A5073270719- Genomics and Phylogenetic Studies
- Colorectal Cancer Treatments and Studies
- Protein Tyrosine Phosphatases
- Salmonella and Campylobacter epidemiology
- Biochemical and Molecular Research
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Epigenetics and DNA Methylation
- Marine Ecology and Invasive Species
- Spondyloarthritis Studies and Treatments
- RNA modifications and cancer
- Poxvirus research and outbreaks
- Bacteriophages and microbial interactions
- Identification and Quantification in Food
- Gut microbiota and health
- Cervical Cancer and HPV Research
- Head and Neck Cancer Studies
- Sperm and Testicular Function
- Genomics and Chromatin Dynamics
- Listeria monocytogenes in Food Safety
- Animal Genetics and Reproduction
- Plant Virus Research Studies
- Bone and Joint Diseases
- RNA Research and Splicing
- Diabetes and associated disorders
National Institute of Health Dr. Ricardo Jorge
2022-2025
Instituto Gulbenkian de Ciência
2014-2025
Universidade Nova de Lisboa
2020-2024
NovaBiotics (Norway)
2021-2024
University of Lisbon
2003-2024
Unidade em Ciências Biomoleculares Aplicadas
2022-2024
Escola Bahiana de Medicina e Saúde Pública
2024
University of Surrey
2023
University of Aveiro
2023
Instituto Nacional de Saúde
2023
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets all supported species; large-scale whole multiple species alignments across vertebrates clade-specific eutherian mammals, primates, birds fish; variation data 17 regulation annotations based ENCODE other sets. are accessible through the browser at http://www.ensembl.org tools...
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human data as well key model organisms such mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) Tasmanian devil (Sarcophilus harrisii) bringing total number of supported to 61 release 64 (September 2011). Of these, 55 appear main website six are provided preview site (Pre!Ensembl; http://pre.ensembl.org)...
The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified May 2022 (refs.
The Ensembl project ( http://www.ensembl.org ) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations set of includes additional data focused variation, comparative, evolutionary, functional regulatory annotation. most advanced resources are provided for key including human, mouse, rat zebrafish...
The accumulation of adaptive mutations is essential for survival in novel environments. However, clonal populations with a high mutational supply, the power natural selection expected to be limited. This due interference - competition clones carrying different beneficial which leads loss many small effect and fixation large ones. If abundant, then mechanisms horizontal transfer genes, allow immediate combination alleles single background, are evolve. relevance complex environments, such as...
ABSTRACT Virtual environments (VEs) are now becoming a promising new technology to be used in the development of interactive learning for children. Perhaps triggered by success computer games, VEs seen as an emergent and engaging way which children can learn experimental sciences other disciplines. Inhabiting these IVEs agents or intelligent characters that responsible events happen environment make it not predictive completely controlled. However, build such environments, particular, if...
Abstract Cancer immunoediting is a dynamic process of crosstalk between tumor cells and the immune system. Herein, we explore fast zebrafish xenograft model to investigate innate contribution this process. Using multiple breast colorectal cancer cell lines zAvatars, find that some are cleared (regressors) while others engraft (progressors) in xenografts. We focus on two human derived from same patient show contrasting engraftment/clearance profiles. polyclonal xenografts mimic intra-tumor...
Pathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters investigate their relationships. Here, we combine genomic epidemiological data of the 2022 mpox outbreak better early viral spread, diversification transmission dynamics. By 52% confirmed cases in Portugal, identified virus sublineages with highest impact on case numbers fitted them into a global context, finding evidence that several international probably emerged or spread...
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of early infections, these methods are resource intensive require samples high viral DNA concentrations. Given atypical clinical presentation cases associated uncertainty regarding load across both course infection...
Abstract Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, transcription machinery fails to identify site continues transcribing beyond gene boundaries, phenomenon designated as readthrough. However, prevalence impact this healthy human tissues remain unexplored. Here, we assessed readthrough almost 3000 transcriptome profiles representing 23 found that 34% expressed protein-coding genes produced...
γδ T cells producing either interleukin-17A (γδ17 cells) or interferon-γ (γδIFN are generated in the mouse thymus, but molecular regulators of their peripheral functions not fully characterized. Here we established an Il17a-GFP:Ifng-YFP double-reporter strain to analyze at unprecedented depth transcriptomes pure γδ17 cell versus γδIFN populations from lymph nodes. Within a very high fraction differentially expressed genes, identify panel 20 new signature genes steady-state cells, which...
When building agents and synthetic characters, in order to achieve believability, we must consider the emotional relations established between users that is, issue of empathy. Defined broad terms as An observer reacting emotionally because he perceives another is experiencing or about experience an emotion, empathy important element creation humans agents. In this paper will focus on role construction providing some requirements for such illustrating presented concepts with a specific system...
Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks recent progress genomics imaging technologies, systemic approaches now used parallel with small-scale studies establish links between genomic information phenotypes, often described at subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets different scales into a global view developmental program. Here,...
New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. Ensembl project collects maintains the regulation data resources on epigenetic transcription factor binding methylation for human mouse, well microarray probe mappings annotations variety chordate...
Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics is the identification genetic clusters their characterization terms geotemporal spread or linkage to clinical demographic data. This task often consists visual exploration (large) phylogenetic trees associated metadata, being time-consuming difficult reproduce.
Drosophila syncytial nuclear divisions limit transcription unit size of early zygotic genes. As mitosis inhibits not only transcription, but also pre-mRNA splicing, we reasoned that constraints on splicing were likely to exist in the embryo, being avoidance a possible explanation why most genes are intronless. We isolated two mutant alleles for subunit NTC/Prp19 complexes, which specifically impaired maternally encoded transcripts. hypothesized requirements efficiency vary during...
Formation of the vertebrate postcranial body axis follows two sequential but distinct phases. The first phase generates pre-sacral structures (the so-called primary body) through activity primitive streak on axial progenitors within epiblast. embryo then switches to generate secondary (post-sacral structures), which depends in tail bud. Here we show that mammalian bud is generated an independent functional developmental module, concurrent functionally different from generating body. This...
Abstract Colorectal cancer (CRC) is a highly diverse disease, where different genomic instability pathways shape genetic clonal diversity and tumor microenvironment. Although intra-tumor heterogeneity has been characterized in primary tumors, its origin consequences CRC outcome not fully understood. Therefore, we assessed intra- inter-tumor of prospective cohort 136 samples. We demonstrate that forged by asynchronous forms molecular alterations, mutational chromosomal collectively boost...
Abstract We estimated comparative primary and booster vaccine effectiveness (VE) of SARS-CoV-2 Omicron BA.5 BA.2 lineages against infection disease progression. During April–June 2022, we implemented a case–case cohort study classified using whole-genome sequencing or spike gene target failure. For the study, adjusted odds ratios (aORs) vaccination logistic regression. VE progression penalized observed no reduced for (aOR 1.07 [95% CI 0.93–1.23]) 0.96 0.84–1.09]) infection. Among...
Abstract Background Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack bioinformatics tools and/or expertise. In order face this challenge, we have previously developed INSaFLU, a free web-based platform for virus next-generation sequencing data analysis. Here, considerably expanded its component new module (TELEVIR) metagenomic identification. Results The routine was strengthened with workflows functionalities, including...
<title>Abstract</title> Probe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance two Illumina probe-based panels, Respiratory Urinary Pathogen ID panels (RPIP UPIP), using 99 clinical samples from 15 different sample types (e.g., cerebrospinal fluid,...
Cognitive judgement bias in decision-making under ambiguity occurs both animals and humans, with some individuals interpreting ambiguous stimulus as positive (optimism) others negative (pessimism). We hypothesize that is a personality trait pessimistic would be more reactive to stressors therefore susceptible stress-related diseases than optimistic ones. Here, we show zebrafish judgment consistent behavioral over time, fish express phenotype-specific neurogenomic responses stress....
<title>Abstract</title> In 2024, unprecedented outbreaks of dengue virus (DENV) and Oropouche (OROV) were reported in Latin America the Caribbean. We describe a case co-infection with DENV serotype 3 OROV imported into Portugal from Cuba. RT-PCR next-generation sequencing confirmed presence both viruses 35-year-old male patient. Our findings highlight importance comprehensive multi-arbovirus diagnostics, particularly travelers regions experiencing concurrent outbreaks.
Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results hindering optimal communication at intersectoral international levels. Through a collaborative effort involving eleven European institutes spanning food, animal, human health sectors, we aimed to assess inter-pipeline clustering congruence across all resolution levels perform an in-depth comparative analysis...