Joao Carlos Setubal

Pós-doutorado

Idiomas

Áreas de atuação

Organização de eventos

Participação em eventos

Participação em bancas

Orientou

Produções bibliográficas

• ZAMUNÉR, CAIO FELIPE CAVICCHIA ; Carhuaricra-Huaman, Dennis ; RAGUPATHY, ROOBINIDEVI ; REDFERN, JAMES ; RODRIGUEZ-CUEVA, CARMEN L. ; Behlau, Franklin ; ENRIGHT, MARK C. ; FERREIRA, HENRIQUE ; Setubal, João C. . Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes. Microbial Genomics , v. 11, p. 1338, 2025.

• NASCIMENTO FILHO, EDSON G. ; VIEIRA, MÔNICA L. ; DIAS, MERIELLEN ; MENDES, MARIA A. ; SANCHEZ, FABIO B. ; Setubal, João C. ; HEINEMANN, MARCOS B. ; SOUZA, GISELE O. ; PIMENTA, DANIEL C. ; NASCIMENTO, ANA L.T.O. . Global proteome of the saprophytic strain Leptospira biflexa and comparative analysis with pathogenic strain Leptospira interrogans uncover new pathogenesis mechanisms. Journal of Proteomics , v. 297, p. 105125, 2024.

• FLORES, VINICIUS S. ; AMGARTEN, DEYVID E. ; IHA, BRUNO KOSHIN VÁZQUEZ ; RYON, KRISTA A. ; DANKO, DAVID ; TIERNEY, BRADEN T. ; MASON, CHRISTOPHER ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS . Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Scientific Reports , v. 14, p. 7913, 2024.

• Carhuaricra-Huaman, Dennis ; GONZALEZ, IRYS H.L. ; RAMOS, PATRICIA L. ; DA SILVA, ALINE M. ; Setubal, Joao C. . Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths ( Bradypus variegatus ), the first from a non-human host. PeerJ , v. 12, p. e17206, 2024.

• RIBEIRO, DILSON FAGUNDES ; DE MATOS, JÉSSICA PEREIRA ; ROCHA, LORRANA CACHUITE MENDES ; DA SILVA, ANA KARLA ; DE PAULA, CAMILA HENRIQUES ; CORDEIRO, ISABELLA FERREIRA ; DE CARVALHO LEMES, CAMILA GRACYELLE ; SANCHEZ, ANGÉLICA BIANCHINI ; GARCIA, CAMILA CARRIÃO MACHADO ; SETUBAL, JOÃO CARLOS ; DE SOUZA, ROBSON FRANCISCO ; DE MELLO VARANI, ALESSANDRO ; ALMEIDA, NALVO FRANCO ; MOREIRA, LEANDRO MARCIO . From cactus to crop: genomic insights of a beneficial and non-pathogenic Curtobacterium flaccumfaciens strain and the evolution of its pathosystem. MOLECULAR GENETICS AND GENOMICS , v. 299, p. 105, 2024.

• CARRAU, ANALÍA ; TANO, JOSEFINA ; MOYANO, LAURA ; RIPA, MARÍA BELÉN ; PETROCELLI, SILVANA ; PISKULIC, LAURA ; MOREIRA, LEANDRO MARCIO ; PATANÉ, JOSÉ SALVATORE LEISTER ; SETUBAL, JOÃO CARLOS ; ORELLANO, ELENA GRACIELA . A novel BLUF photoreceptor modulates the Xanthomonas citri subsp. citri-host plant interaction. PHOTOCHEMICAL SCIENCES (ONLINE) , v. 1, p. 1, 2023.

• INAGUE, ALEX ; ALECRIM, LILIAN COSTA ; MONTEIRO, JHONATAS SIRINO ; YOSHINAGA, MARCOS YUKIO ; SETUBAL, JOÃO CARLOS ; MIYAMOTO, SAYURI ; GIORDANO, RICARDO JOSÉ . Oxygen-induced pathological angiogenesis promotes intense lipid synthesis and remodeling in the retina. Iscience , v. 26, p. 106777, 2023.

• RODRIGUEZ CARNERO, LUIS ANTONIO ; KURAMOTO, ANDRÉIA ; CAMPOS DE OLIVEIRA, LÉA ; MONTEIRO, JHONATAS SIRINO ; SETUBAL, JOÃO CARLOS ; CUNHA-NETO, EDÉCIO ; CERDEIRA SABINO, ESTER ; GIORDANO, RICARDO JOSÉ . Anti-Trypanosoma cruzi antibody profiling in patients with Chagas disease treated with benznidazole assessed by genome phage display. PLoS Neglected Tropical Diseases , v. 17, p. e0011019, 2023.

• SINGH, NITIN K. ; WOOD, JASON M. ; PATANE, JOSE ; MOURA, LIVIA MARIA SILVA ; LOMBARDINO, JONATHAN ; SETUBAL, JOÃO CARLOS ; VENKATESWARAN, KASTHURI . Characterization of metagenome-assembled genomes from the International Space Station. Microbiome , v. 11, p. 125, 2023.

• BOETTGER, BRUNO C. ; PIROUPO, CARLOS M. ; Setubal, João C. ; GIRARDELLO, RAQUEL ; PIGNATARI, ANTÔNIO C. C. . Co-carriage of Plasmid NDM and Chromosomal KPC in Klebsiella pneumoniae ST255 Human Wound Isolate in Brazil. CURRENT MICROBIOLOGY , v. 80, p. 394, 2023.

• DE SOUZA XAVIER COSTA, NATÁLIA ; RIBEIRO JÚNIOR, GABRIEL ; DO NASCIMENTO, ELLEN CAROLINE TOLEDO ; DE BRITO, JÔSE MARA ; ANTONANGELO, LEILA ; FARIA, CAROLINE SILVÉRIO ; MONTEIRO, JHONATAS SIRINO ; SETUBAL, JOÃO CARLOS ; PINHO, JOÃO RENATO REBELLO ; PEREIRA, ROBERTA VERCIANO ; SEELAENDER, MARILIA ; DE CASTRO, GABRIELA SALIM ; LIMA, JOANNA D. C. C. ; DE ALMEIDA MONTEIRO, RENATA APARECIDA ; DUARTE-NETO, AMARO NUNES ; SALDIVA, PAULO HILÁRIO NASCIMENTO ; FERRAZ DA SILVA, LUIZ FERNANDO ; DOLHNIKOFF, MARISA ; MAUAD, THAIS . COVID-19 induces more pronounced extracellular matrix deposition than other causes of ARDS. RESPIRATORY RESEARCH , v. 24, p. 281, 2023.

• LAUX, MARCELE ; PIROUPO, CARLOS MORAIS ; SETUBAL, JOÃO CARLOS ; GIANI, ALESSANDRA . The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade. HARMFUL ALGAE , v. 129, p. 102518, 2023.

• PATANÉ, JOSÉ S.L. ; Moreira, Leandro M. ; DE MELO TEIXEIRA, MARCUS ; MARTINS JR, JOAQUIM ; Setubal, João C. ; VARANI, ALESSANDRO M. . New insights into plant natriuretic peptide evolution: From the lysogenic conversion in Xanthomonas to the lateral transfer to the whitefly Bemisia tabaci. GENE , v. 821, p. 146326, 2022.

• ANTUNES, KRIST H. ; STEIN, RENATO T. ; FRANCESCHINA, CAROLINE ; DA SILVA, EMANUELLE F. ; DE FREITAS, DEISE N. ; SILVEIRA, JOSIANE ; MOCELLIN, MAGÁLI ; LEITÃO, LIDIANE ; FACHI, JOSÉ L. ; PRAL, LAÍS P. ; GONZALEZ, AMANDA ; OLIVEIRA, SARAH ; DUARTE, LEONARDO ; CASSÃO, GISELE ; GONÇALVES, JOÃO I.B. ; REIS, TATIANE M. ; ABBADI, BRUNO L ; DORNELLES, MAIELE ; SPEROTTO, NATHÁLIA D.M. ; SETUBAL, J. C. ; et.al . Short-chain fatty acid acetate triggers antiviral response mediated by RIG-I in cells from infants with respiratory syncytial virus bronchiolitis. EBIOMEDICINE , v. 77, p. 103891, 2022.

• NAKAMURA­GOUVEA, NATALIA ; ALVES­LIMA, CICERO ; BENITES, L. FELIPE ; IHA, CINTIA ; MARACAJA­COUTINHO, VINICIUS ; ALIAGA­TOBAR, VICTOR ; AMARAL, MARCELLA ; YOKOYA, NAIR S ; MARINHO­SORIANO, ELIANE ; GRAMINHA, MARCIA A S ; COLLÉN, JONAS ; CABRAL OLIVEIRA, MARIANA ; Setubal, Joao Carlos ; COLEPICOLO, PIO . Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta: Gracilariales). JOURNAL OF PHYCOLOGY , v. 1, p. 13238, 2022.

• PALMEIRA, ONDINA ; MATOS, LARISSA R.B. ; NASLAVSKY, MICHEL S. ; BUENO, HELOISA M.S. ; SOLER, JÚLIA P. ; Setubal, João C. ; ZATZ, MAYANA . Longitudinal 16S rRNA gut microbiota data of infant triplets show partial susceptibility to host genetics. Iscience , v. 25, p. 103861, 2022.

• HARADA, LILIAM K ; SILVA, ERICA C ; ROSSI, FERNANDO PN ; CIEZA, BASILIO ; OLIVEIRA, THAIS J ; PEREIRA, CARLA ; TOMAZETTO, GEIZECLER ; SILVA, BIANCA B ; SQUINA, FABIO M ; VILA, MARTA MDC ; Setubal, João C ; HA, TAEKJIP ; da Silva, Aline M ; BALCÃO, VICTOR M . Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa. Future Microbiology , v. 17, p. 111-141, 2022.

• JUSTO AREVALO, SANTIAGO ; ZAPATA SIFUENTES, DANIELA ; CUBA PORTOCARRERO, ANDREA ; BRESCIA REÁTEGUI, MICHELLA ; MONGE PIMENTEL, CLAUDIA ; FARAGE MARTINS, LAYLA ; MARQUES PIERRY, PAULO ; MORAIS PIROUPO, CARLOS ; GUERRA SANTA CRUZ, ALCIDES ; QUIÑONES AGUILAR, MAURO ; SHAKER FARAH, CHUCK ; SETUBAL, JOÃO CARLOS ; DA SILVA, ALINE MARIA . Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD. APPLIED AND ENVIRONMENTAL MICROBIOLOGY , v. 88, p. 14, 2022.

• BUTARELLI, ANA CAROLINA DE ARAÚJO ; FERREIRA, LUCAS SALOMÃO DE SOUSA ; RIYUZO, RAQUEL ; DALL?AGNOL, HIVANA MELO BARBOSA ; PIROUPO, CARLOS MORAIS ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS ; DALL?AGNOL, LEONARDO TEIXEIRA . Diversity assessment of photosynthesizers: comparative analysis of pre-cultivated and natural microbiome of sediments from Cerrado biome in Maranhão, Brazil. Environmental Science and Pollution Research , v. 1, p. 1, 2022.

• DA PAIXÃO, VINICIUS FERREIRA ; SOSA, OMAR JULIO ; DA SILVA PELLEGRINA, DIOGO VIEIRA ; DAZZANI, BIANCA ; CORRÊA, THALITA BUENO ; RISÉRIO BERTOLDI, ESTER ; DA CRUZ E ALVES-DE-MORAES, LUÍS BRUNO ; DE OLIVEIRA PESSOA, DIOGO ; DE PAIVA OLIVEIRA, VICTORIA ; ALBERTO CHIONG ZEVALLOS, RICARDO ; RUSSO, LILIAN CRISTINA ; LUIS FORTI, FABIO ; EDUARDO FERREIRA, JOÃO ; CARIOCA FREITAS, HELANO ; JUKEMURA, JOSÉ ; MACHADO, MARCEL CERQUEIRA CÉSAR ; DIRLEI BEGNAMI, MARIA ; SETUBAL, JOÃO CARLOS ; BASSÈRES, DANIELA SANCHEZ ; MORAES REIS, EDUARDO ; et.al . Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma. CELLULAR ONCOLOGY , v. 45, p. 479-504, 2022.

• MARQUIONI, VINÍCIUS ; ROSSI, FERNANDO PACHECO NOBRE ; MENDONÇA, DEBORAH CEZAR ; MARTINS, LAYLA FARAGE ; Behlau, Franklin ; SETUBAL, JOÃO CARLOS ; DA SILVA, ALINE MARIA ; NOVO-MANSUR, MARIA TERESA MARQUES . Isolation and characterization of vB_XciM_LucasX, a new jumbo phage that infects Xanthomonas citri and Xanthomonas fuscans. PLoS One , v. 17, p. e0266891, 2022.

• UCEDA-CAMPOS, GUILLERMO ; FEITOSA-JUNIOR, OSEIAS R. ; SANTIAGO, CAIO R. N. ; PIERRY, PAULO M. ; ZAINI, PAULO A. ; DE SANTANA, WESLEY O. ; MARTINS-JUNIOR, JOAQUIM ; BARBOSA, DEIBS ; DIGIAMPIETRI, Luciano A. ; Setubal, João C. ; DA SILVA, ALINE M. . Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems. Microorganisms , v. 10, p. 914, 2022.

• AMGARTEN, DEYVID ; IHA, BRUNO KOSHIN VÁZQUEZ ; PIROUPO, CARLOS MORAIS ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS . vHULK, a New Tool for Bacteriophage Host Prediction Based on Annotated Genomic Features and Neural Networks. PHAGE , v. 00, p. 1-9, 2022.

• CARHUARICRA HUAMAN, DENNIS E. ; LUNA ESPINOZA, LUIS R. ; RODRÍGUEZ CUEVA, CARMEN L. ; DURAN GONZALES, CARLA G. ; ROSADIO ALCÁNTARA, RAÚL H. ; Setubal, João C. ; MATURRANO HERNÁNDEZ, LENIN . Genomic Characterization of Salmonella Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru. Microorganisms , v. 10, p. 1726, 2022.

• BALCÃO, VICTOR M ; BASU, AAKASH ; CIEZA, BASILIO ; ROSSI, FERNANDO N ; PEREIRA, CARLA ; VILA, MARTA MDC ; Setubal, João C ; HA, TAEKJIP ; da Silva, Aline M . Pseudomonas -tailed lytic phages: genome mechanical analysis and putative correlation with virion morphogenesis yield. Future Microbiology , v. 17, p. 1009-1026, 2022.

• DE MENEZES, TATIANE A. ; DE FREITAS, MAYANNE A.M. ; LIMA, MICHELE S. ; SOARES, ANA CAROLINA ; LEAL, CAMILLE ; BUSCH, MILEANE DE S. ; TSCHOEKE, DIOGO A. ; DE O. VIDAL, LUCIANA ; ATELLA, GEORGIA C. ; KRUGER, RICARDO H. ; Setubal, João ; VASCONCELOS, AGNALDO A. ; DE MAHIQUES, MICHEL M. ; SIEGLE, EDUARDO ; ASP, NILS EDVIN ; COSENZA, CARLOS ; HAJDU, EDUARDO ; DE REZENDE, CARLOS E. ; THOMPSON, CRISTIANE C. ; THOMPSON, FABIANO L. ; et.al . Fluxes of the Amazon River plume nutrients and microbes into marine sponges. SCIENCE OF THE TOTAL ENVIRONMENT , v. 847, p. 157474, 2022.

• ERJEFÄLT, JONAS S. ; DE SOUZA XAVIER COSTA, NATÁLIA ; JÖNSSON, JIMMIE ; COZZOLINO, OLGA ; DANTAS, KATIA CRISTINA ; CLAUSSON, CARL-MAGNUS ; SIDDHURAJ, PREMKUMAR ; LINDÖ, CAROLINE ; ALYAMANI, MANAR ; LOMBARDI, SUZETE CLEUSA FERREIRA SPINA ; MENDRONI JÚNIOR, ALFREDO ; ANTONANGELO, LEILA ; FARIA, CAROLINE SILVÉRIO ; DUARTE-NETO, AMARO NUNES ; DE ALMEIDA MONTEIRO, RENATA APARECIDA ; REBELLO PINHO, JOÃO RENATO ; GOMES-GOUVÊA, MICHELE SOARES ; VERCIANO PEREIRA, ROBERTA ; MONTEIRO, JHONATAS SIRINO ; SETUBAL, JOÃO CARLOS ; et.al . Diffuse alveolar damage patterns reflect the immunological and molecular heterogeneity in fatal COVID-19. EBIOMEDICINE , v. 83, p. 104229, 2022.

• OLIVEIRA, VALERIA MAIA ; ANDREOTE, FERNANDO DINI ; CORTELO, PATRICIA CARDOSO ; CASTRO-GAMBOA, IAN ; COSTA-LOTUFO, LETICIA V. ; POLIZELI, MARIA DE LOURDES T. M. ; THIEMANN, OTÁVIO H. ; SETUBAL, JOÃO CARLOS . Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology. BIOTA NEOTROPICA (ONLINE. EDIÇÃO EM INGLÊS) , v. 22, p. 22, 2022.

• LADIN, ZACHARY S. ; FERRELL, BARBRA ; DUMS, JACOB T. ; MOORE, RYAN M. ; LEVIA, DELPHIS F. ; SHRIVER, W. GREGORY ; D?AMICO, VINCENT ; TRAMMELL, TARA L. E. ; SETUBAL, JOÃO CARLOS ; WOMMACK, K. ERIC . Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems. Scientific Reports , v. 11, p. 1629, 2021.

• DE PEDRO-JOVÉ, R. ; PUIGVERT, M. ; SEBASTIÀ, P. ; MACHO, A. P. ; Monteiro, J. S. ; COLL, N. S. ; SETÚBAL, J. C. ; VALLS, M. . Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection. BMC GENOMICS , v. 22, p. 170, 2021.

• PESSOA, DIOGO DE OLIVEIRA ; RIUS, FLÁVIA EICHEMBERGER ; PAPAIZ, DEBORA D'ANGELO ; AYUB, ANA LUÍSA PEDROSO ; MORAIS, ALICE SANTANA ; DE SOUZA, CAMILA FERREIRA ; DA PAIXÃO, VINICIUS FERREIRA ; SETUBAL, JOÃO CARLOS ; NEWTON-BISHOP, JULIA ; NSENGIMANA, JÉRÉMIE ; AZEVEDO, HATYLAS ; REIS, EDUARDO MORAES ; JASIULIONIS, MIRIAM GALVONAS . Transcriptional signatures underlying dynamic phenotypic switching and novel disease biomarkers in a linear cellular model of melanoma progression. NEOPLASIA , v. 23, p. 439-455, 2021.

• TEIXEIRA, ANDRÉ AZEVEDO REIS ; CARNERO, LUIS RODRIGUEZ ; KURAMOTO, ANDRÉIA ; TANG, FENNY HUI FEN ; GOMES, CARLOS HERNIQUE ; PEREIRA, NATALIA BUENO ; DE OLIVEIRA, LÉA CAMPOS ; GARRINI, REGINA ; MONTEIRO, JHONATAS SIRINO ; SETUBAL, JOÃO CARLOS ; SABINO, ESTER CERDEIRA ; Pasqualini, Renata ; COLLI, WALTER ; Arap, Wadih ; ALVES, MARIA JÚLIA MANSO ; CUNHA-NETO, EDÉCIO ; GIORDANO, RICARDO JOSÉ . A refined genome phage display methodology delineates the human antibody response in patients with Chagas disease. iScience , v. 24, p. 102540, 2021.

• FERREIRA, LUCAS SALOMÃO DE SOUSA ; BUTARELLI, ANA CAROLINA DE ARAÚJO ; SOUSA, RAISSA DA COSTA ; OLIVEIRA, MARIENE AMORIM DE ; MORAES, PABLO HENRIQUE GONÇALVES ; RIBEIRO, IGOR SANTANA ; SOUSA, PEDRO FELIPE RODRIGUES ; DALL'AGNOL, HIVANA MELO BARBOSA ; LIMA, ALEX RANIERI JERÔNIMO ; GONÇALVES, EVONNILDO COSTA ; SIVONEN, KAARINA ; FEWER, DAVID ; RIYUZO, RAQUEL ; PIROUPO, CARLOS MORAIS ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS ; DALL'AGNOL, LEONARDO TEIXEIRA . High-Quality Draft Genome Sequence of Pantanalinema sp. GBBB05, a Cyanobacterium From Cerrado Biome. FRONTIERS IN ECOLOGY AND EVOLUTION , v. 9, p. 336, 2021.

• GIRARDELLO, RAQUEL ; PIROUPO, CARLOS MORAIS ; MARTINS, JOAQUIM ; MAFFUCCI, MARCIA HELENA ; CURY, ANA PAULA ; FRANCO, MARIA RENATA GOMES ; MALTA, FERNANDA DE MELLO ; ROCHA, NATÁLIA CONCEIÇÃO ; PINHO, JOÃO RENATO REBELLO ; ROSSI, FLAVIA ; DUARTE, ALBERTO JOSÉ DA SILVA ; SETUBAL, JOÃO CARLOS . Genomic Characterization of mcr-1.1-Producing Escherichia coli Recovered From Human Infections in São Paulo, Brazil. Frontiers in Microbiology , v. 12, p. 1454, 2021.

• FABRO, ALEXANDRE TODOROVIC ; MACHADO-RUGOLO, JULIANA ; BALDAVIRA, CAMILA MACHADO ; PRIETO, TABATHA GUTIERREZ ; FARHAT, CECÍLIA ; ROTEA MANGONE, FLAVIA REGINA ; BATAH, SABRINA SETEMBRE ; CRUVINEL, HELOÍSA RESENDE ; ALDÁ, MAIARA ALMEIDA ; MONTEIRO, JHONATAS SIRINO ; PÁDUA, ADRIANA INACIO ; MORAIS, SIRLEI SIANI ; ANTÔNIO DE OLIVEIRA, ROGÉRIO ; SANTOS, MARCEL KOENIGKAM ; BADDINI-MARTINEZ, JOSÉ ANTÔNIO ; SETUBAL, JOÃO CARLOS ; RAINHO, CLAUDIA APARECIDA ; YOO, HUGO HYUNG BOK ; SILVA, PEDRO LEME ; NAGAI, MARIA APARECIDA ; et.al . 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 , v. 12, p. 1287, 2021.

• VIEIRA, LUCAS MACIEL ; JORGE, NATASHA ANDRESSA NOGUEIRA ; DE SOUSA, JOÃO BATISTA ; SETUBAL, JOÃO CARLOS ; Stadler, Peter F. ; WALTER, MARIA EMÍLIA MACHADO TELLES . Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction. FRONTIERS IN ONCOLOGY , v. 11, p. 1670, 2021.

• ASSIS, RENATA A.B. ; VARANI, ALESSANDRO M. ; SAGAWA, CINTIA H.D. ; PATANÉ, JOSÉ S.L. ; SETUBAL, JOÃO CARLOS ; UCEDA-CAMPOS, GUILLERMO ; DA SILVA, ALINE MARIA ; ZAINI, PAULO A. ; Almeida, Nalvo F. ; MOREIRA, LEANDRO MARCIO ; DANDEKAR, ABHAYA M. . A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence. GENOMICS , v. 113, p. 2513-2525, 2021.

• CASARO, MATEUS B. ; THOMAS, ANDREW M. ; MENDES, EDUARDO ; FUKUMORI, CLAUDIO ; RIBEIRO, WILLIAN R. ; OLIVEIRA, FERNANDO A. ; CRISMA, AMANDA R. ; MURATA, GILSON M. ; BIZZARRO, BRUNA ; SÁ-NUNES, ANDERSON ; Setubal, Joao C. ; MAYER, MARCIA P. A. ; MARTINS, FLAVIANO S. ; VIEIRA, ANGÉLICA T. ; ANTIORIO, ANA T. F. B. ; TAVARES-DE-LIMA, WOTHAN ; CAMARA, NIELS O. S. ; CURI, RUI ; DIAS-NETO, Emmanuel ; FERREIRA, CAROLINE M. ; et.al . A probiotic has differential effects on allergic airway inflammation in A/J and C57BL/6 mice and is correlated with the gut microbiome. Microbiome , v. 9, p. 134, 2021.

• ROSSMANN, MAIKE ; THOMAS, ANDREW MALTEZ ; GUIMA, SUZANA SATO ; MARTINS, LAYLA FARAGE ; INDERBITZIN, PATRIK ; KNIGHT-CONNONI, VICTORIA ; DA SILVA, ALINE MARIA ; Setubal, João C. . Microbiomes of Field-Grown Maize and Soybean in Southeastern and Central Brazil Inferred by High-Throughput 16S and Internal Transcribed Spacer Amplicon Sequencing. Microbiology Resource Announcements , v. 10, p. 528, 2021.

• RANGEL, LUIZ THIBÉRIO ; SOUCY, SHANNON M ; Setubal, João C ; GOGARTEN, JOHANN PETER ; FOURNIER, GREGORY P . An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets. Genome Biology and Evolution , v. 13, p. evab187, 2021.

• BRAGA, LUCAS PALMA PEREZ ; PEREIRA, ROBERTA VERCIANO ; MARTINS, LAYLA FARAGE ; MOURA, LIVIA MARIA SILVA ; SANCHEZ, FABIO BELTRAME ; PATANÉ, JOSÉ SALVATORE LEISTER ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS . Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC GENOMICS , v. 22, p. 652, 2021.

• BRAGA, LUCAS P. P. ; COUTINHO, FELIPE H. ; AMGARTEN, DEYVID E. ; KOT, WITOLD ; HANSEN, LARS ; Setubal, João C. ; PHILIPPOT, LAURENT . Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis. Environmental Microbiology Reports , v. 13, p. 348-354, 2021.

• RODRIGUEZ CARNERO, LUIS ANTONIO ; REIS TEIXEIRA, ANDRÉ AZEVEDO ; FEN TANG, FENNY HUI ; KURAMOTO, ANDRÉIA ; MANSO ALVES, MARIA JÚLIA ; COLLI, WALTER ; SETUBAL, JOÃO CARLOS ; CUNHA-NETO, EDÉCIO ; Pasqualini, Renata ; Arap, Wadih ; GIORDANO, RICARDO JOSÉ . Protocol for design, construction, and selection of genome phage (gPhage) display libraries. STAR Protocols , v. 2, p. 100936, 2021.

• PRATA, ISADORA OLIVEIRA ; CUBILLOS, ELIANA FERNANDA GALINDO ; KRÜGER, ARNE ; BARBOSA, DEIBS ; MARTINS, JOAQUIM ; SETUBAL, JOÃO CARLOS ; WUNDERLICH, GERHARD . Plasmodium falciparum Acetyl-CoA Synthetase Is Essential for Parasite Intraerythrocytic Development and Chromatin Modification. ACS Infectious Diseases , v. 7, p. 3224-3240, 2021.

• LEMES, CAMILA G. C. ; VILLA, MORGHANA M. ; FELESTRINO, ÉRICA B. ; PERUCCI, LUIZA O. ; ASSIS, RENATA A. B. ; CORDEIRO, ISABELLA F. ; FONSECA, NATASHA P. ; GUERRA, LARA C. C. ; CANESCHI, WASHINGTON L. ; MORAES, LAURO Â. G. ; DO CARMO, FLÁVIO F. ; KAMINO, LUCIANA H. Y. ; VALE, PEDRO N. C. ; GUIMA, SUZANA E. S. ; Setubal, João C. ; SALGADO, ANDRÉ A. R. ; Moreira, Leandro M. . 16S rRNA Gene Amplicon Sequencing Data of the Iron Quadrangle Ferruginous Caves (Brazil) Shows the Importance of Conserving This Singular and Threatened Geosystem. DIVERSITY , v. 13, p. 494, 2021.

• SOARES, DOUGLAS M. M. ; ATUM, SAMIR V. F. ; BECHARA, ETELVINO J. H. ; Setubal, João C. ; STEVANI, CASSIUS V. ; FREIRE, RENATO S. . Exploring the Microbiota of the Guarapiranga Water Reservoir With Long-Read Sequencing Technology. FRONTIERS IN MARINE SCIENCE , v. 8, p. 791101, 2021.

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• MORAES, LAURO ÂNGELO GONÇALVES DE ; FELESTRINO, ÉRICA BARBOSA ; ASSIS, RENATA DE ALMEIDA BARBOSA ; MATOS, DIOGO ; LIMA, JOUBERT DE CASTRO ; LIMA, LEANDRO DE ARAÚJO ; ALMEIDA, NALVO FRANCO ; SETUBAL, JOÃO CARLOS ; GARCIA, CAMILA CARRIÃO MACHADO ; MOREIRA, LEANDRO MARCIO . TabPath: interactive tables for metabolic pathway analysis. BIOINFORMATICS , v. 34, p. 1040-1042, 2017.

• ASSIS, RENATA DE A. B. ; POLLONI, LORRAINE CRISTINA ; Patané, José S. L. ; THAKUR, SHALABH ; FELESTRINO, ÉRICA B. ; DIAZ-CABALLERO, JULIO ; DIGIAMPIETRI, LUCIANO ANTONIO ; GOULART, LUIZ RICARDO ; Almeida, Nalvo F. ; NASCIMENTO, RAFAEL ; DANDEKAR, ABHAYA M. ; ZAINI, PAULO A. ; Setubal, João C. ; Guttman, David S. ; MOREIRA, LEANDRO MARCIO . Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. Scientific Reports , v. 7, p. 16133, 2017.

• ROSSI, F ; GIRARDELLO, R ; MORAIS, C ; CURY, AP ; MARTINS, LF ; SILVA, AM ; ABDALA, E ; SETUBAL, JC ; DUARTE, AJ . Plasmid-mediated mcr-1 in carbapenem-susceptible Escherichia coli ST156 causing a blood infection: an unnoticeable spread of colistin resistance in Brazil?. Clinics , v. 72, p. 642-644, 2017.

• GUARISCHI-SOUSA, RODRIGO ; PUIGVERT, MARINA ; COLL, NÚRIA S. ; SIRI, MARÍA INÉS ; PIANZZOLA, MARÍA JULIA ; VALLS, MARC ; Setubal, João C. . Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031. Standards in Genomic Sciences , v. 11, p. 7, 2016.

• LIMA-JUNIOR, JAMES DALTRO ; VIANA-NIERO, CRISTINA ; CONDE OLIVEIRA, DANIEL V. ; MACHADO, GABRIEL ESQUITINI ; RABELLO, MICHELLE CRISTIANE DA SILVA ; MARTINS-JUNIOR, JOAQUIM ; MARTINS, LAYLA FARAGE ; DIGIAMPIETRI, LUCIANO ANTONIO ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS ; RUSSELL, DANIEL A. ; JACOBS-SERA, DEBORAH ; POPE, WELKIN H. ; HATFULL, GRAHAM F. ; LEÃO, SYLVIA CARDOSO . 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 (Online) , v. 16, p. 111, 2016.

• ANTUNES, LUCIANA PRINCIPAL ; MARTINS, LAYLA FARAGE ; PEREIRA, ROBERTA VERCIANO ; THOMAS, ANDREW MALTEZ ; BARBOSA, DEIBS ; LEMOS, LEANDRO NASCIMENTO ; SILVA, GIANLUCA MAJOR MACHADO ; MOURA, LIVIA MARIA SILVA ; EPAMINO, GEORGE WILLIAN CONDOMITTI ; DIGIAMPIETRI, LUCIANO ANTONIO ; LOMBARDI, KAREN CRISTINA ; RAMOS, PATRICIA LOCOSQUE ; QUAGGIO, RONALDO BENTO ; DE OLIVEIRA, JULIO CEZAR FRANCO ; PASCON, RENATA CASTIGLIONI ; CRUZ, JOÃO BATISTA DA ; DA SILVA, ALINE MARIA ; SETUBAL, JOÃO CARLOS . Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. Scientific Reports , v. 6, p. 38915, 2016.

• PAEZ-ESPINO, DAVID ; CHEN, I.-MIN A. ; PALANIAPPAN, KRISHNA ; RATNER, ANNA ; CHU, KEN ; SZETO, ERNEST ; PILLAY, MANOJ ; HUANG, JINGHUA ; MARKOWITZ, VICTOR M. ; NIELSEN, TORBEN ; HUNTEMANN, MARCEL ; K. REDDY, T. B. ; PAVLOPOULOS, GEORGIOS A. ; SULLIVAN, MATTHEW B. ; CAMPBELL, BARBARA J. ; CHEN, FENG ; MCMAHON, KATHERINE ; HALLAM, STEVE J. ; DENEF, VINCENT ; SETUBAL, J. C. ; et.al . IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Research (Online) , v. 45, p. D457-D465, 2016.

• ALMEIDA, DIEGO DANTAS ; KITAJIMA, JOÃO PAULO ; NISHIYAMA, MILTON YUTAKA ; CONDOMITTI, GEORGE WILLIAN ; OLIVEIRA, URSULA CASTRO DE ; SETÚBAL, JOÃO CARLOS ; JUNQUEIRA-DE-AZEVEDO, INÁCIO L. M. . The complete mitochondrial genome of Bothrops jararaca (Reptilia, Serpentes, Viperidae). Mitochondrial DNA Part B , v. 1, p. 907-908, 2016.

• Setubal, Joao C . Desconcertos na Ciência. Revista Brasileira de Psicanálise (Impresso) , v. 50, p. 145-152, 2016.

• THOMAS, ANDREW M. ; JESUS, ELIANE C. ; LOPES, ADEMAR ; AGUIAR, SAMUEL ; BEGNAMI, MARIA D. ; ROCHA, RAFAEL M. ; CARPINETTI, PAOLA AVELAR ; CAMARGO, ANAMARIA A. ; HOFFMANN, CHRISTIAN ; FREITAS, HELANO C. ; SILVA, ISRAEL T. ; Nunes, Diana N. ; Setubal, João C. ; DIAS-NETO, Emmanuel . Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling. Frontiers in Cellular and Infection Microbiology , v. 6, p. 00179, 2016.

• ZHANG, YUNZENG ; JALAN, NEHA ; ZHOU, XIAOFENG ; GOSS, ERICA ; Jones, Jeffrey B ; Setubal, João C ; DENG, XIAOLING ; WANG, NIAN . Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas. The ISME Journal (Print) , v. 15, p. 1-11, 2015.

• SCHWARTZ, ALLISON R. ; Potnis, Neha ; TIMILSINA, SUJAN ; WILSON, MARK ; PATANÉ, JOSÉ ; MARTINS, JOAQUIM ; MINSAVAGE, GERALD V. ; DAHLBECK, DOUGLAS ; AKHUNOVA, ALINA ; ALMEIDA, NALVO ; VALLAD, GARY E. ; BARAK, JERI D. ; WHITE, FRANK F. ; MILLER, SALLY A. ; RITCHIE, DAVID ; GOSS, ERICA ; BART, REBECCA S. ; Setubal, João C. ; Jones, Jeffrey B. ; STASKAWICZ, BRIAN J. ; 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 (Online) , v. 6, p. 535, 2015.

• Setubal, Joao C. ; ALMEIDA, NALVO . TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Print) , v. 12, p. 499-499, 2015.

• ANDERSON, LETÍCIA ; AMARAL, MURILO S. ; BECKEDORFF, FELIPE ; SILVA, LUCAS F. ; DAZZANI, BIANCA ; OLIVEIRA, KATIA C. ; ALMEIDA, GIULLIANA T. ; GOMES, MONETE R. ; PIRES, DAVID S. ; Setubal, João C. ; DeMarco, Ricardo ; VERJOVSKI-ALMEIDA, Sergio . Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq. PLoS Neglected Tropical Diseases (Online) , v. 9, p. e0004334, 2015.

• FERREIRA, ARI J. S. ; SIAM, RANIA ; Setubal, João C. ; MOUSTAFA, AHMED ; SAYED, AHMED ; CHAMBERGO, FELIPE S. ; DAWE, ADAM S. ; GHAZY, MOHAMED A. ; SHARAF, HAZEM ; OUF, AMGED ; ALAM, INTIKHAB ; ABDEL-HALEEM, ALYAA M. ; LEHVASLAIHO, HEIKKI ; RAMADAN, EMAN ; ANTUNES, ANDRÉ ; STINGL, ULRICH ; ARCHER, JOHN A. C. ; JANKOVIC, BORIS R. ; SOGIN, MITCHELL ; BAJIC, VLADIMIR B. ; et.al . Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses. Plos One , v. 9, p. e97338, 2014.

• TORTO-ALALIBO, TRUDY ; PURWANTINI, ENDANG ; LOMAX, JANE ; SETUBAL, JOãO C. ; MUKHOPADHYAY, BISWARUP ; TYLER, BRETT M. . Genetic resources for advanced biofuel production described with the Gene Ontology. Frontiers in Microbiology (Online) , v. 5, p. 5:528, 2014.

• PURWANTINI, ENDANG ; TORTO-ALALIBO, TRUDY ; LOMAX, JANE ; SETUBAL, JOãO C. ; TYLER, BRETT M. ; MUKHOPADHYAY, BISWARUP . Genetic resources for methane production from biomass described with the Gene Ontology. Frontiers in Microbiology (Online) , v. 5, p. 634, 2014.

• THOMAS, ANDREW ; GLEBER-NETTO, FREDERICO ; FERNANDES, GUSTAVO ; AMORIM, MARIA ; BARBOSA, LUISA ; FRANCISCO, ANA ; GUERRA DE ANDRADE, ARTHUR ; Setubal, João ; KOWALSKI, LUIZ ; NUNES, DIANA ; DIAS-NETO, Emmanuel . Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms. BMC Microbiology (Online) , v. 14, p. 250, 2014.

• RAJASEKARAN, PARTHIBAN ; ALEXANDER, JEFFRY C. ; SELEEM, MOHAMED N. ; JAIN, NEETA ; SRIRANGANATHAN, NAMMALWAR ; WATTAM, ALICE R. ; Setubal, João C. ; BOYLE, STEPHEN M. . Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages. International Journal of Antimicrobial Agents (Print) , v. 41, p. 500, 2013.

• MARTINS, L. F. ; ANTUNES, L. P. ; PASCON, R. ; OLIVEIRA, Julio Cezar de ; DIGIAMPIETRI, Luciano A. ; BARBOSA, D. ; PEIXOTO, B. M. ; VALLIM, M. A. ; VIANA-NIERO, C. ; Ostroski, Eric H ; TELLES, G. ; DIAS, Z. ; CRUZ, J. B. ; JULIANO NETO, L. ; VERJOVSKI-ALMEIDA, Sergio ; da Silva, Aline M ; Setubal, J.C. . Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms. Plos One , v. 8, p. e61928, 2013.

• JALAN, NEHA ; KUMAR, DIBYENDU ; ANDRADE, MAXUEL O ; YU, FAHONG ; Jones, Jeffrey B ; GRAHAM, JAMES H ; White, Frank F ; Setubal, João C ; WANG, NIAN . Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. BMC Genomics , v. 14, p. 551, 2013.

• WULFF, NELSON ARNO ; ZHANG, SHUJIAN ; Setubal, João C ; Almeida, Nalvo F ; MARTINS, ELAINE C ; Harakava, Ricardo ; KUMAR, DIBYENDU ; RANGEL, LUIZ T ; FOISSAC, XAVIER ; BOVE, JOSEPH ; GABRIEL, DEAN W . The complete genome sequence of Candidatus Liberibacter americanus, associated with citrus Huanglongbing.. Molecular Plant-Microbe Interactions , v. 27, p. 131107142521009, 2013.

• SAYED, A. ; GHAZY, M. A. ; Ferreira, A. J. S. ; SETUBAL, J. C. ; CHAMBERGO, F. S. ; OUF, A. ; ADEL, M. ; DAWE, A. S. ; ARCHER, J. A. C. ; BAJIC, V. B. ; 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 (Print) , v. 289, p. 1675-1687, 2013.

• PASCHOAL, A. R. ; MARACAJA-COUTINHO, V. ; Setubal, Joao C ; SIMOES, Z. L. P. ; VERJOVSKI-ALMEIDA, Sergio ; DURHAM, A. M. . Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA Biology , v. 9, p. 274-282, 2012.

• Dos Santos, Patricia C ; Fang, Zhong ; Mason, Steven W ; Setubal, João C ; Dixon, Ray . Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genomics , v. 13, p. 162, 2012.

• Dias, Zanoni ; Dias, Ulisses ; Setubal, Joao C . SIS: a program to generate draft genome sequence scaffolds for prokaryotes. BMC Bioinformatics , v. 13, p. 96, 2012.

• Wattam, A. R. ; INZANA, T. J. ; Williams, K. P. ; Mane, S. P. ; Shukla, M. ; Almeida, N. F. ; Dickerman, A. W. ; MASON, S. ; MORIYON, I. ; O'CALLAGHAN, D. ; WHATMORE, A. M. ; Sobral, B. W. ; Tiller, R. V. ; Hoffmaster, A. R. ; Frace, M. A. ; DE CASTRO, C. ; MOLINARO, A. ; Boyle, S. M. ; De, B. K. ; SETUBAL, J. C. ; et.al . Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway. MBIO , v. 3, p. e00246-12-e00246-12, 2012.

• WILSON, M. L. ; CAI, Y. ; HANLON, R. ; TAYLOR, S. ; CHEVREUX, B. ; SETUBAL, J. C. ; Tyler, B. M. ; PECCOUD, J. . Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic Acids Research (Online) , v. 41, p. e25-e25, 2012.

• SLATER, S. ; Setubal, Joao C ; HOUMIEL, K. ; SUN, J. ; KAUL, R. ; GOLDMAN, B. ; FARRAND, S. ; Almeida, Nalvo F ; BURR, T. ; NESTER, E. W. ; RHOADS, D. ; WELCH, R. ; WOOD, Derek W. . The Genome of Agrobacterium tumefaciens C58: Reconciliation of sequence data, updated annotation, and distribution of linear chromosome in genus Agrobacterium.. Applied and Environmental Microbiology (Print) , p. 1414-1417, 2012.

• Wibberg, Daniel ; Blom, Jochen ; Jaenicke, Sebastian ; Kollin, Florian ; Rupp, Oliver ; Scharf, Birgit ; Schneiker-Bekel, Susanne ; Sczcepanowski, Rafael ; Goesmann, Alexander ; Setubal, Joao Carlos ; Schmitt, Rüdiger ; Pühler, Alfred ; Schlüter, Andreas . 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 , v. 155, p. 50-62, 2011.

• Potnis, Neha ; Krasileva, Ksenia ; Chow, Virginia ; Almeida, Nalvo F ; Patil, Prabhu B ; Ryan, Robert P ; Sharlach, Molly ; Behlau, Franklin ; Dow, J Max ; Momol, MT ; White, Frank F ; Preston, James F ; Vinatzer, Boris A ; Koebnik, Ralf ; Setubal, João C ; Norman, David J ; Staskawicz, Brian J ; Jones, Jeffrey B . Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics , v. 12, p. 146, 2011.

• Zhang, Hongtao ; Setubal, Joao Carlos ; Zhan, Xiaobei ; Zheng, Zhiyong ; Yu, Lijun ; Wu, Jianrong ; Chen, Dingqiang . 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 , v. 38, p. 667-677, 2011.

• COLLEN, J. ; COLLEN, P. N. ; REIS, Marcelo da Silva ; PEDERSEN, M. ; SETUBAL, J. C. ; Varani, A. ; Colepicolo, P. ; OLIVEIRA, Mariana Cabral de . Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta). Journal of Applied Phycology , v. 24, p. 641-647, 2011.

• Cai, Rongman ; Lewis, James ; Yan, Shuangchun ; Liu, Haijie ; Clarke, Christopher R. ; Campanile, Francesco ; Almeida, Nalvo F. ; Studholme, David J. ; Lindeberg, Magdalen ; Schneider, David ; Zaccardelli, Massimo ; Setubal, Joao C. ; Morales-Lizcano, Nadia P. ; Bernal, Adriana ; Coaker, Gitta ; Baker, Christy ; Bender, Carol L. ; Leman, Scotland ; Vinatzer, Boris A. . The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity. PLoS Pathogens , v. 7, p. e1002130, 2011.

• Hamilton, T. L. ; LUDWIG, M. ; DIXON, R. ; Boyd, E. S. ; dos SANTOS, P. C. ; SETUBAL, J. C. ; BRYANT, D. A. ; Dean, D. R. ; PETERS, J. W. . Transcriptional Profiling of Nitrogen Fixation in Azotobacter vinelandii. Journal of Bacteriology (Print) , v. 193, p. 4477-4486, 2011.

• Staquicini, F. I. ; Cardo-Vila, M. ; Kolonin, M. G. ; Trepel, M. ; Edwards, J. K. ; Nunes, D. N. ; Sergeeva, A. ; Efstathiou, E. ; Sun, J. ; Almeida, N. F. ; Tu, S.-M. ; Botz, G. H. ; Wallace, M. J. ; O'Connell, D. J. ; Krajewski, S. ; Gershenwald, J. E. ; Molldrem, J. J. ; Flamm, A. L. ; Koivunen, E. ; SETUBAL, J. C. ; 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 , v. 108, p. 1-6, 2011.

• Jalan, N. ; Aritua, V. ; Kumar, D. ; Yu, F. ; Jones, J. B. ; Graham, J. H. ; SETUBAL, J. C. ; 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 (Print) , v. 193, p. 6342-6357, 2011.

• Moreira, Leandro M ; Almeida, Nalvo F ; Potnis, Neha ; Digiampietri, Luciano A ; Adi, Said S ; Bortolossi, Julio C ; da Silva, Ana C ; da Silva, Aline M ; de Moraes, Fabricio E ; de Oliveira, Julio C ; de Souza, Robson F ; Fancincani, Agda P ; Ferraz, Andre L ; Ferro, Maria I ; Furlan, Luiz R ; Gimenez, Daniele F ; Jones, Jeffrey B ; Kitajima, Elliot W ; Laia, Marcelo L ; SETUBAL, J. C. ; 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 , v. 11, p. 238, 2010.

• Warren, Andrew S ; Archuleta, Jeremy ; Feng, Wu-chun ; Setubal, Joao Carlos . Missing genes in the annotation of prokaryotic genomes. BMC BIOINFORMATICS , v. 11, p. 131, 2010.

• Almeida, Nalvo F. ; Yan, Shuangchun ; Cai, Rongman ; Clarke, Christopher R. ; Morris, Cindy E. ; Schaad, Norman W. ; Schuenzel, Erin L. ; Lacy, George H. ; Sun, Xiaoan ; Jones, Jeffrey B. ; Castillo, Jose A. ; Bull, Carolee T. ; Leman, Scotland ; Guttman, David S. ; Setubal, João C. ; Vinatzer, Boris A. . PAMDB, A Multilocus Sequence Typing and Analysis Database and Website for Plant-Associated Microbes. Phytopathology , v. 100, p. 208-215, 2010.

• BALAJI, P. ; FENG, W. ; LIN, H. ; ARCHULETA, J. ; MATSUOKA, S. ; Warren, A. ; Setubal, J. ; Lusk, Ewing ; Thakur, R. ; Foster, I. ; Katz, D. S. ; Jha, S. ; Shinpaugh, K. ; Coghlan, S. ; Reed, D. . Global-scale distributed I/O with ParaMEDIC. Concurrency and Computation , v. 22, p. 2266-2281, 2010.

• Tiller, R. V. ; Gee, J. E. ; Frace, M. A. ; Taylor, T. K. ; SETUBAL, J. C. ; Hoffmaster, A. R. ; De, B. K. . Characterization of novel Brucella strains originating from wild native rodent species in North Queensland, Australia. Applied and Environmental Microbiology (Print) , v. 76, p. 5837-5845, 2010.

• TORTO-ALALIBO, T. ; Collmer, C. W. ; GWINN-GIGLIO, M. ; Lindeberg, M. ; Meng, S. ; Chibucos, M. C. ; Tseng, T.-T. ; Lomax, J. ; Biehl, B. ; Ireland, A. ; Bird, D. ; Dean, R. A. ; Glasner, J. D. ; PERNA, N. ; SETUBAL, J. C. ; COLLMER, A. ; Tyler, B. M. . Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology. Microbiology and Molecular Biology Reviews , v. 74, p. 479-503, 2010.

• Shulaev, Vladimir ; Sargent, Daniel J ; Crowhurst, Ross N ; Mockler, Todd C ; Folkerts, Otto ; Delcher, Arthur L ; Jaiswal, Pankaj ; Mockaitis, Keithanne ; Liston, Aaron ; Mane, Shrinivasrao P ; Burns, Paul ; Davis, Thomas M ; Slovin, Janet P ; Bassil, Nahla ; Hellens, Roger P ; Evans, Clive ; Harkins, Tim ; Kodira, Chinnappa ; Desany, Brian ; SETUBAL, J. C. ; et.al . The genome of woodland strawberry (Fragaria vesca). Nature Genetics (Print) , v. 43, p. 109-116, 2010.

• DIAS-NETO, Emmanuel ; Nunes, Diana N. ; Giordano, Ricardo J. ; Sun, Jessica ; Botz, Gregory H. ; Yang, Kuan ; Setubal, João C. ; Pasqualini, Renata ; Arap, Wadih ; HO, Paulo Lee . Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis. Plos One , v. 4, p. e8338, 2009.

• Chibucos, Marcus C. ; Tseng, Tsai-Tien ; Setubal, João C. . Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology , v. 17, p. 312-319, 2009.

• SETUBAL, J. C. ; dos Santos, P. ; Goldman, B. S. ; Ertesvag, H. ; Espin, G. ; Rubio, L. M. ; Valla, S. ; Almeida, N. F. ; Balasubramanian, D. ; Cromes, L. ; Curatti, L. ; Du, Z. ; Godsy, E. ; GOODNER, B. ; Hellner-Burris, K. ; Hernandez, J. A. ; Houmiel, K. ; Imperial, J. ; Kennedy, C. ; Larson, T. J. ; et.al . Genome Sequence of Azotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes. Journal of Bacteriology (Print) , v. 191, p. 4534-4545, 2009.

• Wattam, A. R. ; Williams, K. P. ; Snyder, E. E. ; Almeida, N. F. ; Shukla, M. ; Dickerman, A. W. ; Crasta, O. R. ; Kenyon, R. ; Lu, J. ; Shallom, J. M. ; Yoo, H. ; Ficht, T. A. ; Tsolis, R. M. ; Munk, C. ; Tapia, R. ; Han, C. S. ; Detter, J. C. ; Bruce, D. ; Brettin, T. S. ; SETUBAL, J. C. ; et.al . Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle. Journal of Bacteriology (Print) , v. 191, p. 3569-3579, 2009.

• Slater, S. C. ; Goldman, B. S. ; GOODNER, B. ; SETUBAL, J. C. ; Farrand, S. K. ; NESTER, E. W. ; Burr, T. J. ; Banta, L. ; Dickerman, A. W. ; Paulsen, I. ; OTTEN, L. ; Suen, G. ; Welch, R. ; Almeida, N. F. ; Arnold, F. ; Burton, O. T. ; Du, Z. ; Ewing, A. ; Godsy, E. ; Heisel, S. ; et.al . Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria. Journal of Bacteriology (Print) , v. 191, p. 2501-2511, 2009.

• Tseng, Tsai-Tien ; Tyler, Brett M ; Setubal, João C . Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiology (Online) , v. 9, p. S2, 2009.

• Warren, Andrew S ; Setubal, João . The Genome Reverse Compiler: an explorative annotation tool. BMC Bioinformatics , v. 10, p. 35, 2009.

• Gillespie, Joseph J. ; Ammerman, Nicole C. ; Dreher-Lesnick, Sheila M. ; Rahman, M. Sayeedur ; Worley, Micah J. ; Setubal, Joao C. ; Sobral, Bruno S. ; Azad, Abdu F. . An Anomalous Type IV Secretion System in Rickettsia Is Evolutionarily Conserved. Plos One , v. 4, p. e4833, 2009.

• Almeida, Nalvo F. ; Yan, Shuangchun ; Lindeberg, Magdalen ; Studholme, David J. ; Schneider, David J. ; Condon, Bradford ; Liu, Haijie ; Viana, Carlos J. ; Warren, Andrew ; Evans, Clive ; Kemen, Eric ; MacLean, Dan ; Angot, Aurelie ; Martin, Gregory B. ; Jones, Jonathan D. ; Collmer, Alan ; Setubal, Joao C. ; Vinatzer, Boris A. . 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 , v. 22, p. 52-62, 2009.

• Gillespie, Joseph J. ; Williams, Kelly ; Shukla, Maulik ; Snyder, Eric E. ; Nordberg, Eric K. ; Ceraul, Shane M. ; Dharmanolla, Chitti ; Rainey, Daphne ; Soneja, Jeetendra ; Shallom, Joshua M. ; Vishnubhat, Nataraj Dongre ; Wattam, Rebecca ; Purkayastha, Anjan ; Czar, Michael ; Crasta, Oswald ; SETUBAL, J. C. ; Azad, Abdu F. ; Sobral, Bruno S. . Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life. Plos One , v. 3, p. e2018, 2008.

• Yan, S. ; Liu, H. ; Mohr, T. J. ; Jenrette, J. ; Chiodini, R. ; Zaccardelli, M. ; SETUBAL, J. C. ; Vinatzer, B. A. . 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 , v. 74, p. 3171-3181, 2008.

• Venancio, Thiago M ; DeMarco, Ricardo ; Almeida, Giulliana T ; Oliveira, Katia C ; Setubal, João C ; VERJOVSKI-ALMEIDA, Sergio . Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions. BMC Genomics , v. 8, p. 407, 2007.

• Yu, G.X. ; Snyder, E.E. ; Boyle, S.M. ; Crasta, O.R. ; Czar, M. ; Mane, S.P. ; Purkayastha, A. ; Sobral, B. ; Setubal, J.C. . A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. Nucleic Acids Research , v. 35, p. 3953-3962, 2007.

• Snyder, E. E. ; Kampanya, N. ; Lu, J. ; Nordberg, E. K. ; Karur, H. R. ; Shukla, M. ; Soneja, J. ; Tian, Y. ; Xue, T. ; Yoo, H. ; Zhang, F. ; Dharmanolla, C. ; Dongre, N. V. ; Gillespie, J. J. ; Hamelius, J. ; Hance, M. ; Huntington, K. I. ; Jukneliene, D. ; Koziski, J. ; SETUBAL, J. C. ; et.al . PATRIC: The VBI PathoSystems Resource Integration Center. Nucleic Acids Research , v. 35, p. D401-D406, 2007.

• LORENZINI, D ; SILVAJR, P ; SOARES, M ; ARRUDA, P ; SETUBAL, J ; DAFFRE, S . Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana. Developmental and Comparative Immunology , v. 30, p. 545-556, 2006.

• SETUBAL, J. C. . Lipoprotein computational prediction in spirochaetal genomes. Microbiology (Reading) , v. 152, p. 113-121, 2006.

• SETUBAL, J ; MOREIRA, L ; DASILVA, A . Bacterial phytopathogens and genome science. Current Opinion in Microbiology , v. 8, p. 595-600, 2005.

• Moreira, Leandro M. ; De Souza, Robson F. ; DIGIAMPIETRI, Luciano A. ; Da Silva, Ana C.R. ; Setubal, Joao C. . Comparative Analyses of Xanthomonas and Xylella Complete Genomes. Journal of Integrative Biology / Omics (Larchmont) , v. 9, p. 43-76, 2005.

• HANCE, M. E. ; Czar, M. J. ; Azad, Abdu F. ; Purkayastha, A. ; Snyder, Eric E. ; Crasta, O. R. ; SETUBAL, J. C. ; Sobral, B. W. . The Pathogen Resource Integration Center: Implications for Rickettsial Research. Annals of the New York Academy of Sciences , v. 1063, p. 459-465, 2005.

• SETUBAL, J. C. ; SILVA, Ana Claudia Rasera da ; ALMEIDA JR, Nalvo Franco de ; FERRO, Jesus ; FURLAN, Luiz Roberto ; MOREIRA, Leandro ; SOUZA, Robson de ; OLIVEIRA, Julio Cezar de . COMPARATIVE GENOMICS ANALYSES OF CITRUS-ASSOCIATED BACTERIA. Annual Review of Phytopathology (Print) , Estados Unidos, v. 42, p. 163-184, 2004.

• SETUBAL, J. C. ; NASCIMENTO, Ana Lucia Tabet ; VERJOVSKI-ALMEIDA, Sergio ; SLUYS, Marie Anne Van ; MONTEIRO-VITORELLO, Claudia B. ; CAMARGO, Luis Eduardo Aranha ; DIGIAMPIETRI, Luciano A. ; HARTSKEERL, Rudy ; HO, Paulo Lee ; MARQUES, Marilis ; OLIVEIRA, Mariana Cabral de ; HAAKE, David ; MARTINS, Elizabeth . Genome features of Leptospira interrogans serovar Copenhageni. Brazilian Journal of Medical and Biological Research , v. 37, n.2, p. 459-477, 2004.

• Nascimento, A. L. T. O. ; Setubal, J.C. . Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis. Journal of Bacteriology , estados unidos, v. 186, n.7, p. 2164-2172, 2004.

• DeMarco, R. ; Setubal, J.C. . Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni. Journal of Virology , estados unidos, v. 78, n.6, p. 2967-2978, 2004.

• MONTEIRO-VITORELLO, Claudia B. ; Camargo, Luis E. A. ; Van Sluys, Marie A. ; Kitajima, João P. ; Truffi, Daniela ; do Amaral, Alexandre M. ; Harakava, Ricardo ; de Oliveira, Julio C. F. ; Wood, Derek ; de Oliveira, Mariana C. ; Miyaki, Cristina ; Takita, Marco A. ; da Silva, Ana C. R. ; Furlan, Luis R. ; Carraro, Dirce M. ; Camarotte, Giovana ; Almeida, Nalvo F. ; Carrer, Helaine ; Coutinho, Luiz L. ; SETUBAL, J. C. ; et.al . The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli. Molecular Plant-Microbe Interactions , v. 17, p. 827-836, 2004.

• Van Sluys, M. A. ; Setubal, J.C. . Comparative Analyses of the Complete Genome Sequences of Pierce's Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa. Journal of Bacteriology , EUA, v. 185, n.3, p. 1018-1026, 2003.

• VERJOVSKI-ALMEIDA, Sergio ; DeMarco, Ricardo ; Martins, Elizabeth A L ; Guimarães, Pedro E M ; Ojopi, Elida P B ; Paquola, Apuã C M ; Piazza, João P ; Nishiyama, Milton Y ; Kitajima, João P ; Adamson, Rachel E ; Ashton, Peter D ; Bonaldo, Maria F ; Coulson, Patricia S ; Dillon, Gary P ; Farias, Leonardo P ; Gregorio, Sheila P ; Ho, Paulo L ; Leite, Ricardo A ; Malaquias, L Cosme C ; SETUBAL, J. C. ; et.al . Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genetics , Reino Unido, v. 35, p. 148-157, 2003.

• Digiampietri, Luciano A ; MEDEIROS, Claudia Maria Bauzer ; Setubal, João C. . A data model for comparative genomics. Revista Tecnologia da Informação , v. 3, p. 35-40, 2003.

• PIAZZA, J. P. ; Setubal, João C . New ways for automatic detection of contaminants in EST projects. Revista Tecnologia da Informação , v. 3, p. 36-41, 2003.

• da Silva, A. C. R. ; Ferro, J. A. ; Reinach, F. C. ; Farah, C. S. ; Furlan, L. R. ; Quaggio, R. B. ; Monteiro-Vitorello, C. B. ; Sluys, M. A. Van ; Almeida, N. F. ; Alves, L. M. C. ; do Amaral, A. M. ; Bertolini, M. C. ; Camargo, L. E. A. ; Camarotte, G. ; Cannavan, F. ; Cardozo, J. ; Chambergo, F. ; Ciapina, L. P. ; Cicarelli, R. M. B. ; SETUBAL, J. C. ; et.al . Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature (London) , Londres, v. 417, p. 459-463, 2002.

• SETUBAL, J. C. ; SILVA, Ana Claudia Rasera da ; SIMPSON, A. J. G. ; KITAJIMA, Joao Paulo ; FERRO, Jesus ; SLUYS, Marie Anne Van ; MONTEIRO-VITORELLO, Claudia B. ; CAMARGO, Luis Eduardo Aranha ; MENCK, Carlos F. M. ; OLIVEIRA, Mariana Cabral de . C OMPARATIVE G ENOMIC A NALYSIS OF P LANT -A SSOCIATED B ACTERIA . Annual Review of Phytopathology (Print) , EUA, v. 40, p. 169-189, 2002.

• WERNECK, R. ; SETUBAL, J. C. . Finding minimum congestion spanning trees. ACM Journal of Experimental Algorithmics , v. 6, p. 1-20, 2001.

• Wood, D. W. ; Setubal, J.C. . The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58. Science , USA, v. 294, p. 2317-2323, 2001.

• SETUBAL, J. C. ; SIMPSON, A. J. G. ; REINACH, F. ; ARRUDA, P. ; KITAJIMA, Joao Paulo ; Van Sluys, Marie A. ; VERJOVSKI-ALMEIDA, Sergio ; ZAGO, M. ; ZATZ, M. ; MEIDANIS, J. . The genome sequence of the plant pathogen Xylella fastidiosa.. Nature (London) , Londres, v. 406, p. 151-157, 2000.

• CHERKASSKY, B. ; GOLDBERG, A. ; MARTIN, P. ; SETUBAL, J. C. ; STOLFI, J. . Augment Or Push? A Computational Study Of Bipartite Matching And Unit Capacity Maximum Flow Algorithms. ACM Journal of Experimental Algorithmics, EUA, v. 3, n.8, p. 1-40, 1998.

• ANDERSON, R. ; SETUBAL, J. C. . A Parallel Implementation Of The Push-Relabel Algorithm For The Maximum Flow Problem. Journal of Parallel and Distributed Computing, EUA, v. 29, n.1, p. 17-26, 1995.

• Setubal, Joao Carlos ; Stadler, Peter F. (Org.) ; Stoye, Jens (Org.) . Comparative Genomics. 1. ed. New York: Humana Press, 2024. 600p .

• Setubal, João C. ; Stoye, Jens (Org.) ; Stadler, Peter F. (Org.) . Comparative Genomics. 1. ed. New York: Springer, 2018. v. 1. 481p .

• Setubal, João C. ; ALMEIDA JR, N. F. (Org.) . Advances in Bioinformatics and Computational Biology 8th Brazilian Symposium on Bioinformatics, BSB 2013. 1. ed. Springer, 2013. v. 1. 215p .

• Setubal, J.C. ; VERJOVSKI-ALMEIDA, Sergio (Org.) . Brazilian Symposium on Bioinformatics, BSB2005. Berlim: Springer, 2005. 258p .

• SETUBAL, J. C. ; MEIDANIS, J. . Introduction To Computational Molecular Biology. Boston, Mass. EUA: PWS Publishing Company, 1997. 296p .

• MEIDANIS, J. ; SETUBAL, J. C. . Uma Introducao A Biologia Computacional. RECIFE: IX ESCOLA DE COMPUTACAO, 1994. 132p .

• SANCHEZ, FABIO BELTRAME ; Sato Guima, Suzana Eiko ; SETUBAL, JOÃO CARLOS . How to Obtain and Compare Metagenome-Assembled Genomes. Methods in Molecular Biology. 1ed.: Springer US, 2024, v. 2802, p. 135-163.

• Carhuaricra-Huaman, Dennis ; SETUBAL, JOÃO CARLOS . Step-by-Step Bacterial Genome Comparison. Methods in Molecular Biology. 1ed.: Springer US, 2024, v. 2801, p. 107-134.

• Carhuaricra-Huaman, Dennis ; SETUBAL, JOÃO CARLOS . Protein-Coding Gene Families in Prokaryote Genome Comparisons. Methods in Molecular Biology. 1ed.: Springer US, 2024, v. 2802, p. 33-55.

• ROSSI, FERNANDO PACHECO NOBRE ; Flores, Vinicius Sousa ; UCEDA-CAMPOS, GUILLERMO ; Amgarten, Deyvid Emanuel ; SETUBAL, JOÃO CARLOS ; DA SILVA, ALINE MARIA . Comparative Analyses of Bacteriophage Genomes. Methods in Molecular Biology. 1ed.: Springer US, 2024, v. 2802, p. 427-453.

• Patané, José S. L. ; MARTINS, JOAQUIM ; SETUBAL, JOÃO CARLOS . A Guide to Phylogenomic Inference. Methods in Molecular Biology. 1ed.: Springer US, 2024, v. 2802, p. 267-345.

• Patané, José S. L. ; MARTINS, JOAQUIM ; Setubal, João C. . Phylogenomics. Methods in Molecular Biology. 1ed.: Springer New York, 2018, v. , p. 103-187.

• Setubal, João C. ; Almeida, Nalvo F. ; WATTAM, ALICE R. . Comparative Genomics for Prokaryotes. Methods in Molecular Biology. 1ed.: Springer New York, 2018, v. , p. 55-78.

• Setubal, João C. ; Stadler, Peter F. . Gene Phylogenies and Orthologous Groups. Methods in Molecular Biology. 1ed.: Springer New York, 2018, v. , p. 1-28.

• Maltez Thomas, Andrew ; Prata Lima, Felipe ; Maria Silva Moura, Livia ; Maria da Silva, Aline ; DIAS-NETO, Emmanuel ; Setubal, João C. . Comparative Metagenomics. Methods in Molecular Biology. 1ed.: Springer New York, 2018, v. , p. 243-260.

• DURHAM, A. ; Setubal, João C ; BARRERA, J. . Intersdisciplinaridade em ação na pesquisa e pós-graduação em bioinformática. In: Arlindo Philippi Jr; Valdir Fernandes. (Org.). Práticas da interdisciplinaridade no ensino e na pesquisa. 1aed.Barueri: Manole, 2015, v. , p. 619-642.

• Potnis, Neha ; Setubal, João C ; BART, R. ; SHANTARAJ, D. ; Jones, Jeffrey B . High-throughput DNA sequencing technology as a tool in understanding plant-pathogenic bacteria. In: Nian Wang; Jeffrey Jones; George Sundin; Frank White; Saskia Hougenhout; Caroline Roper; Leonardo de la Fuente; Jong Hyun Ham. (Org.). Virulence mechanisms of plant-pathogenic bacteria. 1aed.Saint Paul: APS Press, 2015, v. , p. 183-196.

• Setubal, João C. ; ALMEIDA JR, N. F. . The Azotobacter vinelandii genome: an update. In: Frans de Bruijn. (Org.). Biological Nitrogen Fixation. 1aed.Londres: Wiley-Blackwell, 2015, v. 1, p. 225-234.

• SALDANHA, H. ; RIBEIRO, E. ; BORGES, C. ; ARAUJO, A. ; GALLON, R. ; HOLANDA, M. ; WALTER, M. E. ; TOGAWA, R. ; Setubal, J.C. . Towards a hybrid federated cloud platform to efficiently execute bioinformatics workflows. Bioinformatics. Rijeka: InTech, 2012, v. , p. 1-25.

• Setubal, J.C. ; Wood, Derek ; BURR, T. ; FARRAND, S. ; GOLDMAN, B. ; GOODNER, B. ; OTTEN, L. ; SLATER, S. . The Genomics of Agrobacterium: Insights into Pathogenicity, Biocontrol, and Evolution. In: R. Jackson. (Org.). Plant Pathogenic Bacteria: Genomics and Molecular Biology. London: Caister Academic Press, 2008, v. , p. -.

• Setubal, J.C. . Similarity Search (theory). In: A. Gruber; A. M. Durham; C. Huynhtop; and H. del Portillo. (Org.). Bioinformatics in Tropical Disease Research: A Practical and Case-Study Approach. Bethesda, MD: National Library of Medicine, 2008, v. , p. -.

• SLATER, S. ; GOODNER, B. ; Setubal, J.C. ; GOLDMAN, B. ; Wood, Derek ; NESTER, E. W. . The Agrobacterium tumefaciens C58 genome. In: T. Tzfira and V. Citovsky. (Org.). Agrobacterium. New York: Springer, 2008, v. , p. -.

• Purkayastha, A. ; Crasta, Oswald R ; Eckart, J. D. ; Czar, M. J. ; Meng, X. J. ; Setubal, Joao C. ; Sobral, B. W. . Bioinformatics resources for the study of viruses at the Virginia Bioinformatics Institute. In: R. Holland Cheng; Tatsuo Miyamura. (Org.). Structure-based Study of Virus Replication. Stockholm: World Scientific Publishing Company, 2008, v. , p. 267-288.

• SETUBAL, J. C. ; SILVA, Ana Claudia Rasera da . Genomic approaches to the study of plant pathogenic bacteria. In: R. Goodman. (Org.). Encyclopedia of Plant and Crop Sciences. : Marcel Dekker, 2004, v. , p. 524-526.

• SETUBAL, J. C. ; WOOD, Derek W. ; NESTER, E. W. . Genome sequence analysis of prokaryotic plant pathogens. In: M. Gillings, A. Holmes. (Org.). Plant Microbiology. Oxford: BIOS Scientific Publishers, 2004, v. , p. 223-241.

• SETUBAL, J. C. . Bioinformática. In: Luis Mir. (Org.). Genômica. : Editora Atheneu, 2004, v. , p. 105-118.

• ANDERSON, R. ; SETUBAL, J. C. . Goldberg's Algorithm For Maximum Flow In Perspective: A Computational Study. In: D. S. Johnson; C. McGeoch. (Org.). FIRST DIMACS IMPLEMENTATION CHALLENGE -- NETWORK FLOWS AND MATCHING. EUA: AMERICAN MATHEMATICAL SOCIETY, 1993, v. , p. 1-18.

• SETUBAL, J. C. . A origem e o sentido da Bioinformatica. ComCiencia, Campinas, SP, 10 ago. 2003.

• SETUBAL, J. C. . Ciencia Genetica e acao digital (A helice dupla e o computador). Pesquisa FAPESP encarte especial, Sao Paulo, p. 37 - 37, 01 maio 2003.

• DIAS, Z. ; DIAS, U. M. ; HEATH, L. ; SETUBAL, J. C. . Sorting Genomes Using Almost-Symmetric Inversions. In: 27th ACM Symposium on Applied Computing, 2012, Riva del Garda. Proceedings of the 27th ACM Symposium on Applied Computing, 2012.

• Warren, A. ; Setubal, Joao C . Using Entropy Estimates for DAG-Based Ontologies. In: 15th Bio-Ontologies Special Interest Group Meeting of ISMB 2012, 2012, Los Angeles. Proceedings of 15th Bio-Ontologies Special Interest Group Meeting of ISMB 2012, 2012. v. 1. p. 1-6.

• DIAS, Z. ; DIAS, U. M. ; Setubal, Joao C. . Using inversion signatures to generate draft genome sequence scaffolds. In: ACM Interantional Conference on Bioinformatics, Computational Biology and Biomedicine, 2011, Chicago. Proceedings of ACM-BCB 2011, 2011.

• DIAS, U. M. ; DIAS, Z. ; Setubal, Joao C . A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes. In: RECOMB - Comparative Genomics, 2010, Ottawa, Canada. Proceedings of RECOMB-CG 2010, 2010. p. 1-10.

• YANG, K. ; Setubal, Joao C . Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes. In: ACM International Conference on Bioinformatics and Computational Biology 2010, 2010, Niagara Falls, USA. Proceedings of ACM-BCB 2010, 2010.

• MYERS, E. ; FISHER, P. S. ; IRWIN, K. ; Baek, J. ; Setubal, Joao C . The Complexity and Application of Syntactic Pattern Recognition Using Finite Inductive Strings. In: Pattern Recognition in Bioinformatics 2010, 2010, Nijmegen. Proceedings of Pattern Recognition in Bioinformatics 2010, 2010.

• BALAJI, P. ; FENG, W. ; LIN, H. ; ARCHULETA, J. ; MATSUOKA, S. ; Warren, A. ; Setubal, J.C. . Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer. In: International Supercomputing Conference, 2008, Heidelberg. Proceedings of the International Supercomputing Conference, 2008.

• DIGIAMPIETRI, Luciano A. ; MEDEIROS, Claudia Maria Bauzer ; Setubal, J.C. ; BARGA, R. . Traceability Mechanisms for Bioinformatics Scientific Workflows. In: Workshop on Semantic e-Science, AAAI, 2007, Vancouver. Proceedings of the Workshop on Semantic e-Science, AAAI, 2007.

• SETUBAL, J. C. ; MEDEIROS, Claudia Maria Bauzer ; DIGIAMPIETRI, Luciano A. . A framewok based on Web services orchestration for bioinformatics workflow management. In: III Brazilian Workshop on Bioinformatics, 2004, Brasilia, 2004.

• DIGIAMPIETRI, Luciano A. ; MEDEIROS, Claudia Maria Bauzer ; SETUBAL, J. C. . A data model for comparative genomics. In: II Brazilian Workshop on Bioinformatics, 2003, Macaé. Anais do II WOB, 2003.

• PIAZZA, J. P. ; SETUBAL, J. C. . New Ways for automatic detection of contaminants in EST projects. In: II Brazilian Workshop on Bioinformatics, 2003, Macaé. Anais do II WOB, 2003.

• SETUBAL, J. C. . Uma proposta de plano pedagógico para a matéria Computação e Algoritmos. In: Workshop de Educacao em Informatica - Curso de Qualidade, 2000, Curitiba, PR. Anais do WEI - Curso de Qualidade, 2000. p. 1-20.

• WERNECK, R. ; SETUBAL, J. C. ; CONCEICAO, A. . Finding Minimum Congestion Spanning Trees. In: Third Workshop on Algorithm Engineering, 1999, Londres. Lecture Notes in Computer Science. Frankfurt: Springer-Verlag, 1999. v. 1668. p. 60-71.

• CHERKASSKY, B. ; GOLDBERG, A. V. ; MARTIN, P. ; SETUBAL, J. C. ; STOLFI, J. . Augment Or Push? A Computational Study Of Bipartite Matching And Unit Capacity Maximum Flow Algorithms. In: Workshop on Algorithm Engineering, 1997, Veneza. Anais. Veneza, Italia, 1997. p. 1-12.

• MEIDANIS, J. ; SETUBAL, J. C. . Multiple Alignment Of DNA Sequences With Gap Flexibility. In: Latin American Theoretical Informatics, 1995, Valparaiso. Lecture Notes in Computer Science. Alemanha: Springer-Verlag, 1995. v. 911. p. 411-426.

• CRUZ, C. F. B. ; SETUBAL, J. C. . Uma Adaptacao do Algoritmo de Edmonds Para Execucao Em Paralelo. In: II Oficina Nacional de Problemas Combinatorios, 1995, Campinas. Anais. Campinas, SP, 1995. p. 39-49.

• ANDERSON, R. ; SETUBAL, J. C. . On The Parallel Implementation of Goldberg's Maximum Flow Algorithm. In: Symposium on Parallel Algorithms and Architectures, 1992. Proceedings of the Symposium on Parallel Algorithms and Architectures. San Diego, EUA. p. 168-177.

• SETUBAL, J. C. ; KOWALTOWSKI, T. . Fig, Uma Linguagem Para Especificacao de Figuras. In: XV Seminario integrado de software e hardware, 1988. Anais. Salvador, BA. p. 67-77.

• Baker, S. C. ; Jukneliene, D. ; Purkayastha, Anjan ; Snyder, E. E. ; Crasta, O. R. ; Czar, M. J. ; Setubal, Joao C ; Sobral, B. W. . Developing bioinformatic resources for coronaviruses. In: Toward Control of SARS and other Nidovirus Diseases, 2006, Colorado Springs. Proceedings of the Xth Nidovirus Symposium, 2005. v. 581. p. 395-398.

• SETUBAL, J. C. ; PEREZ, Marcelo ; CARRIÃO, Patricia Farah . Parsing BLAST results to find pseudogenes in bacterial genomes. In: III Brazilian Workshop on Bioinformatics, 2004, Brasilia, 2004.

• SETUBAL, J. C. ; ALMEIDA JR., Nalvo Franco de ; VIANA, Carlos ; CARVALHO, Marcelo de . A method to determine homologous protein families based on graph cliques and profiles. In: III Brazilian Workshop on Bioinformatics, 2004, Brasilia, 2004.

• SETUBAL, J. C. ; PEREZ, Marcelo ; CARRIÃO, Patricia Farah . A relational database for COG data. In: II Brazilian Workshop on Bioinformatics, 2003, Macaé. Anais do II WOB, 2003.

• SETUBAL, J. C. ; ALMEIDA JR, Nalvo Franco de . Detection of related genes in prokaryotes using syntenic regions. In: DIMACS Workshop on whole genome comparison, 2001, Rutgers University, New Jersey. Abstracts of the DIMACS Workshop on whole genome comparison, 2001. p. 15-17.

• WOOD, Derek W. ; SETUBAL, J. C. ; OKURA, V. K. ; CHEN, L. ; KITAJIMA, Joao Paulo ; NESTER, E. W. ; OLSON, M. V. . Sequencing and analysis of the Agrobacterium tumefaciens genome. In: 10th Int'l congress on Molecular plant-microbe interactions, 2001, Madison, WI, EUA. poster session, 2001.

• SETUBAL, J. C. ; MEIDANIS, J. . The Bioinformatics Of The Xylella Fastidiosa Genome Project. In: II Annual Conference on Computational Genomics, 1998, Renton, Virginia. Abstract Book of the II Annual Conference on Computational Genomics. EUA: The Institute of Genomic Research, 1998.

• SETUBAL, J. C. ; MACEDO, P. ; CACERES, E. . Solving The Maximum Flow Problem in Parallel, with Distributed Memory, and Asynchronously. In: Workshop em Paralelismo e Otimizacao Combinatoria, 1998, Búzios, RJ. Anais do Workshop em Paralelismo e Otimizacao Combinatoria. Buzios, RJ, 1998. p. 1-4.

• SETUBAL, J. C. . New Experimental Results For Bipartite Matching. In: NETFLOW'93, 1993. Proceedings. San Miniato, Italia. p. 211-216.

• João C. Setubal . Bacteriophage Genomes in MetaSUB data. 2024. (Apresentação de Trabalho/Conferência ou palestra).

• João C. Setubal . Bacteriophage Genomes in MetaSUB data. 2024. (Apresentação de Trabalho/Conferência ou palestra).

• João C. Setubal . An Anecdote regarding Metagenome Data Access, and lessons we can learn from it. 2024. (Apresentação de Trabalho/Conferência ou palestra).

• João C. Setubal . MetaSUB explorations: phages and bacteria. 2023. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, João C. . Prediction of bacterial phenotypes from genomes using machine learning. 2023. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, Joao Carlos . The Composting Microbiome. 2021. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, Joao Carlos . Metagenome-assembled genomes: what they are and how we can believe them. 2021. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, João C . Microbiomes and their analysis. 2020. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, João C . Genome-resolved composting. 2020. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, Joao C. . Genome-resolved composting. 2019. (Apresentação de Trabalho/Conferência ou palestra).

• Setubal, João C . A microbial-molecular view of what happens when organic waste from a Zoo is composted. 2018. (Apresentação de Trabalho/Conferência ou palestra).

• SETUBAL, J. C. ; WERNECK, R. . A program for building contig scaffolds in double-barrelled shotgun genome sequencing. Campinas: Instituto de Computacao, Unicamp, 2001 (Relatório Técnico).

• SETUBAL, J. C. ; ALMEIDA JR, Nalvo Franco de ; TOMPA, M. . On the use of don´t care regions in the alignment of protein sequences. Campinas: Instituto de Computação, UNICAMP, 1999 (Relatório Técnico).

• SETUBAL, J. C. ; ALMEIDA JR, Nalvo Franco de . Um Modelo oculto de Markov para determinar promotores em seqüências de DNA. Campinas: IC-Unicamp, 1998 (Relatório Técnico).

• SETUBAL, J. C. ; OLIVEIRA, J. R. S. . Uma abordagem uniforme para problemas de comparação de seqüências. Campinas: Instituto de Computação, UNICAMP, 1997 (Relatório Técnico).

• SETUBAL, J. C. ; MENEZES, R. P. . Modelos de computação paralela e projeto de algoritmos. Campinas: Instituto de Computação, UNICAMP, 1995 (Relatório Técnico).

Outras produções

Projetos de pesquisa

• 2023 - Atual

  B3: Biologia de Bactérias e Bacteriófagos, Descrição: Trata-se de um Centro de Pesquisa, Inovação e Difusão (CEPID) financiado pela FAPESP. , Situação: Em andamento; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (20) / Mestrado acadêmico: (10) / Doutorado: (50) . , Integrantes: Joao Carlos Setubal - Integrante / Henrique Ferreira - Integrante / Shaker Chuck Farah - Coordenador / Frederico Gueiros-Filho - Integrante / Beny Spira - Integrante / Regina Baldini - Integrante / Cristina Martinez - Integrante / Robson Francisco de Souza - Integrante / Cristiane de Carvalho Guzzo - Integrante / Marcelo Brocchi - Integrante / Sandro Marana - Integrante / Germán Sgro - Integrante / Marilis do Vale Marques - Integrante / Rodrigo Galhardo - Integrante / Marcio Vinicius Bertacine Dias - Integrante / Roberto Kopke Salinas - Integrante / José Freire da Silva Neto - Integrante / Marco Aurélio Takita - Integrante / Rita de Cássia Café Ferreira - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro.

• 2022 - Atual

  O conjunto de ferramentas computacionais bigDiscovery (bigD) em bioinformática e genômica, Descrição: Neste projeto pretendemos desenvolver oito ferramentas de bioinformática com diversas aplicações, sendo as principais biotecnologia e saúde humana. A filosofia geral do projeto é dada pelas seguintes diretrizes:1. Iremos produzir ferramentas para uso público (de livre acesso, sem custo para usuários, código aberto), a serem disponibilizadas em repositórios como GitHub e CRAN, e associadas a publicações como BMC Bioinformatics, Bioinformatics, entre outras.2. Em cada ferramenta, teremos a parceria de pelo menos um pesquisador bioinformata com um pesquisador de ciências da vida, tal que este último seja um especialista na área de aplicação da ferramenta.3. Os implementadores das ferramentas serão predominantemente alunos de pós-graduação dos pesquisadores participantes, em sua maioria alunos do programa de pós-graduação interunidades em Bioinformática da Universidade de São Paulo. Esperamos também contar com a participação de um bolsista DTI e um bolsista de Iniciação Tecnológica e Industrial.4. Para cada ferramenta, os pesquisadores e os implementadores formarão uma equipe. As diversas equipes manterão contato constante ao longo do projeto, para garantir sinergia de trabalho entre os diversos sub-projetos.. , Situação: Em andamento; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Coordenador / Nalvo Franco de Almeida Jr - Integrante / DA SILVA, ALINE MARIA - Integrante / Ricardo Giordano - Integrante / VARANI, ALESSANDRO DE MELLO - Integrante / Eduardo Reis - Integrante / Mario Murakami - Integrante / João Eduardo Ferreira - Integrante / Gecele Matos Paggi - Integrante / Gabriela Persinoti - Integrante.

• 2018 - Atual

  Caracterização do microbioma de solos, rizosfera, e plantas de soja e milho em regiões de plantio dessas culturas, Projeto certificado pela empresa INDIGO BRAZIL AGRICULTURA LTDA. em 13/01/2021., Descrição: Levantamento do microbioma por meio de sequenciamento do gene rRNA de 16S de amostras de solos, rizosfera, e plantas de soja e milho em regiões de plantio dessas culturas. , Situação: Em andamento; Natureza: Pesquisa. , Alunos envolvidos: Mestrado acadêmico: (1) Doutorado: (1) . , Integrantes: Joao Carlos Setubal - Coordenador / da Silva, Aline M - Integrante / Maltez Thomas, Andrew - Integrante / Suzana Guima - Integrante / Maike Rossmann - Integrante.

• 2014 - 2020

  Bioinformática, Genômica, e Associados (BIGA), Descrição: O objetivo deste projeto é realizar avanços no estado da arte em biologia computacional1 por meio de trabalho interdisciplinar em projetos biológicos motivadores. Esses projetos têm em comum entre si necessidades sofisticadas de bioinformática; além disso, vários dos temas importantes da biologia computacional aparecem de forma recorrente em muitos desses projetos, permitindo assim uma sinergia na análise dos dados e no desenvolvimento de novas ferramentas. A área científica geral que permeia os projetos motivadores é a área de Ciências Genômicas. Usamos este termo para designar todas as investigações biológicas que dependem direta ou indiretamente do conhecimento do genoma dos organismos de interesse. Recaem portanto nesta definição várias das técnicas conhecidas como ?ômicas?, tais como a genômica, a transcritômica e a proteômica. O advento das tecnologias de sequenciamento de nova geração (NGS) barateou extraordinariamente os custos de sequenciamento, tanto para DNA quanto RNA. Isso abriu novos horizontes de pesquisa em variadas áreas, mas ao mesmo tempo trouxe demandas novas e intensas de processamento computacional, exigindo a adaptação de antigas técnicas e a formulação de novas. É neste contexto que se insere este projeto.. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Coordenador / Nalvo Franco de Almeida Jr - Integrante / Jesus Ferro - Integrante / Leandro Moreira - Integrante., Financiador(es): Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Auxílio financeiro.

• 2012 - 2015

  PlantSimLab: A Simulation Laboratory for Plant Biology, Descrição: The goal of the project is to develop a network modeling tool, PlantSimLab, that enables plant biologists to build, validate, and use intuitive computer models, with a user interface that does not require mathematical or modeling expertise. No such tool is currently available.. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Brett Tyler - Integrante / Reinhard Laubenbacher - Coordenador / John McDowell - Integrante., Financiador(es): National Science Foundation - Auxílio financeiro.

• 2012 - 2014

  Modelos computacionais para familias de proteinas relevantes em bioenergia microbiana, Descrição: Criação de modelos ocultos de Markov que representem famílias de proteinas de processos microbianos relevantes para aplicações biotecnológicas em bioenergia. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Coordenador / Claudia B. Monteiro-Vitorello - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro.

• 2012 - Atual

  Estudos da diversidade microbiana do Parque Zoológico de São Paulo, Descrição: Este projeto tem por objetivo geral coletar, analisar e prospectar dados moleculares de três microbiomas existentes no Parque Zoológico do Estado de São Paulo: compostagem vegetal da mata atlântica, lago, e fezes de macacos bugio. O projeto fará uso de diversas metodologias, sendo as principais a metagenômica por pirossequenciamento, a identificação dos isolados microbianos por espectrofotometria de massa, e bioinformática. O projeto inclui pesquisadores da USP (campi Butantan e Zona Leste), da UNIFESP (campi Vila Clementino e Diadema), e da Fundação Parque Zoológico de São Paulo. O projeto trará novos resultados sobre a biodiversidade de microorganismos e de biomas específicos, com prospecção e o estabelecimento de coleções de linhagens microbianas; desenvolvimento de estratégias para a rápida identificação e transferência de linhagens com potencial de aplicação biotecnológica e industrial; e bioprospecção de produtos microbianos.. , Situação: Em andamento; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (3) / Mestrado acadêmico: (2) / Doutorado: (3) . , Integrantes: Joao Carlos Setubal - Coordenador / Sergio verjovski-Almeida - Integrante / Luciano A. Digiampietri - Integrante / Julio Cezar de Oliveira - Integrante / da Silva, Aline M - Integrante / Renata Pascon - Integrante / Marcelo Vallim - Integrante / Luiz Juliano Neto - Integrante / João Batista da Cruz - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro.

• 2011 - 2015

  The Oomycete-Soybean Coordinated Agricultural Project, Descrição: The Oomycete-Soybean Coordinated Agricultural Project (CAP) is a community, transdisciplinary effort of 28 co-project directors at 17 institutions. The Virginia Bioinformatics Institute at Virginia Tech is the lead institution. Brett Tyler is the lead PD. The project is funded by the the Agriculture and Food Research Initiative (AFRI) of the National Institute of Food and Agriculture (NIFA), an agency within the U.S. Department of Agriculture (USDA).. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Brett Tyler - Coordenador / John McDowell - Integrante., Financiador(es): United States Department of Agriculture - Auxílio financeiro.

• 2011 - 2014

  Commoditizing Data-Intensive Biocomputing in the Cloud, Descrição: Criação de infra-estrutura de sofware para utilização da Cloud Azure da Microsoft para problemas de larga escala em genômica. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Doutorado: (2) . , Integrantes: Joao Carlos Setubal - Integrante / Feng, Wu-chun - Coordenador.

• 2010 - 2014

  Gene Ontology Terms for Microbial Energy Processes, Descrição: Novos termos da Gene Ontology sao criados para processos de bioenergia em micro-organismos. Esses termos sao usados na anotacao de genomas microbianos relevantes para bioenergia.. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Brett Tyler - Integrante / T. Murali - Integrante / Biswarup Mukhopadhyay - Coordenador.

• 2007 - 2010

  The Phylofacts Encyclopedia of Microbial Genes and Genomes, Descrição: Banco de dados, ferramentas computacionais de construcao e analise, e interface web para familias de proteinas em microorganismos. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Kimmen Sjolander - Coordenador., Financiador(es): National Science Foundation - Auxílio financeiro.

• 2006 - 2009

  Genome sequencing and annotation of Azotobacter vinelandii, Descrição: Sequenciamento e anotacao/analise do genoma da bacteria A. vinelandii. , Situação: Em andamento; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Wood, Derek - Coordenador / Dennis Dean - Integrante., Financiador(es): National Science Foundation - Auxílio financeiro.

• 2005 - 2008

  Gene ontology terms for standardized annotation of plant-associated microbe genomes, Descrição: Geracao de novos termos da Gene Ontology para funcoes, processos e componentes relacionados com interacao microbio-plantas (e animais), e aplicacao desses novos termos na anotacao de genomas especificos. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Brett Tyler - Coordenador., Financiador(es): United State Department of Agriculture USDA - Auxílio financeiro / National Science Foundation - Auxílio financeiro.

• 2004 - 2009

  Genome sequencing of agrobacterium biovar type strains, Descrição: sequenciamento e analise de a. vitis s4 e a. radiobacter k84. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (0) / Especialização: (0) / Mestrado acadêmico: (0) / Mestrado profissional: (0) / Doutorado: (0) . , Integrantes: Joao Carlos Setubal - Integrante / Derek W. Wood - Coordenador., Financiador(es): National Science Foundation - Auxílio financeiro.

• 2004 - 2009

  PathoSystems Resource Integration Center, Descrição: Banco de dados genomicos e correlatos para bacterias e virus constantes da lista de prioridades do NIAID/NIH. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Integrante / Sobral, B. - Coordenador.

• 2001 - 2004

  Projeto transcriptoma Schistosoma mansoni, Descrição: Projeto objetivou sequenciamento e analise de 180.000 sequencias de ESTs do parasita humano Schistosoma mansoni. O projeto é liderado pelo Prof. Sergio Verjovski-Almeida, do IQ-USP. Minha participacao se deu realizando a bioinformatica, em colaboracao com o grupo do prof. Verjovski-Almeida. Participa tambem meu aluno de mestrado Joao Paulo Piazza. O projeto já conseguiu uma publicação importante (Nature Genetics), mas há intenção de se prosseguir com as análises. Projeto financiado pela FAPESP e CNPq. Coube ao LBI/IC o valor de R$ 80 mil (FAPESP) e US$12500 (CNPq).. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (0) / Especialização: (0) / Mestrado acadêmico: (1) / Mestrado profissional: (0) / Doutorado: (0) . , Integrantes: Joao Carlos Setubal - Coordenador / Joao Paulo Kitajima - Integrante / Joao Paulo Piazza - Integrante., Financiador(es): Conselho Nacional de Desenvolvimento Científico e Tecnológico - Auxílio financeiro / Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro., Número de produções C, T & A: 2

• 2001 - 2004

  Projeto genoma Leifsonia xyli, Descrição: O projeto objetiva o sequenciamento completo e analise do genoma da bacteria Leifsonia xyli, que causa doencas em cana de açúcar. É um projeto realizado pela rede AEG/ONSA do estado de São Paulo. O Laboratório de Bioinformática do IC/Unicamp coordenado por mim realiza toda a bioinformática desse projeto.. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (3) / Especialização: (0) / Mestrado acadêmico: (1) / Mestrado profissional: (0) / Doutorado: (1) . , Integrantes: Joao Carlos Setubal - Coordenador / Joao Paulo Kitajima - Integrante / Luciano A. Digiampietri - Integrante / Marcelo Perez - Integrante / Patricia Farah Carrião - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro / Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa., Número de produções C, T & A: 2

• 2001 - 2004

  Projeto genoma Leptospira interrogans, Descrição: O projeto objetivou o sequenciamento completo e análise do genoma da bactéria Leptospira interrogans serovar Copenhageni, causadora da leptospirose. O LBI/IC realizou toda a bioinformática desse projeto. O projeto já tem um manuscrito aceito para publicação, a qual deve ocorrer em 2004.. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (3) / Especialização: (0) / Mestrado acadêmico: (1) / Mestrado profissional: (0) / Doutorado: (1) . , Integrantes: Joao Carlos Setubal - Coordenador / Joao Paulo Kitajima - Integrante / Luciano A. Digiampietri - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro / Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa.

• 2000 - 2002

  Projeto genoma Xanthomonas citri, Descrição: Sequenciamento, anotacao e analise dos genomas das bacterias Xanthomonas citri e campestris. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Coordenador / Joao Paulo Kitajima - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro.

• 1997 - 2000

  Projeto genoma Xylella fastidiosa, Descrição: Sequenciamento, anotaco e analise do genoma da bacteria Xylella fastidiosa. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Joao Carlos Setubal - Coordenador / João Meidanis - Integrante., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Auxílio financeiro.

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