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
Mamede de CarvalhoFaculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, PortugalVerified email at fm.ul.pt
m gromichoInstituto Medicina MolecularVerified email at medicina.ulisboa.pt
Joana P. GonçalvesAssistant Professor at TU DelftVerified email at tudelft.nl
Helena AidosLASIGE, Dep. Informática, Faculdade de Ciências, Universidade de LisboaVerified email at fc.ul.pt
Isabel Sá-CorreiaDistinguished Professor, Instituto Superior Técnico, Universidade de Lisboa and iBBVerified email at tecnico.ulisboa.pt
Susana PintoTranslational and Clinical Physiology Unit, Instituto de Medicina Molecular, Lisboa, PortugalVerified email at sapo.pt
Miguel Cacho TeixeiraFull Professor of Biological Sciences, Bioengineering Dept, Instituto Superior Técnico, UniversidadeVerified email at tecnico.ulisboa.pt
André V. CarreiroFraunhofer Portugal - AICOSVerified email at fraunhofer.pt
Nuno P. MiraAssistant Professor, Instituto Superior TécnicoVerified email at ist.utl.pt
Diogo F. SoaresLASIGE, Informática, Faculdade de Ciências, Universidade de LisboaVerified email at ciencias.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
Eduardo N. CastanhoLASIGE, Informática, Faculdade de Ciências, Universidade de LisboaVerified email at fc.ul.pt
Pedro T. MonteiroINESC-ID / IST - Universidade de LisboaVerified email at tecnico.ulisboa.pt
Yves MoreauUniversity of LeuvenVerified email at esat.kuleuven.be
Pedro TomásINESC-ID, Instituto Superior Técnico, Universidade de LisboaVerified email at inesc-id.pt
Sofia PiresLASIGEVerified email at lasige.di.fc.ul.pt
Alexandra M CarvalhoAssistant Professor, Instituto Superior Técnico, Technical University of LisbonVerified email at tecnico.ulisboa.pt

Sara C. Madeira

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

Verified email at fc.ul.pt - Homepage

Machine Learning Data Mining Biomedical Informatics Bioinformatics Biclustering & Triclustering


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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	2719	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	365	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	283	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	241	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, 2010	147	2010
BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data JP Gonçalves, SC Madeira, AL Oliveira BMC research notes 2, 1-11, 2009	93	2009
BicPAM: Pattern-based biclustering for biomedical data analysis R Henriques, SC Madeira Algorithms for Molecular Biology 9, 1-30, 2014	92	2014
A structured view on pattern mining-based biclustering R Henriques, C Antunes, SC Madeira Pattern Recognition 48 (12), 3941-3958, 2015	86	2015
Triclustering algorithms for three-dimensional data analysis: A comprehensive survey R Henriques, SC Madeira ACM Computing Surveys (CSUR) 51 (5), 95, 2018	84	2018
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	80	2011
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series SC Madeira, AL Oliveira Algorithms for Molecular Biology 4, 1-39, 2009	78	2009
BicPAMS: Software for biological data analysis with pattern-based biclustering R Henriques, FL Ferreira, SC Madeira BMC Bioinformatics 18 (1), 82, 2017	75	2017
A linear time biclustering algorithm for time series gene expression data SC Madeira, AL Oliveira Algorithms in Bioinformatics, 39-52, 2005	74	2005
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	56	2017
BicSPAM: Flexible biclustering using sequential patterns R Henriques, SC Madeira BMC bioinformatics 15 (1), 130, 2014	54	2014
BSig: Evaluating the statistical significance of biclustering solutions R Henriques, SC Madeira Data Mining and Knowledge Discovery 32 (1), 124-161, 2017	52	2017
BicNET: flexible module discovery in large-scale biological networks using biclustering R Henriques, SC Madeira Algorithms for Molecular Biology 11, 1-30, 2016	49	2016
Neuropsychological predictors of conversion from mild cognitive impairment to Alzheimer’s disease: a feature selection ensemble combining stability and predictability T Pereira, FL Ferreira, S Cardoso, D Silva, A de Mendonça, M Guerreiro, ... BMC Medical Informatics and Decision Making 18 (1), 1-20, 2018	48	2018
Spreading in ALS: The relative impact of upper and lower motor neuron involvement M Gromicho, M Figueiral, H Uysal, J Grosskreutz, M Kuzma‐Kozakiewicz, ... Annals of Clinical and Translational Neurology, 2020	45	2020
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	44	2015

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