João Carlos Setubal
CV Lattes
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Universidade de São Paulo (USP). Instituto de Química (IQ) (Institutional affiliation for the last research proposal) Birthplace: Brazil
Full Professor in the Biochemistry Department of the Chemistry Institute of the University of Sao Paulo. PhD in Computer Science, University of Washington (1992). Research interests: bioinformatics and computational biology, primarily in genomics, metagenomics, and transcriptomics. (Source: Lattes Curriculum)
| News published in Agência FAPESP Newsletter about the researcher |
| Novel genetic signature that can predict some kinds of breast cancer is identified |
| Intestinal bacteria can be used to predict occurrence of colorectal cancer |
- Aging and genetic disorders: genomics and metagenomics, AP.TEM
Abstract
Healthy aging and longevity are a growing topic of interest. They depend on the complex interplay between nuclear and mitochondrial DNA, the environment and the microbiota, that is, the whole set of bacteria living in the different parts of our body with their whole set of genes. Understanding this complex nature versus nurture balance is one of the greatest challenges in human genetics...
- Studies of microbial diversity in the Zoological Park of the State of São Paulo, AP.BTA.TEM
Abstract
This project has as general objectives the collection, analysis, and investigation of molecular data from three microbiomes found in the Zoological Park of São Paulo state. These microbiomes are: Atlantic Rain Forest vegetation compost, water from a lake, and stool sample from Alouatta monkeys. The choice of microbiomes seeks to cover to some extent the environmental diversity found in ...
- Computational models for microbial bioenergy protein families, AP.R
Abstract
The goal of this project is to generate Hidden Markov Models for microbial protein families that have relevance inbioenergy. These models will allow the automated propagation of manual annotations of the genes that code for theseproteins. This project is associated with another project being carried out in the USA, which has as objectives thecreation of new Gene Ontology (GO) terms for ...
- Augment or push? a computational study of bipartite matching and unit capacity maximum flow algorithms, AR.EXT
- Differential expression isoform analysis from oxygen induced retinopathy in a murine model, BP.IC
Abstract
Angiogenesis is the creation of new blood vessels from pre-existing ones. It occurs naturally in physiological and pathological process, such as retinopathies and cancer. Through RNA sequencing (RNA-Seq), it is possible to study these differences between tissues at cell level in the moment of sequencing. RNA-seq data enables the identification and quantification of gene expression of th...
- Determination and analysis of gene regulation network of angiogenesis in a murine model, BP.DR
Abstract
Angiogenesis is the process which new blood vessels form from pre-existing vessels. Many diseases are dependent of neovascularization to growth in the organism, like Cancer and retinopathies. These diseases are known as angiogenesis-dependent diseases. The formation of blood vessels in a adult organism occur under delicate control of gene expression, and dysregulation of this process co...
- Unraveling the role of phages on the evolution of plant beneficial and pathogenic rhizobacteria, BP.PD
Abstract
Many beneficial and pathogenic rhizobacteria are both well described and characterized in literature. We know who they are and what they do. However, we don't know why and how they evolve pathogenic or beneficial traits. Viruses infecting bacteria (phages) modulate host niche adaptation. Genomic evidences demonstrate that prophages contribute to the evolution of virulence. Most of the...
- Microbial community profiling of human cancers, BP.DR
Abstract
The microbial mass present in the human species is ten times greater than that of human cells. We know now that this metagenome influences us greatly, playing a role in our metabolism, tissue development, inflammation and immunity. Certain body habitats suffer greater exposure to the outside world than others, increasing the importance of the human microbiome on such body sites. Studyin...
- Diversity analysis of bacteriophages associated to microbial community during the composting process, BP.MS
Abstract
Metagenomic studies have defined the structure and diversity of microbial communities in environmental samples. The data bring light to the uncultured microbial majority and help us to understand what are the organisms acting in complex processes. The thematic project in which this proposal is inserted (process 2011/50870-6) aims to characterize the diversity in different environmental ...
(Only some records are available in English at this moment)
- Screening for ecogenomic signatures of phage-bacteria interactions in natural microbiomes exposed to environmental disturbances, BE.EP.PD
Abstract
Phages, the viruses of bacteria, are capable of establishing either antagonistic or mutualistic interactions with their hosts. Evidence so far clearly demonstrates the importance of phages for microbiome functioning. However little is known about how phage-bacteria interactions at the community-level respond to environmental changes. Environmental disturbances can change microbial commu...
- Identification of microbial biomarkers for colorectal cancer using strain-level metagenomic profiling, BE.EP.DR
Abstract
Colorectal cancer (CRC) is the third most common cancer in the world, affecting more than 1.3 million people every year. CRCs can be divided into sporadic, inflammatory and hereditary forms. Genetics can, however, explain only a small proportion of disease variance. Using 16S rRNA amplicon sequencing, several bacterial species have been implicated in the development of CRC, but high-res...
- Phage orthologous clusters: a database of phage information, BE.EP.MS
Abstract
Phages studies have been experiencing a resurgence of scientific interest due to recent evidences that show their importance in microbial ecology, carbon and other nutrients cycling and potential applications as anti-bacterial therapeutics in clinical, agricultural and food processing fields. They are also theorized as Nature reservoirs of genetic diversity, being responsible for new ge...
- Angiogenic pathological signature and its prognostic power, BE.EP.DR
Abstract
The branching of pre-existing blood vessels to form new ones (angiogenesis) is a physiological process vital to any vertebrate. But this vital process is also involved on the initiation and progress of diseases including cancers, age-related macular degeneration and retinopathies, amongst others. We hypothesized that, while the macroscopic process of remains the same, there are molecul...
(Only some records are available in English at this moment)
| 1 / 1 | Ongoing research grants |
| 7 / 3 | Completed research grants |
| 2 / 2 | Ongoing scholarships in Brazil |
| 27 / 7 | Completed scholarships in Brazil |
| 1 / 1 | Ongoing scholarships abroad |
| 5 / 4 | Completed scholarships abroad |
| 43 / 18 | All research grants and scholarships |
| Associated processes | |
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
| Publications | 19 |
| Citations | 166 |
| Cit./Article | 8.7 |
| Data from Web of Science | |
BRAGA, STEFANIA PEGORIN; DOS SANTOS, ALEXANDRE PAES; PAGANINI, THAIS; BARBOSA, DEIBS; CONDOMITTI EPAMINO, GEORGE WILLIAN; MORAIS, CARLOS; MARTINS, LAYLA FARAGE; SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS; VALLIM, MARCELO AFONSO; et al. First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans. Brazilian Journal of Microbiology, v. 50, n. 4, p. 1051-1062, OCT 2019. Web of Science Citations: 0. (16/07360-0, 11/50870-6, 16/14542-8)
AL ASSAL, KARINA; PRIFTI, EDI; BELDA, EUGENI; SALA, PRISCILA; CLEMENT, KARINE; DAO, MARIA-CARLOTA; DORE, JOEL; LEVENEZ, FLORENCE; TADDEI, CARLA R.; FONSECA, DANIELLE CRISTINA; et al. 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, v. 12, n. 2, FEB 2020. Web of Science Citations: 2. (15/01507-7, 11/09612-3)
BRAGA, LUCAS P. P.; SPOR, AYME; KOT, WITOLD; BREUIL, MARIE-CHRISTINE; HANSEN, LARS H.; SETUBAL, JOAO C.; PHILIPPOT, LAURENT. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. MICROBIOME, v. 8, n. 1, APR 6 2020. Web of Science Citations: 0. (18/19247-0)
THOMAS, ANDREW M.; JESUS, ELIANE C.; LOPES, ADEMAR; AGUIAR, JR., SAMUEL; BEGNAMI, MARIA D.; ROCHA, RAFAEL M.; CARPINETTI, PAOLA AVELAR; CAMARGO, ANAMARIA A.; HOFFMANN, CHRISTIAN; FREITAS, HELANO C.; et al. Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, v. 6, DEC 9 2016. Web of Science Citations: 19. (15/01507-7, 13/07914-8)
LEMOS, LEANDRO N.; PEREIRA, ROBERTA V.; QUAGGIO, RONALDO B.; MARTINS, LAYLA F.; MOURA, LIVIA M. S.; DA SILVA, AMANDA R.; ANTUNES, LUCIANA P.; DA SILVA, ALINE M.; SETUBAL, JOAO C.. Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting. FRONTIERS IN MICROBIOLOGY, v. 8, APR 19 2017. Web of Science Citations: 9. (13/05325-5)
PUIGVERT, MARINA; GUARISCHI-SOUSA, RODRIGO; ZULUAGA, PAOLA; COLL, NURIA S.; MACHO, ALBERTO P.; SETUBAL, JOAO C.; VALLS, MARC. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii. FRONTIERS IN PLANT SCIENCE, v. 8, MAR 20 2017. Web of Science Citations: 5. (12/15197-1)
KINKER, GABRIELA SARTI; THOMAS, ANDREW MALTEZ; CARVALHO, VINICIUS JARDIM; LIMA, FELIPE PRATA; FUJITA, ANDRE. Deletion and low expression of NFKBIA are associated with poor prognosis in lower-grade glioma patients. SCIENTIFIC REPORTS, v. 6, APR 7 2016. Web of Science Citations: 4. (15/01507-7, 14/27287-0, 13/03447-6, 15/01587-0, 14/09576-5)
AMGARTEN, DEYVID; BRAGA, LUCAS P. P.; DA SILVA, ALINE M.; SETUBAL, JOAO C.. MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins. FRONTIERS IN GENETICS, v. 9, AUG 7 2018. Web of Science Citations: 13. (11/50870-6, 14/16450-8)
THOMAS, ANDREW MALTEZ; MANGHI, PAOLO; ASNICAR, FRANCESCO; PASOLLI, EDOARDO; ARMANINI, FEDERICA; ZOLFO, MORENO; BEGHINI, FRANCESCO; MANARA, SERENA; KARCHER, NICOLAI; POZZI, CHIARA; et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine, v. 25, n. 4, p. 667+, APR 2019. Web of Science Citations: 24. (16/23527-2, 14/26897-0)
FACHI, JOSE LUIS; FELIPE, JAQUELINE DE SOUZA; PRAL, LAIS PASSARIELLO; DA SILVA, BRUNA KARADI; CORREA, RENAN OLIVEIRA; PEREIRA DE ANDRADE, MIRELLA CRISTINY; DA FONSECA, DENISE MORAIS; BASSO, PAULO JOSE; SARAIVA CAMARA, NIELS OLSEN; DE SALES E SOUZA, ERICKA LORENNA; et al. Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism. CELL REPORTS, v. 27, n. 3, p. 750+, APR 16 2019. Web of Science Citations: 3. (15/01507-7, 12/10653-9, 13/06810-4, 17/25679-7, 18/01753-6, 17/16280-3, 17/06577-9, 17/26366-2, 16/23142-3, 14/03002-7, 15/06134-4, 17/01451-7, 18/02208-1)
BRAGA, LUCAS P. P.; SOUCY, SHANNON M.; AMGARTEN, DEYVID E.; DA SILVA, ALINE M.; SETUBAL, JOAO C.. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. FRONTIERS IN ECOLOGY AND EVOLUTION, v. 6, JAN 26 2018. Web of Science Citations: 5. (11/50870-6)
PYLRO, VICTOR S.; MORAIS, DANIEL K.; DE OLIVEIRA, FRANCISLON S.; DOS SANTOS, FAUSTO G.; LEMOS, LEANDRO N.; OLIVEIRA, GUILHERME; ROESCH, LUIZ F. W.. BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies. MICROBIAL ECOLOGY, v. 72, n. 2, p. 443-447, AUG 2016. Web of Science Citations: 14. (13/05325-5)
ERILL, IVAN; PUIGVERT, MARINA; LEGRAND, LUDOVIC; GUARISCHI-SOUSA, RODRIGO; VANDECASTEELE, CELINE; SETUBAL, JOAO C.; GENIN, STEPHANE; GUIDOT, ALICE; VALLS, MARC. Comparative Analysis of Ralstonia solanacearum Methylomes. FRONTIERS IN PLANT SCIENCE, v. 8, APR 13 2017. Web of Science Citations: 2. (12/15197-1)
LIMA-JUNIOR, JAMES DALTRO; VIANA-NIERO, CRISTINA; CONDE OLIVEIRA, DANIEL V.; MACHADO, GABRIEL ESQUITINI; DA SILVA RABELLO, MICHELLE CRISTIANE; MARTINS-JUNIOR, JOAQUIM; MARTINS, LAYLA FARAGE; DIGIAMPIETRI, LUCIANO ANTONIO; DA SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS; et al. Characterization of mycobacteria and mycobacteriophages isolated from compost at the Sao Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U. BMC Microbiology, v. 16, JUN 17 2016. Web of Science Citations: 2. (11/18326-4, 14/01825-6, 11/50870-6, 12/04911-5)
WOOD‚ D.W.; SETUBAL‚ J.C.; KAUL‚ R.; MONKS‚ D.E.; KITAJIMA‚ J.P.; OKURA‚ V.K.; ZHOU‚ Y.; CHEN‚ L.; WOOD‚ G.E.; ALMEIDA JR‚ N.F.; et al. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science, v. 294, n. 5550, p. 2317-2323, 2001.
ANTUNES, LUCIANA PRINCIPAL; MARTINS, LAYLA FARAGE; PEREIRA, ROBERTA VERCIANO; THOMAS, ANDREW MALTEZ; BARBOSA, DEIBS; LEMOS, LEANDRO NASCIMENTO; MACHADO SILVA, GIANLUCA MAJOR; SILVA MOURA, LIVIA MARIA; CONDOMITTI EPAMINO, GEORGE WILLIAN; DIGIAMPIETRI, LUCIANO ANTONIO; et al. Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics. SCIENTIFIC REPORTS, v. 6, DEC 12 2016. Web of Science Citations: 28. (11/50870-6)
AMGARTEN, DEYVID; MARTINS, LAYLA FARAGE; LOMBARDI, KAREN CRISTINA; ANTUNES, LUCIANA PRINCIPAL; SILVA DE SOUZA, ANA PAULA; NICASTRO, GIANLUCCA GONCALVES; KITAJIMA, ELLIOTT WATANABE; QUAGGIO, RONALDO BENTO; UPTON, CHRIS; SETUBAL, JOAO CARLOS; et al. Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, v. 18, MAY 4 2017. Web of Science Citations: 6. (15/14334-3, 11/50870-6, 14/16450-8)
WIRBEL, JAKOB; PYL, PAUL THEODOR; KARTAL, ECE; ZYCH, KONRAD; KASHANI, ALIREZA; MILANESE, ALESSIO; FLECK, JONAS S.; VOIGT, ANITA Y.; PALLEJA, ALBERT; PONNUDURAI, RUBY; et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine, v. 25, n. 4, p. 679+, APR 2019. Web of Science Citations: 30. (16/23527-2)
RANGEL, LUIZ THIBERIO; MARDEN, JEREMIAH; COLSTON, SOPHIE; SETUBAL, JOAO CARLOS; GRAF, JOERG; GOGARTEN, JOHANN PETER. Identification and characterization of putative Aeromonas spp. T3SS effectors. PLoS One, v. 14, n. 6, JUN 4 2019. Web of Science Citations: 0. (14/23975-0, 12/17196-2)
SILVA, NATALIA MARIA; SILVA ARAUJO DE OLIVEIRA, ALINE MARCIA; PEGORIN, STEFANIA; GIUSTI, CAMILA ESCANDURA; FERRARI, VITOR BATISTA; BARBOSA, DEIBS; MARTINS, LAYLA FARAGE; MORAIS, CARLOS; SETUBAL, JOAO CARLOS; VASCONCELLOS, SUZAN PANTAROTO; et al. Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting. PLoS One, v. 14, n. 4, APR 18 2019. Web of Science Citations: 0. (11/50870-6, 16/23639-5)
(References retrieved automatically from State of São Paulo Research Institutions)
JUNIOR, Lidio Nunes de Abreu. O problema da designação e sua variante parametrica. Dissertação (Mestrado) - Instituto de Computação. Universidade Estadual de Campinas (UNICAMP). (97/11222-0)
CRUZ, Carlos Fernando Bella. Algoritmos para emparelhamento em grafos e uma implementação paralela. Dissertação (Mestrado) - Instituto de Matemática, Estatística e Computação Científica. Universidade Estadual de Campinas (UNICAMP). (94/04158-5)