15 documents found, page 1 of 2
Forecasting biotoxin contamination in mussels across production areas of the Po...
Cruz, Rafaela C.; Reis Costa, Pedro; Krippahl, Ludwig; Lopes, Marta B.Harmful algal blooms (HABs) and the consequent contamination of shellfish are complex processes depending on several biotic and abiotic variables, turning prediction of shellfish contamination into a challenging task. Not only the information of interest is dispersed among multiple sources, but also the complex temporal relationships between the time-series variables require advanced machine methods to model su...
Time-lagged correlation analysis of Shellfish toxicity reveals predictive links...
Patrício, André; Lopes, Marta B.; Reis Costa, Pedro; Costa, Rafael S.; Henriques, Rui; Vinga, SusanaDiarrhetic Shellfish Poisoning (DSP) is an acute intoxication caused by the consumption of contaminated shellfish, which is common in many regions of the world. To safeguard human health, most countries implement programs focused on the surveillance of toxic phytoplankton abundance and shellfish toxicity levels, an effort that can be complemented by a deeper understanding of the underlying phenomena. In this wo...
The role of network science in glioblastoma
Lopes, Marta B.; Martins, Eduarda P.; Vinga, Susana; Costa, Bruno MarquesNetwork science has long been recognized as a well-established discipline across many biological domains. In the particular case of cancer genomics, network discovery is challenged by the multitude of available high-dimensional heterogeneous views of data. Glioblastoma (GBM) is an example of such a complex and heterogeneous disease that can be tackled by network science. Identifying the architecture of molecula...
A review of recent machine learning advances for forecasting harmful Algal Bloo...
Cruz, Rafaela C.; Reis Costa, Pedro; Vinga, Susana; Krippahl, Ludwig; Lopes, Marta B.Harmful algal blooms (HABs) are among the most severe ecological marine problems worldwide. Under favorable climate and oceanographic conditions, toxin-producing microalgae species may proliferate, reach increasingly high cell concentrations in seawater, accumulate in shellfish, and threaten the health of seafood consumers. There is an urgent need for the development of effective tools to help shellfish farmers...
TCox : correlation-based regularization applied to colorectal cancer survival data
Peixoto, Carolina; Lopes, Marta B.; Martins, Marta; Costa, Luis; Vinga, SusanaColorectal cancer (CRC) is one of the leading causes of mortality and morbidity in the world. Being a heterogeneous disease, cancer therapy and prognosis represent a significant challenge to medical care. The molecular information improves the accuracy with which patients are classified and treated since similar pathologies may show different clinical outcomes and other responses to treatment. However, the high...
Twiner: correlation-based regularization for identifying common cancer gene sig...
Lopes, Marta B.; Casimiro, Sandra; Vinga, SusanaBackground: Breast and prostate cancers are typical examples of hormone-dependent cancers, showing remarkable similarities at the hormone-related signaling pathways level, and exhibiting a high tropism to bone. While the identification of genes playing a specific role in each cancer type brings invaluable insights for gene therapy research by targeting disease-specific cell functions not accounted so far, ident...
Robust identification of target genes and outliers in triple-negative breast ca...
Segaert, Pieter; Lopes, Marta B.; Casimiro, Sandra; Vinga, Susana; Rousseeuw, Peter J.Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal. Our analysis i...
Ensemble outlier detection and gene selection in triple-negative breast cancer ...
Lopes, Marta B.; Veríssimo, André; Carrasquinha, Eunice; Casimiro, Sandra; Beerenwinkel, Niko; Vinga, SusanaBackground: Learning accurate models from 'omics data is bringing many challenges due to their inherent high-dimensionality, e.g. the number of gene expression variables, and comparatively lower sample sizes, which leads to ill-posed inverse problems. Furthermore, the presence of outliers, either experimental errors or interesting abnormal clinical cases, may severely hamper a correct classification of patients...
Monitoring the ex-vivo expansion of human mesenchymal stem/stromal cells in xen...
Rosa, Filipa; Sales, Kevin C.; Carmelo, Joana G.; Fernandes-Platzgummer, Ana; Silva, Cláudia L. da; Lopes, Marta B.; Calado, CecíliaHuman mesenchymal stem/stromal cells (MSCs) have received considerable attention in the field of cell-based therapies due to their high differentiation potential and ability to modulate immune responses. However, since these cells can only be isolated in very low quantities, successful realization of these therapies requires MSCs ex-vivo expansion to achieve relevant cell doses. The metabolic activity is one of...
A comprehensive high-throughput FTIR spectroscopy-based method for evaluating t...
Rosa, Filipa; Sales, Kevin C.; Cunha, Bernardo R.; Couto, Andreia; Lopes, Marta B.; Calado, CecíliaReporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the ...