Research lines

The project that gave rise to the laboratory: sequencing and analysing the genome of Rhodnius prolixus, the kissing bug, the main vector of Chagas disease in Latin America. From there the line expanded into the biology of other arthropods of medical and agricultural interest — immunity, blood-feeding, reproduction, and the relationship between the insect and the parasites it transmits. The resulting data (genome assemblies, gene predictions and RNAseq tracks) are made publicly available through the laboratory's genome browser.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Rafael Dias MesquitaBiochemistry | Bioinformatics | Genomics | Transcriptomics | Gene and protein annotation

Genome assembly and annotation — from organising raw sequencing reads to gene prediction and comparative analysis across species. Besides the Rhodnius prolixus genome, this line includes identifying sex-linked genes, expanded gene families, and polymorphisms associated with traits of interest such as insecticide resistance.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Rafael Dias MesquitaBiochemistry | Bioinformatics | Genomics | Transcriptomics | Gene and protein annotationBernardo Saraiva VelozoBioinformatics | Genomics | Oncology | Scientific researchMárcio Wilson Dias de BritoBiology | Bioinformatics | R&D | Oncology | Genomics | Transcriptomics | Machine learningNilton SilvaProtein modelling | Genomics | Transcriptomics | Molecular dynamicsAna Beatriz de Almeida MouraGenomics | Metabolic modelling | Bioinformatics | Target protein prospecting

De novo and genome-guided transcriptome assembly, followed by differential expression analysis and clustering of expression profiles. Applied to specific tissues — such as the digestive tract and ovarian tissue of triatomine bugs — and to comparisons across experimental conditions, including work with biomedical relevance, such as expression profiles in oncology models.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Rafael Dias MesquitaBiochemistry | Bioinformatics | Genomics | Transcriptomics | Gene and protein annotationMárcio Wilson Dias de BritoBiology | Bioinformatics | R&D | Oncology | Genomics | Transcriptomics | Machine learningNilton SilvaProtein modelling | Genomics | Transcriptomics | Molecular dynamics

Homology-based three-dimensional protein modelling, protein–ligand docking and molecular dynamics simulations, applied to predicting mutations in antibiotic target proteins and to rational drug design. In parallel, the technological prospecting of enzymes of biotechnological interest — identifying candidates from genomic and transcriptomic data for industrial and environmental applications.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Rafael Dias MesquitaBiochemistry | Bioinformatics | Genomics | Transcriptomics | Gene and protein annotationVicente Salgado PiresBioinformatics | Protein modelling | Rational drug design | Molecular dynamicsNilton SilvaProtein modelling | Genomics | Transcriptomics | Molecular dynamicsVictória Gabriela da Silva TrindadeBiotechnology | Biochemistry | Enzyme prospectingGabriel Stamato NunesBiotechnology | Biochemistry | Microbiology | Enzyme prospectingAna Beatriz de Almeida MouraGenomics | Metabolic modelling | Bioinformatics | Target protein prospecting

Reconstructing genome-scale metabolic networks from an organism's annotated genome and analysing them in silico — for instance through flux balance analysis — to predict how metabolism responds to changes in growth conditions or to genetic modifications. This line links the laboratory's gene and enzyme annotation work to metabolic engineering, focusing on production routes for compounds of biotechnological interest such as long-chain alcohols and fatty acids.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Caroline Azevedo de AraújoSystems biology | Genome-scale metabolic modelling | Metabolic engineeringAna Beatriz de Almeida MouraGenomics | Metabolic modelling | Bioinformatics | Target protein prospecting

Applying machine learning methods to large biological datasets produced or reanalysed by the laboratory — genome sequences, expression profiles and interaction networks. The aim is to extract patterns beyond the reach of conventional analysis: classifying samples, selecting genes and expression signatures with biomarker potential, and supporting the functional annotation of genes and proteins.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Márcio Wilson Dias de BritoBiology | Bioinformatics | R&D | Oncology | Genomics | Transcriptomics | Machine learningSabrina Atella BarreiraBiomedicine | Biochemistry | Molecular Biology | Oncology | Multi-omics marker prediction

Applying the laboratory's genomics, transcriptomics and molecular modelling techniques to direct biomedical questions — from variant and expression-pattern analysis in oncology models to the computational prediction of mutations that lead to bacterial antibiotic resistance, a public health problem estimated to cause hundreds of thousands of deaths per year worldwide.

Who works on this line today

Current laboratory members whose research falls in this area — not necessarily authors of the publications listed below.

Bernardo Saraiva VelozoBioinformatics | Genomics | Oncology | Scientific researchMárcio Wilson Dias de BritoBiology | Bioinformatics | R&D | Oncology | Genomics | Transcriptomics | Machine learningSabrina Atella BarreiraBiomedicine | Biochemistry | Molecular Biology | Oncology | Multi-omics marker prediction