Joana P. Goncalves, Alexandre P. Francisco, Yves Moreau, Sara C. Madeira (2012), Interactogeneous: Disease Gene Prioritization Using Heterogeneous Networks and Full Topology Scores, In PLoS ONE Volume 7 p.1-13.

Joana P. Gonçalves, Ricardo S. Aires, Alexandre P. Francisco, Sara C. Madeira (2012), Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks, In PLoS ONE Volume 7.

Daniela Nitsch, Léon-Charles Tranchevent, Joana P. Goncalves, Josef Korbinian Vogt, Sara C. Madeira, Yves Moreau (2011), PINTA: A web server for network-based gene prioritization from expression data, In Nucleic Acids Research Volume 39 p.W334-W338.

Joana P. Goncalves, Alexandre P. Francisco, Nuno P. Mira, Miguel C. Teixeira, Isabel Sá-Correia, Arlindo L. Oliveira, Sara C. Madeira (2011), TFRank: Network-based prioritization of regulatory associations underlying transcriptional responses, In Bioinformatics Volume 27 p.3149-3157.

Daniela Nitsch, Joana P. Goncalves, Fabian Ojeda, Bart de Moor, Yves Moreau (2010), Candidate gene prioritization by network analysis of differential expression using machine learning approaches, In BMC Bioinformatics Volume 11 p.1-16.

Joana P. Gonçalves, Sara C. Madeira, Yves Moreau (2010), Network-based disease candidate gene prioritization: Towards global diffusion in heterogeneous association networks, In CEUR Workshop Proceedings p.53-64.

Joana P. Goncalves, Sara Cordeiro Madeira (2010), e-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs, In Advances in Bioinformatics p.181-191.

Joana P. Gonçalves, Sara C. Madeira, Arlindo L. Oliveira (2009), BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data, In BMC Research Notes Volume 2.

Joana P. Goncalves, Mário Grãos, Andre X. C. N. Valente (2009), POLAR MAPPER: A computational tool for integrated visualization of protein interaction networks and mRNA expression data, In Journal of the Royal Society Interface Volume 6 p.881-896.