-16181-0, Springer.
• K. Yang and J.C. Setubal. Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes. Proceedings of the ACM International Conference on Bioinformatics and Computational Biology 2010.
• 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.
• 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.
• Baker SC, Jukneliene D, Purkayastha A, Snyder EE, Crasta OR, Czar MJ, Setubal JC, Sobral BW. Developing bioinformatic resources for coronaviruses. In: Stanley Perlman and Kathryn Holmes (eds.), The Nidoviruses: Toward Control of SARS and other Nidovirus Diseases. Proceedings of the Xth Nidovirus Symposium. Advances in Experimental Medicine and Biology, Volume 581, pp. 395-398, Springer, 2006.
• Shallom JM, Dongre N, Dharmanolla C, Purkayastha A, Czar M, Crasta O, Setubal J, Sobral B. The PathoSystems Resource Integration center: implications for viral pathogens. Journal of Clinical Virology 36: S205-S205, 2006.
• 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.
• J. P. Piazza and J. C. Setubal. DNA sequence organism determination by sequence composition analysis. Poster at the Intelligent Systems for Molecular Biology 2005.
• 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.
• 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.
• 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.
• 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.
• 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.
• J. C. Setubal. Bioinformatics challenges for the 21st century. Proceedings of the 20th Meeting on Genetics and Crop Improvement, ESALQ-USP, 2003 (in Portuguese).
• 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.
• 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).
• J. C. Setubal. Syllabus proposal for Theoretical Computer Science. Proceedings of the 2000 Computer Science Teaching Workshop (WEI), Curitiba (Brazil), 2000 (in Portuguese).
• 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.
• 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.
• 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).
• 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.
• 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).
• J. C. Setubal. Sequential and Parallel Experimental Results with Bipartite Matching Algorithms. Technical Report IC--96--09, Instituto de Computação, Unicamp, 1996.
• 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.
• 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.
• 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.
• 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.
• 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

• J. C. Setubal. Desconcertos na Ciência. (Disconcertments in Science) Revista Brasileira de Psicanálise 50(3):145-152, 2016 (in Portuguese).
• J. C. Setubal. The Origin and Meaning of Bioinformatics, Revista ComCiencia, 46, 2003 (in Portuguese).
• 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).