Santiago Gisler, Joana P. Gonçalves, Waseem Akhtar, Johann de Jong, Alexey V. Pindyurin, Lodewyk F.A. Wessels, Maarten van Lohuizen (2019), Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency, In Nature Communications Volume 10 p.1-14.

Joana P. Gonçalves, Sara Cordeiro Madeira (2014), LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification, In IEEE - ACM Transactions on Computational Biology and Bioinformatics Volume 11 p.801-813.

Kai Sun, Joana P. Gonçalves, Chris Larminie, Nataša Pržulj (2014), Predicting disease associations via biological network analysis, In BMC Bioinformatics Volume 15 p.1-13.

Miguel Cacho Teixeira, Pedro Tiago Monteiro, Joana Fernandes Guerreiro, Joana Pinho Goncalves, Nuno Pereira Mira, Sandra Costa dos Santos, Tania Rodrigues Cabrito, Margarida Palma, Catarina Costa, Alexandre Paulo Francisco, Sara Cordeiro Madeira, Arlindo Limede Oliveira, Ana Teresa Freitas, Isabel Sa-Correia (2014), The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae, In Nucleic Acids Research Volume 42 p.D161-D166.

Joana P. Gonçalves, Sara C. Madeira (2013), Heuristic approaches for time-lagged biclustering, In Proc. of the 12th Int. Workshop on Data Mining in Bioinformatics, BIOKDD 2013 - Held in Conj. with the 19th ACM SIGKDD Int. Conf. on Knowledge Discovery and Data Mining, SIGKDD 2013 p.1-9, ACM.

Joana P. Goncalves, Yves Moreau, Sara C. Madeira (2012), AliBiMotif: Integrating alignment and biclustering to unravel Transcription Factor Binding Sites in DNA sequences, In International Journal of Data Mining and Bioinformatics Volume 6 p.196-215.

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.