Sara C. Madeira

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Arlindo L OliveiraDistinguished Professor, Instituto Superior Técnico / INESC-IDVerified email at tecnico.ulisboa.pt
Rui HenriquesAssistant Professor at IST, Associate Researcher at INESC-IDVerified email at tecnico.ulisboa.pt
Joana P. GonçalvesAssistant Professor at TUDelftVerified email at joanagoncalves.org
Isabel Sá-CorreiaDistinguished Professor, Instituto Superior Técnico, Universidade de Lisboa and iBBVerified email at tecnico.ulisboa.pt
Mamede de CarvalhoFaculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, PortugalVerified email at fm.ul.pt
Miguel Cacho TeixeiraAssociate professor with Habilitation, Bioengineering Dept, Instituto Superior Técnico, UniversidadeVerified email at tecnico.ulisboa.pt
Susana PintoTranslational and Clinical Physiology Unit, Instituto de Medicina Molecular, Lisboa, PortugalVerified email at sapo.pt
Nuno P. MiraAssistant Professor, Instituto Superior TécnicoVerified email at ist.utl.pt
André V. CarreiroFraunhofer Portugal - AICOSVerified email at fraunhofer.pt
m gromichoInstituto Medicina MolecularVerified email at medicina.ulisboa.pt
Claudia AntunesAssociate Professor of Computer Science and Engineering, Instituto Superior TecnicoVerified email at tecnico.ulisboa.pt
Telma PereiraInstituto Superior Técnico & LASIGE, Universidade de LisboaVerified email at ist.utl.pt
Pedro T. MonteiroINESC-ID / IST - Universidade de LisboaVerified email at tecnico.ulisboa.pt
Yves MoreauUniversity of LeuvenVerified email at esat.kuleuven.be
Joaquin DopazoHead of the Clinical Bioinformatics Area, FPS, Hospital Virgen del Rocio, Sevilla, SpainVerified email at juntadeandalucia.es
Joao Miguel C. SousaIDMEC, Instituto Superior Técnico, Universidade de Lisboa, PortugalVerified email at tecnico.ulisboa.pt
Sofia PiresLASIGEVerified email at lasige.di.fc.ul.pt
Pedro TomásINESC-ID, Instituto Superior Técnico, Universidade de LisboaVerified email at inesc-id.pt
Alexandra M CarvalhoAssistant Professor, Instituto Superior Técnico, Technical University of LisbonVerified email at tecnico.ulisboa.pt
João André CarriçobioMérieux Industry and Researcher, Faculty of Medicine, University of LisbonVerified email at fm.ul.pt

Sara C. Madeira

Associate Professor,LASIGE,Departamento de Informática,Faculdade de Ciências,Universidade de Lisboa

Verified email at fc.ul.pt - Homepage

Data Science Data Mining Machine Learning Bioinformatics Biomedical Informatics


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Biclustering algorithms for biological data analysis: a survey SC Madeira, AL Oliveira IEEE/ACM transactions on computational biology and bioinformatics 1 (1), 24-45, 2004	2569	2004
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling I Medina, J Carbonell, L Pulido, SC Madeira, S Goetz, A Conesa, ... Nucleic acids research 38 (suppl_2), W210-W213, 2010	357	2010
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae MC Teixeira, PT Monteiro, JF Guerreiro, JP Gonçalves, NP Mira, ... Nucleic acids research 42 (D1), D161-D166, 2014	266	2014
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface D Abdulrehman, PT Monteiro, MC Teixeira, NP Mira, AB Lourenco, ... Nucleic acids research 39 (suppl_1), D136-D140, 2010	226	2010
Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm SC Madeira, MC Teixeira, I Sa-Correia, AL Oliveira IEEE/ACM Transactions on Computational Biology and Bioinformatics 7 (1), 153-165, 2008	135	2008
BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data JP Gonçalves, SC Madeira, AL Oliveira BMC research notes 2 (1), 1-11, 2009	82	2009
PINTA: a web server for network-based gene prioritization from expression data D Nitsch, LC Tranchevent, JP Goncalves, JK Vogt, SC Madeira, Y Moreau Nucleic acids research 39 (suppl_2), W334-W338, 2011	76	2011
BicPAM: Pattern-based biclustering for biomedical data analysis R Henriques, SC Madeira Algorithms for Molecular Biology 9 (1), 1-30, 2014	74	2014
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series SC Madeira, AL Oliveira Algorithms for Molecular Biology 4 (1), 1-39, 2009	74	2009
A linear time biclustering algorithm for time series gene expression data SC Madeira, AL Oliveira Algorithms in Bioinformatics, 39-52, 2005	71	2005
A structured view on pattern mining-based biclustering R Henriques, C Antunes, SC Madeira Pattern Recognition 48 (12), 3941-3958, 2015	64	2015
Triclustering algorithms for three-dimensional data analysis: A comprehensive survey R Henriques, SC Madeira ACM Computing Surveys (CSUR) 51 (5), 95, 2018	53	2018
BicPAMS: Software for biological data analysis with pattern-based biclustering R Henriques, FL Ferreira, SC Madeira BMC Bioinformatics 18 (1), 82, 2017	53	2017
BicSPAM: Flexible biclustering using sequential patterns R Henriques, SC Madeira BMC bioinformatics 15 (1), 130, 2014	49	2014
BicNET: flexible module discovery in large-scale biological networks using biclustering R Henriques, SC Madeira Algorithms for Molecular Biology 11 (1), 1-30, 2016	42	2016
Predicting progression of mild cognitive impairment to dementia using neuropsychological data: A supervised learning approach using time windows T Pereira, L Lemos, S Cardoso, D Silva, A Rodrigues, I Santana, ... BMC Medical Informatics and Decision Making 17 (1), 110, 2017	36	2017
Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores JP Gonçalves, AP Francisco, Y Moreau, SC Madeira PloS one 7 (11), e49634, 2012	34	2012
BSig: Evaluating the statistical significance of biclustering solutions R Henriques, SC Madeira Data Mining and Knowledge Discovery 32 (1), 124-161, 2018	32	2018
Comparison of target selection methods in direct marketing S Madeira, JM Sousa European symposium on intelligent technologies, hybrid systems and their …, 2002	31	2002
Prognostic models based on patient snapshots and time windows: Predicting disease progression to assisted ventilation in Amyotrophic Lateral Sclerosis AV Carreiro, PMT Amaral, S Pinto, P Tomás, M de Carvalho, SC Madeira Journal of biomedical informatics 58, 133-144, 2015	27	2015

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