A5070209032- Mosquito-borne diseases and control
- Viral Infections and Vectors
- SARS-CoV-2 and COVID-19 Research
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Malaria Research and Control
- Antibiotic Resistance in Bacteria
- SARS-CoV-2 detection and testing
- Vibrio bacteria research studies
- Vector-Borne Animal Diseases
- Plant Virus Research Studies
- Genetics, Aging, and Longevity in Model Organisms
- Virology and Viral Diseases
- Machine Learning in Bioinformatics
- Parasite Biology and Host Interactions
- Cell Image Analysis Techniques
- Insect symbiosis and bacterial influences
- Cancer Genomics and Diagnostics
- Bacteriophages and microbial interactions
- Dengue and Mosquito Control Research
- BRCA gene mutations in cancer
- Zoonotic diseases and public health
- Insect Resistance and Genetics
- COVID-19 epidemiological studies
Fundação Oswaldo Cruz
2016-2025
The University of Melbourne
2014-2024
We characterized 3 autochthonous dengue virus serotype cases and 1 imported case from 2 states in the North South Regions of Brazil, 15 years after Brazil's last outbreak involving this serotype. also identified a new Asian lineage recently introduced into Americas, raising concerns about future outbreaks.
The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance has become the gold standard methodology used to monitor study this fast-spreading virus its constantly emerging lineages. current deluge of SARS-CoV-2 genomic data generated worldwide put additional pressure on urgent need for streamlined bioinformatics workflows. Here, we describe a workflow developed our group process...
Abstract ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned into general-purpose reference-based genome assembler all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. runs on broad range of infrastructures, from laptop computers high-performance computing (HPC) environments, generates standard well-formatted outputs suited both public...
ABSTRACT The Brazilian western Amazon region is currently experiencing its largest laboratory confirmed Oropouche virus (OROV) outbreak, with nearly 6,000 reported cases in the states of Amazonas (AM), Acre (AC), Rondônia (RO), and Roraima (RR), between August 2022 March 2024. Here, we sequenced analyzed 382 full-length OROV genomes from human samples collected 2024 all four states, aiming to trace origin genetic evolution leading current outbreak. Genomic analyses revealed that recent...
Abstract OGEE is an Online GEne Essentiality database. Gene essentiality not a static and binary property, rather context-dependent evolvable property in all forms of life. In we collect only experimentally tested essential non-essential genes, but also associated gene properties that contributes to essentiality. We tagged conditionally genes show variable statuses across datasets highlight complex interplays between functions environmental/experimental perturbations. v3 contains for 91...
The rapid worldwide spread of chikungunya (CHIKV), dengue (DENV), and Zika (ZIKV) viruses have raised great international concern. Knowledge about the entry routes geographic expansion these arboviruses to mainland Americas remain incomplete controversial. Epidemics caused by continue cause socioeconomic burden globally, particularly in countries where vector control is difficult due climatic or infrastructure factors. Understanding how virus circulates moves from one country another...
Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing analysis coupled with assessment of antibiotic resistance 46 strains (45 A. plus one nosocomialis) originated from five hospitals the city Recife, Brazil, between 2010 2014. An average 3,809 genes were identified per genome, although only 2,006 single copy...
Abstract The Orthobunyavirus oropoucheense in a arthropod borne zoonotic pathogen known to infect sylvatic animals and humans by means of biting midges transmission. Several large-scale human outbreaks Oropouche virus (OROV), primarily confined the Amazon region, were documented over decades. However, since 2022, more widespread OROV have been unfolding Brazil across South America, with cases exported Cuba, Italy, Germany. I In Brazil, has reached established communitary transmission states...
Dengue fever, caused by the dengue virus (DENV), is most important mosquito-borne disease impacting human health globally, it particularly prevalent in tropical regions where Aedes vectors thrive. However, due to a recent expansion of main subtropical and temperate zones last decades there an increasing population at risk. Brazil global hotspot for dengue, accounting 70% all cases reported worldwide 2024. Noteworthy, became endemic even southernmost Brazilian state Rio Grande do Sul, which...
Dengue virus (DENV) infection is a significant global health concern, causing severe morbidity and mortality. While many cases present as mild febrile illness, some progress to life-threatening dengue (SD). Early intervention essential improve outcomes, but current predictive methods lack specificity, burdening healthcare systems in endemic regions. Circulating long non-coding RNAs (lncRNAs) have emerged stable promising biomarkers. This study explored the use of lncRNAs markers for SD....
The availability of whole-genome sequences and associated multi-omics data sets, combined with advances in gene knockout knockdown methods, has enabled large-scale annotation exploration protein functions eukaryotes. Knowing which genes are essential for the survival eukaryotic organisms is paramount an understanding basic mechanisms life, could assist identifying intervention targets pathogens cancer. Here, we studied orthologs among selected species eukaryotes, then employed a systematic...
Abstract Dengue virus serotype 2, genotype Cosmopolitan (DENV-2-GII), is one of the most widespread DENV strains globally. In USA, DENV-2 epidemics have been dominated by Asian-American (DENV-2-GIII), and first cases DENV-2-GII were only described in 2019, Peru, 2021 Brazil. To gain new information about circulation Brazil, we sequenced 237 confirmed sampled between March 2023 revealed that already present all geographic regions The phylogeographic analysis inferred was introduced at least...
Schistosomiasis is a parasitic disease affecting ~200 million people worldwide. Schistosoma haematobium and S. mansoni are two relatively closely related schistosomes (blood flukes), the causative agents of urogenital hepatointestinal schistosomiasis, respectively. The availability genomic, transcriptomic proteomic data sets for these now provides unprecedented opportunities to explore their biology, host interactions schistosomiasis at molecular level. A particularly important group...
SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving large death toll. As of January 2023, Brazil is among countries with highest number registered deaths. Nonpharmacological pharmacological interventions have been heterogeneously implemented in country, which, associated socioeconomic differences between country regions, has led distinct dynamics. Here, we investigate spatiotemporal dispersion lineages Pernambuco state (Northeast Brazil) throughout...
The Mayaro virus (MAYV) is an arbovirus with emerging potential, though a limited understanding of its epidemiology and evolution due to the lack studies surveillance. Here, we investigated 71 MAYV genome sequences from Americas available at GenBank characterized phylogenetic relationship among strains. A analysis showed that were grouped according genotypes L, D, N. Genotype D closely related collected in adjacent years their respective countries, suggesting isolates may have originated...
Millions of livestock animals worldwide are infected with the haematophagous barber's pole worm, Haemonchus contortus, aetiological agent haemonchosis. Despite major significance this parasite and its widespread resistance to current treatments, lack a high-quality genome for well-defined strain from Australia, called Haecon-5, has constrained research in number areas including host-parasite interactions, drug discovery population genetics. To enable these areas, we report here...
Abstract The Orthobunyavirus oropoucheense species encompasses a group of arthropod‐borne zoonotic viruses transmitted by biting midges to animals including humans. Several large‐scale human outbreaks caused the prototype member this species, Oropouche virus (OROV) have been documented since 1970s and were primarily confined Amazon basin. However, 2022, more widespread OROV unfolding in Brazil across South America, with cases exported Cuba, Italy, Spain, USA Germany. In Brazil, has reached...
Chikungunya virus (CHIKV) is an RNA from the Togaviridae family transmitted by mosquitoes in both sylvatic and urban cycles. In humans, CHIKV infection leads to a febrile illness, denominated fever (CHIKF), commonly associated with more intense debilitating outcomes. arrived Brazil 2014 through two independent introductions: Asian/Caribbean genotype entered North region African ECSA was imported Northeast region. Following their initial introduction, genotypes established cycle among large...
Abstract The identification and characterization of essential genes are central to our understanding the core biological functions in eukaryotic organisms, has important implications for treatment diseases caused by, example, cancers pathogens. Given major constraints testing many organisms laboratory, due absence vitro cultures and/or gene perturbation assays most metazoan species, there been a need develop silico tools accurate prediction or inference underpin systems investigations. Major...
Over the years, comprehensive explorations of model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have contributed substantially to our understanding complex biological processes pathways in multicellular generally. Extensive functional genomic–phenomic, genomic, transcriptomic, proteomic data sets enabled discovery characterisation genes that are crucial for life, called ‘essential genes’. Recently, we investigated feasibility inferring essential...
Defining genes that are essential for life has major implications understanding critical biological processes and mechanisms. Although have been identified characterised experimentally using functional genomic tools, it is challenging to predict with confidence such from molecular phenomic data sets computational methods. Using extensive available the model organism Caenorhabditis elegans, we constructed here a machine-learning (ML)-based workflow prediction of on genome-wide scale. We...