Ongoing projects and articles in preparation:
- methodological, with Lodewyk Wessels
- methodology: a novel framework to identify mechanisms of transcriptional regulation involving potential activation delays from temporal transcriptomes and regulatory networks;
- methodological, with Sara Madeira
- methodology: a novel triclustering algorithm for discovery of local aligned patterns from 3D temporal data;
- technological, with Sara Madeira
- software: an upgraded version of the BIGGESTS software including the LateBiclustering algorithm;
- biological, with Lodewyk Wessels in collaboration with Wilbert Zwart (Netherlands Cancer Institute)
- application: study of androgen response in prostate cancer, identification of new therapeutic targets;
- methodology: independent experimental and computational identification of mechanisms of transcriptional regulation with temporal delays;
- preliminary results: notable concordance between mechanisms described in the literature, wet-lab experiments and computational predictions; experimental validation of novel computationally identified mechanisms.
Gonçalves JP and Madeira SC (2014) LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(5):801-813.
Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP, dos Santos SC, Cabrito TR, Palma M, Costa C, Francisco AP, Madeira SC, Oliveira AL, Freitas AT and Sá-Correia I (2014) The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae, Nucleic Acids Research, 42(D1):D161-D166.
Sun K, Gonçalves JP, Larminie C and Przulj N (2014) Predicting disease associations via biological network analysis, BMC Bioinformatics, 15(1):304.
Gonçalves JP, Francisco AP, Moreau Y, and Madeira SC (2012) Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores, PLoS ONE, 11(7):e49634.
Gonçalves JP, Francisco AP, Aires RS and Madeira SC (2012) Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks, PLoS ONE, 7(5):e35977.
Gonçalves JP, Moreau Y and Madeira SC (2012) AliBiMotif: Integrating sequence alignment and biclustering to unravel transcription factor binding sites in DNA sequences, International Journal on Data Mining and Bioinformatics, 6(2):196-215.
Gonçalves JP, Francisco AP, Mira NP, Teixeira MC, Sá-Correia I, Oliveira AL and Madeira SC (2011) TFRank: network-based prioritization of regulatory associations underlying transcriptional responses, Bioinformatics, 27(22):3149-3157.
Nitsch D, Tranchevent L-C, Gonçalves JP, Vogt JK, Madeira SC and Moreau Y (2011) PINTA: a web server for network-based gene prioritization from expression data, Nucleic Acids Research, 39(Web server issue):W334-W338.
Nitsch D, Gonçalves JP, Ojeda F, De Moor B and Moreau Y (2010) Candidate gene prioritization by network analysis of differential expression using machine learning approaches, BMC Bioinformatics, 11:460.
Gonçalves JP, Grãos M and Valente AXCN (2009) Polar Mapper: a computational tool for integrated visualization of protein interaction networks and mRNA expression data, Journal of the Royal Society Interface, 6(39):881-896.
Gonçalves JP and Madeira SC, Heuristic approaches for time-lagged biclustering, Proc. of the Twelfth International Workshop on Data Mining and Bioinformatics (BIOKDD 2013), ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Chicago (KDD 2013), IL, EUA, August 11, 2013.
Gonçalves JP, Madeira SC and Moreau Y, Network-based disease candidate gene prioritization: towards global diffusion in heterogeneous association networks, Proc. of the First International Workshop on Dynamic Networks and Knowledge Discovery (DyNaK 2010), European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD 2010), Barcelona, Spain, September 24, 2010.
Gonçalves JP and Madeira SC (2010) e-BiMotif: Combining sequence alignment and biclustering to unravel structured motifs, Proc. of the Fourth International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), Advances in Bioinformatics, Springer Series Advances in Soft Computing, 74:181-191.
Gonçalves JP (2013) Integrative mining of gene regulation and its perturbations, Ph.D. Thesis, Instituto Superior Técnico, Universidade Técnica de Lisboa, Portugal. Not publicly available, as one chapter is yet to be submitted for publication.
Gonçalves JP (2007) BiGGEsTS - BiclusterinG Gene Expression Time Series, Diploma Thesis, Department of Computer Science and Engineering, Faculty of Engineering, University of Beira Interior, Portugal.
Gonçalves JP and Madeira SC, Heuristic discovery of time-lagged biclusters in gene expression time series, Twelfth Asia-Pacific Bioinformatics Conference (APBC 2014), Xangai, China, 17-19 de Janeiro, 2014.
Gonçalves JP and Madeira SC, Time-coherent triclustering: mining local transcriptional patterns in multiple expression time series, Tenth Asia-Pacific Bioinformatics Conference (APBC 2012), Melbourne, Australia, January 17-19, 2012. Best poster award, selected for oral presentation
Gonçalves JP, Moreau Y and Madeira SC, Time coherent three-dimensional clustering: unraveling local transcriptional patterns in multiple gene expression time series, Ninth European Conference on Computational Biology (ECCB 2010), Ghent, Belgium, September 26-29, 2010.
Brohée S, Gonçalves JP, Nitsch D and Moreau Y, Beegle - a new search engine for discovering novel genes, Ninth European Conference on Computational Biology (ECCB 2010), Ghent, Belgium, September 26-29, 2010.
Gonçalves JP, Madeira SC and Moreau Y, Network-based disease gene prioritization: Are functional associations a promising alternative to protein-protein interactions?, Fourteenth International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, August 12-15, 2010.
Francisco AP, Gonçalves JP and Madeira SC, TFRank: A framework to unravel relevant regulations in regulatory networks using diffusion ranking, Fourteenth International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, August 12-15, 2010.
Nitsch D, Gonçalves JP, Ojeda F and Moreau Y, Prioritizing candidate genes by network analysis of differential expression using machine learning approaches, Fourteenth International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, August 12-15, 2010.
Gonçalves JP, Grãos and Valente AXCN, Polar Mapper: software tool for integrated visualization of protein interaction networks and mRNA expression data, Ninth International Conference on Systems Biology (ICSB 2008), Gothenburg, Sweden, August 23-27, 2008.