Triclustering Algorithms for Three-Dimensional Data Analysis: A Comprehensive Survey.

Sara C. Madeira Sara Cordeiro Madeira University of Lisbon, Instituto Superior Técnico, Portugal https://fenix.tecnico.ulisboa.pt/homepage/ist46399 https://scholar.google.com/citations?user=rpaGL7AAAAAJ https://orcid.org/0000-0002-1459-8096 https://www.wikidata.org/entity/Q38543993 https://www.researcherid.com/rid/C-5494-2008

Rui Henriques Sara C. Madeira Triclustering Algorithms for Three-Dimensional Data Analysis: A Comprehensive Survey. 95:1-95:43 2019 51 ACM Comput. Surv. 5 https://doi.org/10.1145/3195833 db/journals/csur/csur51.html#HenriquesM19

João M. C. Sousa Susana M. Vieira João P. Carvalho Sara C. Madeira Leo A. Celi Stan N. Finkelstein An Architecture Based on Fuzzy Systems for Personalized Medicine in ICUs. 1-6 2019 FUZZ-IEEE https://doi.org/10.1109/FUZZ-IEEE.2019.8858903 conf/fuzzIEEE/2019 db/conf/fuzzIEEE/fuzzIEEE2019.html#SousaVCMCF19

Telma Pereira Sofia Pires Marta Gromicho Susana Pinto Mamede de Carvalho Sara C. Madeira Predicting assisted ventilation in Amyotrophic Lateral Sclerosis using a mixture of experts and conformal predictors. 2019 abs/1907.13070 CoRR http://arxiv.org/abs/1907.13070 db/journals/corr/corr1907.html#abs-1907-13070

Rui Henriques Sara C. Madeira BSig: evaluating the statistical significance of biclustering solutions. 124-161 2018 32 Data Min. Knowl. Discov. 1 https://doi.org/10.1007/s10618-017-0521-2 https://www.wikidata.org/entity/Q61959010 db/journals/datamine/datamine32.html#HenriquesM18

Telma Pereira Francisco L. Ferreira Sandra Cardoso Dina Silva Alexandre de Mendonça Manuela Guerreiro Sara C. Madeira Neuropsychological predictors of conversion from mild cognitive impairment to Alzheimer's disease: a feature selection ensemble combining stability and predictability. 137:1-137:20 2018 18 BMC Med. Inf. & Decision Making 1 https://doi.org/10.1186/s12911-018-0710-y https://www.wikidata.org/entity/Q60043911 db/journals/midm/midm18.html#PereiraFCSMGM18

Sofia Pires Marta Gromicho Susana Pinto Mamede de Carvalho Sara C. Madeira Predicting Non-invasive Ventilation in ALS Patients Using Stratified Disease Progression Groups. 748-757 2018 ICDM Workshops https://doi.org/10.1109/ICDMW.2018.00113 conf/icdm/2018w db/conf/icdm/icdm2018w.html#PiresGPCM18

Telma Pereira Sandra Cardoso Dina Silva Manuela Guerreiro Alexandre de Mendonça Sara C. Madeira Ensemble learning with Conformal Predictors: Targeting credible predictions of conversion from Mild Cognitive Impairment to Alzheimer's Disease. 2018 abs/1807.01619 CoRR http://arxiv.org/abs/1807.01619 db/journals/corr/corr1807.html#abs-1807-01619

Rui Henriques Francisco L. Ferreira Sara C. Madeira BicPAMS: software for biological data analysis with pattern-based biclustering. 82:1-82:16 2017 18 BMC Bioinformatics 1 https://doi.org/10.1186/s12859-017-1493-3 https://www.wikidata.org/entity/Q30837399 db/journals/bmcbi/bmcbi18.html#HenriquesFM17

Rui Henriques Francisco L. Ferreira Sara C. Madeira Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering. 162:1-162:2 2017 18 BMC Bioinformatics 1 https://doi.org/10.1186/s12859-017-1573-4 https://www.wikidata.org/entity/Q42317180 db/journals/bmcbi/bmcbi18.html#HenriquesFM17a

Telma Pereira Luís Lemos Sandra Cardoso Dina Silva Ana Rodrigues Isabel Santana Alexandre de Mendonça Manuela Guerreiro Sara C. Madeira Predicting progression of mild cognitive impairment to dementia using neuropsychological data: a supervised learning approach using time windows. 110:1-110:15 2017 17 BMC Med. Inf. & Decision Making 1 https://doi.org/10.1186/s12911-017-0497-2 https://www.wikidata.org/entity/Q38655025 db/journals/midm/midm17.html#PereiraLCSRSMGM17

Telma Pereira Alexandre de Mendonça Francisco L. Ferreira Sara C. Madeira Manuela Guerreiro Towards a reliable prediction of conversion from Mild Cognitive Impairment to Alzheimer's Disease: stepwise learning using time windows. 19-26 2017 MIH@KDD http://proceedings.mlr.press/v69/pereira17a.html conf/kdd/2017mih db/conf/kdd/mih2017.html#PereiraMFMG17 Telma Pereira Sandra Cardoso Dina Silva Alexandre de Mendonça Manuela Guerreiro Sara C. Madeira Towards Trustworthy Predictions of Conversion from Mild Cognitive Impairment to Dementia: A Conformal Prediction Approach. 155-163 2017 PACBB https://doi.org/10.1007/978-3-319-60816-7_19 https://www.wikidata.org/entity/Q61959014 conf/pacbb/2017 db/conf/pacbb/pacbb2017.html#PereiraCSMGM17 Francisco L. Ferreira Sandra Cardoso Dina Silva Manuela Guerreiro Alexandre de Mendonça Sara C. Madeira Improving Prognostic Prediction from Mild Cognitive Impairment to Alzheimer's Disease Using Genetic Algorithms. 180-188 2017 PACBB https://doi.org/10.1007/978-3-319-60816-7_22 https://www.wikidata.org/entity/Q61959012 conf/pacbb/2017 db/conf/pacbb/pacbb2017.html#FerreiraCSGMM17

Rui Henriques Sara C. Madeira BicNET: Flexible module discovery in large-scale biological networks using biclustering. 14 2016 11 Algorithms for Molecular Biology https://doi.org/10.1186/s13015-016-0074-8 https://www.wikidata.org/entity/Q36923523 db/journals/almob/almob11.html#HenriquesM16

Rui Henriques Sara C. Madeira BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge. 23 2016 11 Algorithms for Molecular Biology https://doi.org/10.1186/s13015-016-0085-5 https://www.wikidata.org/entity/Q31132092 db/journals/almob/almob11.html#HenriquesM16a

Rui Henriques Sara C. Madeira Cláudia Antunes Multi-period classification: learning sequent classes from temporal domains. 792-819 2015 29 Data Min. Knowl. Discov. 3 https://doi.org/10.1007/s10618-014-0376-8 https://www.wikidata.org/entity/Q61959023 db/journals/datamine/datamine29.html#HenriquesMA15

Rui Henriques Cláudia Antunes Sara C. Madeira Generative modeling of repositories of health records for predictive tasks. 999-1032 2015 29 Data Min. Knowl. Discov. 4 https://doi.org/10.1007/s10618-014-0385-7 https://www.wikidata.org/entity/Q61959027 db/journals/datamine/datamine29.html#HenriquesAM15

André Valério Carreiro Pedro M. T. Amaral Susana Pinto Pedro Tomás Mamede de Carvalho Sara C. Madeira Prognostic models based on patient snapshots and time windows: Predicting disease progression to assisted ventilation in Amyotrophic Lateral Sclerosis. 133-144 2015 58 Journal of Biomedical Informatics https://doi.org/10.1016/j.jbi.2015.09.021 https://www.wikidata.org/entity/Q51584813 db/journals/jbi/jbi58.html#CarreiroAPTCM15

Rui Henriques Cláudia Antunes Sara C. Madeira A structured view on pattern mining-based biclustering. 3941-3958 2015 48 Pattern Recognition 12 https://doi.org/10.1016/j.patcog.2015.06.018 https://www.wikidata.org/entity/Q61959018 db/journals/pr/pr48.html#HenriquesAM15

Rui Henriques Sara C. Madeira Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes. 738-752 2015 12 IEEE/ACM Trans. Comput. Biology Bioinform. 4 https://doi.org/10.1109/TCBB.2014.2388206 http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2388206 https://www.wikidata.org/entity/Q40552900 db/journals/tcbb/tcbb12.html#HenriquesM15

Rui Henriques Sara C. Madeira Pattern-Based Biclustering with Constraints for Gene Expression Data Analysis. 326-339 2015 EPIA https://doi.org/10.1007/978-3-319-23485-4_34 https://www.wikidata.org/entity/Q61959025 conf/epia/2015 db/conf/epia/epia2015.html#HenriquesM15 Rui Henriques Sara C. Madeira BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules. 1-15 2015 WABI https://doi.org/10.1007/978-3-662-48221-6_1 https://www.wikidata.org/entity/Q61959019 conf/wabi/2015 db/conf/wabi/wabi2015.html#HenriquesM15

Rui Henriques Sara C. Madeira BicPAM: Pattern-based biclustering for biomedical data analysis. 27 2014 9 Algorithms for Molecular Biology https://doi.org/10.1186/s13015-014-0027-z https://www.wikidata.org/entity/Q30887396 db/journals/almob/almob9.html#HenriquesM14

Rui Henriques Sara C. Madeira BicSPAM: flexible biclustering using sequential patterns. 130 2014 15 BMC Bioinformatics https://doi.org/10.1186/1471-2105-15-130 https://www.wikidata.org/entity/Q35178395 db/journals/bmcbi/bmcbi15.html#HenriquesM14

Miguel Cacho Teixeira Pedro Tiago Monteiro 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 Ana Teresa Freitas Isabel Sá-Correia The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. 161-166 2014 42 Nucleic Acids Research Database-Issue https://doi.org/10.1093/nar/gkt1015 https://www.wikidata.org/entity/Q38494570 db/journals/nar/nar42.html#TeixeiraMGGMSCPCFMOFS14

Joana P. Gonçalves Sara C. Madeira LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification. 801-813 2014 11 IEEE/ACM Trans. Comput. Biology Bioinform. 5 https://doi.org/10.1109/TCBB.2014.2312007 http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2312007 https://www.wikidata.org/entity/Q40554217 db/journals/tcbb/tcbb11.html#GoncalvesM14

André Vale Sara C. Madeira Cláudia Antunes Mining coherent evolution patterns in education through biclustering. 391-392 2014 EDM http://www.educationaldatamining.org/EDM2014/uploads/procs2014/posters/67_EDM-2014-Poster.pdf conf/edm/2014 db/conf/edm/edm2014.html#ValeMA14 Cecília Nunes Dina Silva Manuela Guerreiro Alexandre de Mendonça Alexandra M. Carvalho Sara C. Madeira Class Imbalance in the Prediction of Dementia from Neuropsychological Data. 138-151 2013 EPIA https://doi.org/10.1007/978-3-642-40669-0_13 https://www.wikidata.org/entity/Q61959032 conf/epia/2013 db/conf/epia/epia2013.html#NunesSGMCM13 Joana P. Gonçalves Sara C. Madeira Heuristic approaches for time-lagged biclustering. 1-9 2013 BIOKDD https://doi.org/10.1145/2500863.2500865 https://www.wikidata.org/entity/Q61959033 conf/kdd/2013bio db/conf/kdd/biokdd2013.html#GoncalvesM13 Hugo López-Fernández Miguel Reboiro-Jato Sara C. Madeira Rubén López-Cortés J. D. Nunes-Miranda Hugo Miguel Santos Florentino Fdez-Riverola Daniel Glez-Peña A Workflow for the Application of Biclustering to Mass Spectrometry Data. 145-153 2013 PACBB https://doi.org/10.1007/978-3-319-00578-2_19 https://www.wikidata.org/entity/Q61959031 conf/pacbb/2013 db/conf/pacbb/pacbb2013.html#Lopez-FernandezRMLNSFG13 Rui Henriques Cláudia Antunes Sara C. Madeira Methods for the Efficient Discovery of Large Item-Indexable Sequential Patterns. 100-116 2013 NFMCP https://doi.org/10.1007/978-3-319-08407-7_7 https://www.wikidata.org/entity/Q61959030 conf/pkdd/2013nfmcp db/conf/pkdd/nfmcp2013.html#HenriquesAM13

Joana P. Gonçalves Yves Moreau Sara C. Madeira AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences. 196-215 2012 6 IJDMB 2 https://doi.org/10.1504/IJDMB.2012.048198 https://www.wikidata.org/entity/Q51351826 db/journals/ijdmb/ijdmb6.html#GoncalvesMM12

André Valério Carreiro Artur J. Ferreira Mário A. T. Figueiredo Sara Cordeiro Madeira Towards a Classification Approach using Meta-Biclustering: Impact of Discretization in the Analysis of Expression Time Series. 2012 9 J. Integrative Bioinformatics 3 https://doi.org/10.2390/biecoll-jib-2012-207 https://www.wikidata.org/entity/Q47344520 db/journals/jib/jib9.html#CarreiroFFM12

André Valério Carreiro Artur J. Ferreira Mário A. T. Figueiredo Sara C. Madeira Prognostic Prediction Using Clinical Expression Time Series: Towards a Supervised Learning Approach Based on Meta-biclusters. 11-20 2012 PACBB https://doi.org/10.1007/978-3-642-28839-5_2 https://www.wikidata.org/entity/Q61959036 conf/pacbb/2012 db/conf/pacbb/pacbb2012.html#CarreiroFFM12 Filipe Cristóvão Sara C. Madeira Parallel e-CCC-Biclustering: Mining Approximate Temporal Patterns in Gene Expression Time Series Using Parallel Biclustering. 21-31 2012 PACBB https://doi.org/10.1007/978-3-642-28839-5_3 https://www.wikidata.org/entity/Q61959035 conf/pacbb/2012 db/conf/pacbb/pacbb2012.html#CristovaoM12

Joana P. Gonçalves Alexandre P. Francisco Nuno P. Mira Miguel C. Teixeira Isabel Sá-Correia Arlindo L. Oliveira Sara C. Madeira TFRank: network-based prioritization of regulatory associations underlying transcriptional responses. 3149-3157 2011 27 Bioinformatics 22 https://doi.org/10.1093/bioinformatics/btr546 https://www.wikidata.org/entity/Q44298158 db/journals/bioinformatics/bioinformatics27.html#GoncalvesFMTSOM11

André Valério Carreiro Orlando Anunciação João André Carriço Sara Cordeiro Madeira Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series. 2011 8 J. Integrative Bioinformatics 3 https://doi.org/10.2390/biecoll-jib-2011-175 https://www.wikidata.org/entity/Q43653688 db/journals/jib/jib8.html#CarreiroACM11

Dário Abdulrehman Pedro T. Monteiro Miguel C. Teixeira Nuno P. Mira Artur B. Lourenço Sandra Costa dos Santos Tânia Rodrigues Cabrito Alexandre P. Francisco Sara C. Madeira Ricardo Santos Aires Arlindo L. Oliveira Isabel Sá-Correia Ana T. Freitas YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. 136-140 2011 39 Nucleic Acids Research Database-Issue https://doi.org/10.1093/nar/gkq964 https://www.wikidata.org/entity/Q41582682 db/journals/nar/nar39.html#AbdulrehmanMTMLSCFMAOSF11

Daniela Nitsch Léon-Charles Tranchevent Joana P. Gonçalves Josef Korbinian Vogt Sara C. Madeira Yves Moreau PINTA: a web server for network-based gene prioritization from expression data. 334-338 2011 39 Nucleic Acids Research Web-Server-Issue https://doi.org/10.1093/nar/gkr289 https://www.wikidata.org/entity/Q33908012 db/journals/nar/nar39.html#NitschTGVMM11

Ricardo Santos Aires João A. Carriço Alexandre P. Francisco Sara C. Madeira Baiacu: A Tool for the Visual Analysis of the Saccharomyces Cerevisiae Regulatory Network. 49-56 2011 PACBB https://doi.org/10.1007/978-3-642-19914-1_7 https://www.wikidata.org/entity/Q59845870 conf/pacbb/2011 db/conf/pacbb/pacbb2011.html#AiresCFM11 André Valério Carreiro Orlando Anunciação João A. Carriço Sara C. Madeira Biclustering-Based Classification of Clinical Expression Time Series: A Case Study in Patients with Multiple Sclerosis. 229-239 2011 PACBB https://doi.org/10.1007/978-3-642-19914-1_31 https://www.wikidata.org/entity/Q61959038 conf/pacbb/2011 db/conf/pacbb/pacbb2011.html#CarreiroACM11

Ignacio Medina José Carbonell Luis Pulido Sara C. Madeira Stefan Götz Ana Conesa Joaquín Tárraga Alberto D. Pascual-Montano Rubén Nogales-Cadenas Javier Santoyo Francisco García-García 0002 Martina Marbà David Montaner Joaquín Dopazo Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. 210-213 2010 38 Nucleic Acids Research Web-Server-Issue https://doi.org/10.1093/nar/gkq388 https://www.wikidata.org/entity/Q33579781 db/journals/nar/nar38.html#MedinaCPMGCTPNSGMMD10

Sara C. Madeira Miguel C. Teixeira Isabel Sá-Correia Arlindo L. Oliveira Identification of Regulatory Modules in Time Series Gene Expression Data Using a Linear Time Biclustering Algorithm. 153-165 2010 7 IEEE/ACM Trans. Comput. Biology Bioinform. 1 http://doi.acm.org/10.1145/1719272.1719289 db/journals/tcbb/tcbb7.html#MadeiraTSO10

Joana P. Gonçalves Sara C. Madeira e-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs. 181-191 2010 IWPACBB https://doi.org/10.1007/978-3-642-13214-8_24 conf/isami/2010iwpacbb db/conf/isami/iwpacbb2010.html#GoncalvesM10 Joana P. Gonçalves Sara C. Madeira Yves Moreau Network-Based Disease Candidate Gene Prioritization: Towards Global Diffusion in Heterogeneous Association Networks. 2010 NyNaK http://ceur-ws.org/Vol-655/dynak2010_paper5.pdf conf/pkdd/2010dynak db/conf/pkdd/dynak2010.html#GoncalvesMM10

Sara C. Madeira Arlindo L. Oliveira A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series. 2009 4 Algorithms for Molecular Biology https://doi.org/10.1186/1748-7188-4-8 https://www.wikidata.org/entity/Q33460704 db/journals/almob/almob4.html#MadeiraO09

Sara C. Madeira Arlindo L. Oliveira Efficient Biclustering Algorithms for Time Series Gene Expression Data Analysis. 1013-1019 2009 IWANN (2) https://doi.org/10.1007/978-3-642-02481-8_154 https://www.wikidata.org/entity/Q58883991 conf/iwann/2009-2 db/conf/iwann/iwann2009-2.html#MadeiraO09 Paulo Moura Ricardo Rocha 0001 Sara C. Madeira High Level Thread-Based Competitive Or-Parallelism in Logtalk. 107-121 2009 PADL https://doi.org/10.1007/978-3-540-92995-6_8 https://www.wikidata.org/entity/Q61959044 conf/padl/2009 db/conf/padl/padl2009.html#MouraRM09 Paulo Moura Ricardo Rocha 0001 Sara C. Madeira Thread-Based Competitive Or-Parallelism. 713-717 2008 ICLP https://doi.org/10.1007/978-3-540-89982-2_63 https://www.wikidata.org/entity/Q61959045 conf/iclp/2008 db/conf/iclp/iclp2008.html#MouraRM08 Sara C. Madeira Arlindo L. Oliveira An Efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-series Expression Data. 67-80 2007 conf/apbc/2007 APBC http://www.comp.nus.edu.sg/~wongls/psZ/apbc2007/apbc221a.pdf db/conf/apbc/apbc2007.html#MadeiraO07 Sara C. Madeira Arlindo L. Oliveira A Linear Time Biclustering Algorithm for Time Series Gene Expression Data. 39-52 2005 conf/wabi/2005 WABI https://doi.org/10.1007/11557067_4 https://www.wikidata.org/entity/Q58884040 db/conf/wabi/wabi2005.html#MadeiraO05

Sara C. Madeira Arlindo L. Oliveira Biclustering Algorithms for Biological Data Analysis: A Survey. 24-45 2004 1 IEEE/ACM Trans. Comput. Biology Bioinform. 1 https://doi.org/10.1109/TCBB.2004.2 http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.2 https://www.wikidata.org/entity/Q31067714 db/journals/tcbb/tcbb1.html#MadeiraO04

Sara C. Madeira Arlindo L. Oliveira Catarina S. Conceição A Data Mining Approach to Credit Risk Evaluation and Behaviour Scoring. 184-188 https://doi.org/10.1007/978-3-540-24580-3_25 2003 conf/epia/2003 EPIA db/conf/epia/epia2003.html#MadeiraOC03 João M. C. Sousa Sara C. Madeira Uzay Kaymak Modeling charity donations using target selection for revenue maximization. 654-659 2003 FUZZ-IEEE https://doi.org/10.1109/FUZZ.2003.1209441 conf/fuzzIEEE/2003 db/conf/fuzzIEEE/fuzzIEEE2003.html#SousaMK03 Dário Abdulrehman Ricardo Santos Aires Pedro M. T. Amaral Cláudia Antunes Orlando Anunciação Tânia Rodrigues Cabrito José Carbonell Sandra Cardoso André Valério Carreiro João A. CarriçoJoão André Carriço Alexandra M. Carvalho João P. Carvalho Mamede de Carvalho Leo A. Celi Catarina S. Conceição Ana Conesa Catarina Costa Filipe Cristóvão Joaquín Dopazo Artur J. Ferreira Francisco L. Ferreira Mário A. T. Figueiredo Stan N. Finkelstein Alexandre P. FranciscoAlexandre Paulo Francisco Ana T. FreitasAna Teresa Freitas Francisco García-García 0002 Daniel Glez-Peña Joana P. GonçalvesJoana Pinho Gonçalves Stefan Götz Marta Gromicho Joana Fernandes Guerreiro Manuela Guerreiro Rui Henriques Uzay Kaymak Luís Lemos Rubén López-Cortés Hugo López-Fernández Artur B. Lourenço Martina Marbà Ignacio Medina Alexandre de Mendonça Nuno P. MiraNuno Pereira Mira David Montaner Pedro T. MonteiroPedro Tiago Monteiro Yves Moreau Paulo Moura Daniela Nitsch Rubén Nogales-Cadenas Cecília Nunes J. D. Nunes-Miranda Arlindo L. OliveiraArlindo Limede Oliveira Margarida Palma Alberto D. Pascual-Montano Telma Pereira Susana Pinto Sofia Pires Luis Pulido Miguel Reboiro-Jato Florentino Fernández RiverolaFlorentino Fdez-Riverola Ricardo Rocha 0001 Ana Rodrigues Isabel Sá-Correia Isabel Santana Hugo Miguel Santos Sandra Costa dos Santos Javier Santoyo Dina Silva João Miguel da Costa SousaJoão M. C. Sousa Joaquín Tárraga Miguel C. TeixeiraMiguel Cacho Teixeira Pedro Tomás Léon-Charles Tranchevent André Vale Susana M. Vieira Josef Korbinian Vogt