Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine Basta, Mark S. Keller, Joana P. Gonçalves, L.G. Migas, Raf Van de Plas, R. Lardenoije, More Authors (2024), The chromatin landscape of healthy and injured cell types in the human kidney, In Nature Communications Volume 15.

Sanjay Jain, Liming Pei, Jeffrey M. Spraggins, Michael Angelo, James P. Carson, Niels Gehlenborg, Fiona Ginty, Joana P. Gonçalves, Raf Van de Plas, More Authors (2023), Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP), In Nature Cell Biology Volume 25 p.1089-1100.

Y.I. Tepeli, C.F. Seale, Joana P. Gonçalves (2023), ELISL: early-late integrated synthetic lethality prediction in cancer, In Bioinformatics Volume 40.

Colm Seale, Yasin Tepeli, Joana P. Gonçalves (2022), Overcoming Selection Bias in Synthetic Lethality Prediction, In Bioinformatics Volume 38 p.4360–4368.

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, Association for Computing Machinery (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.