
Joana P. GonçalvesDelft University of Technology | TU · Department of Intelligent Systems
Joana P. Gonçalves
Ph.D. Computer Science
About
25
Publications
4,136
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Citations
Introduction
Additional affiliations
October 2014 - July 2017
October 2014 - July 2017
September 2013 - August 2014
Education
October 2007 - January 2013
September 2005 - February 2006
September 2002 - July 2007
Publications
Publications (25)
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem c...
Motivation
Synthetic lethality (SL) between two genes occurs when simultaneous loss-of-function leads to cell death. This holds great promise for developing anti-cancer therapeutics that target synthetic lethal pairs of endogenously disrupted genes. Identifying novel SL relationships through exhaustive experimental screens is challenging, due to th...
Motivation
Anti-cancer therapies based on synthetic lethality (SL) exploit tumour vulnerabilities for treatment with reduced side effects, by targeting a gene that is jointly essential with another whose function is lost. Computational prediction is key to expedite SL screening, yet existing methods are vulnerable to prevalent selection bias in SL...
Fairness in machine learning seeks to mitigate model bias against individuals based on sensitive features such as sex or age, often caused by an uneven representation of the population in the training data due to selection bias. Notably, bias unascribed to sensitive features is challenging to identify and typically goes undiagnosed, despite its pro...
Motivation
Many tumours show deficiencies in DNA damage response (DDR), which influence tumorigenesis and progression, but also expose vulnerabilities with therapeutic potential. Assessing which patients might benefit from DDR-targeting therapy requires knowledge of tumour DDR deficiency status, with mutational signatures reportedly better predicto...
Motivation
Understanding the factors involved in DNA double-strand break (DSB) repair is crucial for the development of targeted anti-cancer therapies, yet the roles of many genes remain unclear. Recent studies show that perturbations of certain genes can alter the distribution of sequence-specific mutations left behind after DSB repair. This sugge...
Selection bias poses a critical challenge for fairness in machine learning, as models trained on data that is less representative of the population might exhibit undesirable behavior for underrepresented profiles. Semi-supervised learning strategies like self-training can mitigate selection bias by incorporating unlabeled data into model training t...
The Human BioMolecular Atlas Program (HuBMAP) aims to create a spatial atlas of the healthy human body at single cell resolution by applying advanced technologies and disseminating resources to the community. As HuBMAP moves past its first phase creating ontologies, protocols, and pipelines, this Perspective introduces the production phase: to gene...
Anti-cancer therapies based on synthetic lethality (SL) exploit tumour vulnerabilities for treatment with reduced side effects. Since simultaneous loss-of-function of SL genes causes cell death, tumours with known gene disruptions can be treated by targeting SL partners. Computational selection of promising SL candidates amongst all gene combinatio...
Understanding the relationship between diseases based on the underlying biological mechanisms is one of the greatest challenges in modern biology and medicine. Exploring disease-disease associations by using system-level biological data is expected to improve our current knowledge of disease relationships, which may lead to further improvements in...
Identifying patterns in temporal data is key to uncover meaningful relationships in diverse domains, from stock trading to social interactions. Also of great interest are clinical and biological applications, namely monitoring patient response to treatment or characterizing activity at the molecular level. In biology, researchers seek to gain insig...
The YEASTRACT (http://www.yeastract.com) information system is a tool for the analysis and prediction of transcription regulatory associations in Saccharomyces cerevisiae. Last updated in June 2013, this database contains over 200 000 regulatory associations between transcription factors (TFs)
and target genes, including 326 DNA binding sites for 1...
Identifying patterns in temporal data supports complex analyses in several domains, including stock markets (finance) and social interactions (social science). Clinical and biological applications, such as monitoring patient response to treatment or characterizing activity at the molecular level, are also of interest. In particular, researchers see...
Disease gene prioritization aims to suggest potential implications of genes in disease susceptibility. Often accomplished in a guilt-by-association scheme, promising candidates are sorted according to their relatedness to known disease genes. Network-based methods have been successfully exploiting this concept by capturing the interaction of genes...
Transcription Factors (TFs) control transcription by binding to specific sites in the promoter regions of the target genes, which can be modelled by structured motifs. In this paper we propose AliBiMotif, a method combining sequence alignment and a biclustering approach based on efficient string matching techniques using suffix trees to unravel app...
Explaining regulatory mechanisms is crucial to understand complex cellular responses leading to system perturbations. Some strategies reverse engineer regulatory interactions from experimental data, while others identify functional regulatory units (modules) under the assumption that biological systems yield a modular organization. Most modular stu...
Motivation:
Uncovering mechanisms underlying gene expression control is crucial to understand complex cellular responses. Studies in gene regulation often aim to identify regulatory players involved in a biological process of interest, either transcription factors coregulating a set of target genes or genes eventually controlled by a set of regula...
PINTA (available at http://www.esat.kuleuven.be/pinta/; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. Our strategy is meant for biological and m...
Discovering novel disease genes is still challenging for diseases for which no prior knowledge--such as known disease genes or disease-related pathways--is available. Performing genetic studies frequently results in large lists of candidate genes of which only few can be followed up for further investigation. We have recently developed a computatio...
Transcription factors control transcription by binding to specific sites in the DNA sequences of the target genes, which can
be modeled by structured motifs. In this paper, we propose e-BiMotif, a combination of both sequence alignment and a biclustering approach relying on efficient string matching techniques
based on suffix trees to unravel all a...
Disease candidate gene prioritization addresses the association of novel genes with disease susceptibility or progression. Networkbased approaches explore the connectivity properties of biological networks to compute an association score between candidate and diseaserelated genes. Although several methods have been proposed to date, a number of con...
The ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using expression time series, is critical to advance our understanding of complex biological processes. Biclustering has been recognized as an effective method for discovering local temporal expression patterns and unraveling...
Polar Mapper is a computational application for exposing the architecture of protein interaction networks. It facilitates the system-level analysis of mRNA expression data in the context of the underlying protein interaction network. Preliminary analysis of a human protein interaction network and comparison of yeast oxidative stress and heat shock...
Polar Mapper is a computational application for exposing the architecture of protein interaction networks. It facilitates the system-level analysis of mRNA expression data in the context of the underlying protein interaction network. Preliminary analysis of a human protein interaction network and comparison of the yeast oxidative stress and heat sh...