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List of works by Joao Carlos Setubal

A Tropical Composting Operation Unit at São Paulo Zoo as a Source of Bacterial Proteolytic Enzymes

scientific article published on 23 June 2018

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.

scientific article

A framework based on Web service orchestration for bioinformatics workflow management

scientific article published on 30 September 2005

A ligand motif enables differential vascular targeting of endothelial junctions between brain and retina

scientific article published on 22 January 2019

A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea

scientific article

A probiotic has differential effects on allergic airway inflammation in A/J and C57BL/6 mice and is correlated with the gut microbiome

scientific article published on 10 June 2021

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival

scientific article published on 17 December 2019

A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case

scientific article published on 6 June 2007

Abstract 105: Bioinformatic analysis of RNA-Seq data to search for novel diagnostic/prognostic biomarkers of pancreatic ductal adenocarcinoma

scholarly article by Omar J. Sosa et al published 15 July 2016 in Cancer Research

Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms

scientific article

An anomalous type IV secretion system in Rickettsia is evolutionarily conserved

scientific article

Analyses of Seven New Genomes of Xanthomonas citri pv. aurantifolii Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes

scientific article published on 11 October 2019

Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions

scientific article

Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol

scientific article published on 19 November 2020

Analysis of expressed sequence tags from the agarophyte Gracilaria tenuistipitata (Rhodophyta)

Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle

scientific article published on 03 April 2009

Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

scientific article published on 01 December 2019

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

scientific article published in 2018

Bacterial phytopathogens and genome science

scientific article

Brazilian Symposium on Bioinformatics

article

Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism

scientific article published on 01 April 2019

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

scientific article

Characterization of novel Brucella strains originating from wild native rodent species in North Queensland, Australia

scientific article

Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting

scientific article published on 18 April 2019

Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs.

scientific article

Circulating Plasma miRNA and Clinical/Hemodynamic Characteristics Provide Additional Predictive Information About Acute Pulmonary Thromboembolism, Chronic Thromboembolic Pulmonary Hypertension and Idiopathic Pulmonary Hypertension

scientific article published on 28 May 2021

Comparative Analyses of Xanthomonas and Xylella Complete Genomes

article

Comparative Analysis of Ralstonia solanacearum Methylomes

scientific article

Comparative Genomics for Prokaryotes

scientific article

Comparative Genomics of <i>Xylella fastidiosa</i> Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems

scientific article published on 27 April 2022

Comparative Metagenomics

scientific article

Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa.

scientific article

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

scientific article published on 9 September 2011

Comparative genomic analysis of plant-associated bacteria

scientific article

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

scientific article

Comparative genomics analyses of citrus-associated bacteria

scientific article published in January 2004

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway

scientific article

Comparative genomics of early-diverging Brucella strains reveals a novel lipopolysaccharide biosynthesis pathway

scientific article published in 2012

Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis

scientific article

Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper.

scientific article

Comparison of the genomes of two Xanthomonas pathogens with differing host specificities

scientific article

Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction

scientific article published on 10 June 2021

Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant

scientific article published on 05 November 2020

Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031.

scientific article

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

article by Daniel Wibberg et al published August 2011 in Journal of Biotechnology

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

article

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

scientific article

Correction: Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms.

scientific article

Describing commonalities in microbial effector delivery using the Gene Ontology

scientific article published on July 2009

Detection and identification of Xanthomonas pathotypes associated with citrus diseases using comparative genomics and multiplex PCR

scientific article published on 01 October 2019

Developing bioinformatic resources for coronaviruses

scientific article published on January 2006

Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana

scientific article published on 7 October 2005

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

scientific article

Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.

scientific article published on 9 October 2014

Editorial: Computational Methods for Microbiome Analysis

scientific article published on 11 December 2020

First report of cis-1,4-polyisoprene degradation by Gordonia paraffinivorans

scientific article published on 22 August 2019

Gene Phylogenies and Orthologous Groups

scientific article published in January 2018

Genetic resources for advanced biofuel production described with the Gene Ontology

scientific article

Genetic resources for methane production from biomass described with the Gene Ontology

scientific article

Genome features of Leptospira interrogans serovar Copenhageni

scientific article published on 23 March 2004

Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes

scientific article published on 08 May 2009

Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria

scientific article

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting

scientific article

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

scientific article published on 10 September 2021

Global Distribution and Evolution of Mycobacterium bovis Lineages

scientific article published on 07 May 2020

Gut Microbiota Profile of Obese Diabetic Women Submitted to Roux-en-Y Gastric Bypass and Its Association with Food Intake and Postoperative Diabetes Remission

scientific article published on 21 January 2020

High-Quality Draft Genome Sequence of Pantanalinema sp. GBBB05, a Cyanobacterium From Cerrado Biome

scientific article published in 2021

High-quality draft genome sequence resources of eight Xylella fastidiosa strains isolated from citrus, coffee, plum and hibiscus in South America

scientific article published on 10 June 2020

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

scientific article published on 30 October 2016

Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae.

scientific article published on 23 November 2017

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

scientific article published on 06 April 2020

Inhibition of histone methyltransferase EZH2 in Schistosoma mansoni in vitro by GSK343 reduces egg laying and decreases the expression of genes implicated in DNA replication and noncoding RNA metabolism

article

Lipoprotein computational prediction in spirochaetal genomes

scientific article published on January 2006

Longitudinal 16S rRNA gut microbiota data of infant triplets show partial susceptibility to host genetics

scientific article published on 02 February 2022

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

scholarly article by Deyvid Amgarten et al published 2018 in Frontiers in Genetics

Machine learning meets genome assembly

scholarly article by Kleber Padovani de Souza et al published 17 August 2018 in Briefings in Bioinformatics

Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms

scientific article

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

scientific article published on 01 April 2019

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

scientific article

Missing genes in the annotation of prokaryotic genomes ⬇️

scientific article

Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea

scientific article published on 06 February 2019

Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis

scientific article

Non-coding transcription characterization and annotation: a guide and web resource for non-coding RNA databases

scientific article published on March 2012

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii

scientific article

Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

scientific article published on 09 September 2019

PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes

scientific article

PATRIC: the VBI PathoSystems Resource Integration Center

scientific article

Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses.

scientific article published on 13 February 2017

Peptide nucleic acids inhibit growth of Brucella suis in pure culture and in infected murine macrophages

scientific article published on 08 January 2013

Phylogenomics

scientific article

Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

scientific article published on 3 June 2015

Plasmid-mediated mcr-1 in carbapenem-susceptible Escherichia coli ST156 causing a blood infection: an unnoticeable spread of colistin resistance in Brazil?

scientific article published in October 2017

Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas

scientific article published on 17 February 2015

Prophylactic Supplementation of Bifidobacterium longum 51A Protects Mice from Ovariectomy-Induced Exacerbated Allergic Airway Inflammation and Airway Hyperresponsiveness

scientific article published on 11 September 2017

Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology

scientific article

Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection

scientific article

Protocol for design, construction, and selection of genome phage (gPhage) display libraries

scientific article published on 08 November 2021

REGEN: Ancestral Genome Reconstruction for Bacteria

scientific article published on 18 July 2012

Reconciliation of sequence data and updated annotation of the genome of Agrobacterium tumefaciens C58, and distribution of a linear chromosome in the genus Agrobacterium

scientific article

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

scientific article (publication date: 2008)

Role of recombination in the evolution of the model plant pathogen Pseudomonas syringae pv. tomato DC3000, a very atypical tomato strain

scientific article published on 31 March 2008

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

scientific article

Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni.

scientific article published in May 2004

Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni

scientific article

Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq

scientific article published on 31 December 2015

Sequence verification of synthetic DNA by assembly of sequencing reads

scientific article published on 4 October 2012

Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments

scientific article published on 29 November 2019

TCBB Special Section on the Brazilian Symposium on Bioinformatics 2013

article

TabPath: interactive Tables for Metabolic Pathway analysis

scientific article published on 3 November 2017

The Candidatus Liberibacter-Host Interface: Insights into Pathogenesis Mechanisms and Disease Control

scientific article

The Genome Reverse Compiler: an explorative annotation tool

scientific article published on 27 January 2009

The complete genome sequence of 'Candidatus Liberibacter americanus', associated with Citrus huanglongbing.

scientific article

The genome of the natural genetic engineer Agrobacterium tumefaciens C58

scientific article

The genome of woodland strawberry (Fragaria vesca)

scientific article

The pathogen resource integration center: implications for Rickettsial research

scientific article

The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity

scientific article

Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages

scientific article

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling

scientific article published on 09 December 2016

Toward unrestricted use of public genomic data:

scientific article

Transcriptional profiling of nitrogen fixation in Azotobacter vinelandii

scientific article

Transcriptional signatures underlying dynamic phenotypic switching and novel disease biomarkers in a linear cellular model of melanoma progression

scientific article published on 09 April 2021

Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni

scientific article published on 14 September 2003

Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

scientific article published on 20 March 2017

Tributyrin Attenuates Metabolic and Inflammatory Changes Associated with Obesity through a GPR109A-Dependent Mechanism

scientific article published on 01 September 2020

Unifying themes in microbial associations with animal and plant hosts described using the gene ontology

scientific article

Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients

scientific article

Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology

scientific article published on 29 August 2019

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