Software

G-Tric: generating three-way synthetic datasets with triclustering solution

BicPAMS: Software for Biological Data Analysis with Pattern-based Biclustering

BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

João Lobo and Rui Henriques and Sara C. Madeira, G-Tric: generating three-way synthetic datasets with triclustering solution, BMC Bioinformatics, 22(16), Jan. 2021, BioMed Central. [DOI Article link]

Rui Henriques and Sara C. Madeira, BicPAMS: Software for Biological Data Analysis with Pattern-based Biclustering, BMC Bioinformatics, 18(82), Fev. 2017, BioMed Central. [DOI Article link]

Miguel Teixeira and Pedro T. Monteiro and Joana Guerreiro and Joana Gonçalves and Nuno Mira and Sandra dos Santos and Tânia Cabrito and Margarida Palma and Catarina Costa and A. P. Francisco and Sara C. Madeira and Arlindo L. Oliveira and Ana T. Freitas and Isabel Sá-Correia, The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae, Nucleic Acids Research , 42(1), pp. D1-D6, Jan. 2014. [DOI Article link]

Daniela Nitsch and Léon-Charles Tranchevent and Joana P. Gonçalves and Josef Korbinian Vogt and Sara C. Madeira and Yves Moreau, PINTA: a web server for network-based gene prioritization from expression data, Nucleic Acids Research, 39(), pp. W334-W338, Jul. 2011, Oxford University Press. [DOI Article link]

Dario Abdulrehman and Pedro T. Monteiro and Miguel C. Teixeira and Nuno P. Mira and Artur B. Lourenço and Sónia C. dos Santos and Tânia R. Cabrito and A. P. Francisco and Sara C. Madeira and Ricardo Rubén dos Santos Aires and Arlindo L. Oliveira and Isabel Sá-Correia and Ana T. Freitas, YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface, Nucleic Acids Research, 39(1), pp. D136-D140, Jan. 2011, Oxford Journals. [DOI Article link]

Ignacio Medina and Jose Carbonell and Luis Pulido and Sara C. Madeira and Stefan Goetz and Ana Conesa and Joaquin Tarraga and Alberto Pascual-Montano and Ruben Nogales-Cadenas and Javier Santoyo and Francisco Garcia and Martina Marba and David Montaner and Joaquin Dopazo, Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling, Nucleic Acids Research, 38(), pp. W210-W213, Jul. 2010, Oxford Journals. [DOI Article link][bibTeX]

Joana P. Gonçalves and Sara C. Madeira and Arlindo L. Oliveira, BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data, BMC Research Notes, 2(124), pp. , Jul. 2009, BioMed Central. [DOI Article link]