Pedro G. Ferreira
A5089291118- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- RNA modifications and cancer
- Data Mining Algorithms and Applications
- Cancer-related molecular mechanisms research
- Algorithms and Data Compression
- Genetic Associations and Epidemiology
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Advanced Neuroimaging Techniques and Applications
- Genomics and Chromatin Dynamics
- Machine Learning in Bioinformatics
- Advanced MRI Techniques and Applications
- Gene expression and cancer classification
- Cardiovascular Function and Risk Factors
- Advanced Proteomics Techniques and Applications
- Anomaly Detection Techniques and Applications
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Single-cell and spatial transcriptomics
- Cardiac Imaging and Diagnostics
- Machine Learning in Materials Science
- Molecular Biology Techniques and Applications
- Genomics and Rare Diseases
Universidade do Porto
2010-2025
INESC TEC
2020-2025
Hospital of St. Francis Xavier
2023-2024
University of Lisbon
2024
i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto
2015-2023
Lusíada University of Lisbon
2021
University of Minho
2005-2020
National Laboratory of Energy and Geology
2020
Thermo Fisher Scientific (Sweden)
2020
University of Geneva
2013-2017
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these...
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue these is not yet available their characteristic localizations also poorly understood. Because RNA represents direct output genetic information encoded by genomes a significant proportion cell's regulatory capabilities focused on its synthesis, processing, transport, modification translation, generation such crucial for...
The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these...
Abstract Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy general robustness misspecified reference sets. We apply this framework 44 GTEx tissues 100+ from GWAS meta-analysis studies, creating growing public catalog of associations seeks capture the effects variation on human...
Expression, genetic variation, and tissues Human genomes show extensive variation across individuals, but we have only just started documenting the effects of this on regulation gene expression. Furthermore, a few been examined per variant. In order to examine how expression varies among within Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative traits that affect determined which these...
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate impact PMI on expression using data from multiple donors obtained GTEx project. find that many genes change over relatively short PMIs in tissue-specific manner, but this potentially confounding effect biological analysis be minimized taking into account...
Significance In eusocial insect societies, such as ants and some bees wasps, phenotypes are highly plastic, generating alternative (queens workers) from the same genome. The greatest plasticity is found in simple which individuals can switch between adults. genomic, transcriptional, epigenetic underpinnings of largely unknown. contrast to complex societies honeybee, we find that lack distinct transcriptional differentiation coherently patterned DNA methylomes. Instead, defined by subtle...
Abstract Aging is one of the most important biological processes and a known risk factor for many age-related diseases in human. Studying transcriptomic changes tissues across whole body can provide valuable information holistic understanding this fundamental process. In work, we catalogue gene expression nine from nearly two hundred individuals collected by Genotype-Tissue Expression (GTEx) project. general, find aging signatures are very tissue specific. However, enrichment some well-known...
Abstract Predicting the sensitivity of tumors to specific anti-cancer treatments is a challenge paramount importance for precision medicine. Machine learning(ML) algorithms can be trained on high-throughput screening data develop models that are able predict response cancer cell lines and patients novel drugs or drug combinations. Deep learning (DL) refers distinct class ML have achieved top-level performance in variety fields, including discovery. These types unique characteristics may make...
Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome -exome sequencing contributed to the characterization of mutational spectrum disease, but underlying transcriptional profile is still poorly understood. We have performed deep RNA in different subpopulations normal B-lymphocytes CLL cells from a cohort 98 patients, characterized landscape with unprecedented resolution. detected thousands elements differentially expressed between B cells,...
Understanding how alternative phenotypes arise from the same genome is a major challenge in modern biology. Eusociality insects requires evolution of two - workers, who sacrifice personal reproduction, and queens, realize that reproduction. Extensive work on honeybees ants has revealed molecular basis derived queen worker highly eusocial lineages, but we lack equivalent deep-level analyses wasps primitively species, latter which can reveal phenotypic decoupling first occurs early stages...
We make use of a large set fast simulations an intensity mapping experiment with characteristics similar to those expected the Square Kilometre Array (SKA) in order study viability and limits blind foreground subtraction techniques. In particular, we consider different approaches: polynomial fitting, principal component analysis (PCA) independent (ICA). review motivations algorithms for three methods, show that they can all be described, using same mathematical framework, as approaches...
Identification of genetic variants affecting splicing in RNA sequencing population studies is still its infancy. Splicing phenotype more complex than gene expression and ought to be treated as a multivariate recapitulated completely. Here we represent the pattern distribution relative abundances gene's alternative transcript isoforms. We develop statistical framework that uses distance-based approach compute variability ratios across observations, non-parametric analogue analysis variance....
Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework quantify contributions 21 traits as drivers gene expression alternative splicing across 46 tissues 781 individuals from Genotype-Tissue Expression project. demonstrate that ancestry, sex, age, BMI make additive tissue-specific variability, whereas interactions are rare. Variation in dominated by ancestry under genetic control most...
One of the main obstacles to successful treatment cancer is phenomenon drug resistance. A common strategy overcome resistance use combination therapies. However, space possibilities huge and efficient search strategies are required. Machine Learning (ML) can be a useful tool for discovery novel, clinically relevant anti-cancer combinations. In particular, deep learning (DL) has become popular choice modeling effects. Here, we set out examine impact different methodological choices on...
The understanding of soil-geosynthetic interaction under cyclic loading conditions is essential for the safe design geosynthetic-reinforced soil structures subjected to repeated loads, such as those induced by road and railway traffic earthquakes. This paper describes a series large-scale monotonic multistage pullout tests carried out investigate behaviour an HDPE uniaxial geogrid embedded in locally available granite residual loading. effects load level at start stage, frequency amplitude,...