e-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs. - Joana P. Gonçalves; Sara C. Madeira (IWPACBB, 2010)

Network-Based Disease Candidate Gene Prioritization: Towards Global Diffusion in Heterogeneous Association Networks. - Joana P. Gonçalves; Sara C. Madeira; Yves Moreau (NyNaK, 2010)

Candidate gene prioritization by network analysis of differential expression using machine learning approaches. - Daniela Nitsch; Joana P. Gonçalves; Fabian Ojeda; Bart De Moor; Yves Moreau (BMC Bioinform., 2010)

TFRank: network-based prioritization of regulatory associations underlying transcriptional responses. - Joana P. Gonçalves; Alexandre P. Francisco; Nuno P. Mira; Miguel C. Teixeira; Isabel Sá-Correia; Arlindo L. Oliveira; Sara C. Madeira (Bioinform., 2011)

PINTA: a web server for network-based gene prioritization from expression data. - Daniela Nitsch; Léon-Charles Tranchevent; Joana P. Gonçalves; Josef Korbinian Vogt; Sara C. Madeira; Yves Moreau (Nucleic Acids Res., 2011)

AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences. - Joana P. Gonçalves; Yves Moreau; Sara C. Madeira (Int. J. Data Min. Bioinform., 2012)

Heuristic approaches for time-lagged biclustering. - Joana P. Gonçalves; Sara C. Madeira (BIOKDD, 2013)

Predicting disease associations via biological network analysis. - Kai Sun 005; Joana P. Gonçalves; Chris Larminie; Natasa Przulj (BMC Bioinform., 2014)

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. - Miguel Cacho Teixeira; Pedro Tiago Monteiro 001; Joana Fernandes Guerreiro; Joana Pinho Gonçalves; Nuno Pereira Mira; Sandra Costa dos Santos; Tânia Rodrigues Cabrito; Margarida Palma; Catarina Costa; Alexandre Paulo Francisco; Sara Cordeiro Madeira; Arlindo Limede Oliveira; et al. (Nucleic Acids Res., 2014)

LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification. - Joana P. Gonçalves; Sara C. Madeira (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Overcoming selection bias in synthetic lethality prediction. - Colm Seale; Yasin Tepeli; Joana P. Gonçalves (Bioinform., 2022)

DCAST: Diverse Class-Aware Self-Training Mitigates Selection Bias for Fairer Learning. - Yasin Tepeli; Joana P. Gonçalves (CoRR, 2024)

Metric-DST: Mitigating Selection Bias Through Diversity-Guided Semi-Supervised Metric Learning. - Yasin Tepeli; Mathijs de Wolf; Joana P. Gonçalves (CoRR, 2024)