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Alberto D. Pascual-Montano
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Journal Articles
- 2015
 [j26]Edgardo Mejía-Roa [j26]Edgardo Mejía-Roa , Daniel Tabas-Madrid, Javier Setoain, Carlos García , Daniel Tabas-Madrid, Javier Setoain, Carlos García , Francisco Tirado , Francisco Tirado , Alberto D. Pascual-Montano: , Alberto D. Pascual-Montano:
 NMF-mGPU: non-negative matrix factorization on multi-GPU systems. BMC Bioinform. 16: 43:1-43:12 (2015)
 [j25]Javier Setoain, Mònica Franch, Marta Martínez [j25]Javier Setoain, Mònica Franch, Marta Martínez , Daniel Tabas-Madrid, Carlos Oscar Sánchez Sorzano , Daniel Tabas-Madrid, Carlos Oscar Sánchez Sorzano , Annette Bakker , Annette Bakker , Eduardo Gonzalez-Couto, Juan Elvira, Alberto D. Pascual-Montano: , Eduardo Gonzalez-Couto, Juan Elvira, Alberto D. Pascual-Montano:
 NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. Nucleic Acids Res. 43(Webserver-Issue): W193-W199 (2015)
- 2014
 [j24]Joao Miguel da Conceiçao Alves-Cruzeiro, Rubén Nogales-Cadenas, Alberto Domingo Pascual-Montano: [j24]Joao Miguel da Conceiçao Alves-Cruzeiro, Rubén Nogales-Cadenas, Alberto Domingo Pascual-Montano:
 CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. Nucleic Acids Res. 42(Database-Issue): 430-436 (2014)
- 2013
 [j23]Rubén Nogales-Cadenas, Slavica Jonic [j23]Rubén Nogales-Cadenas, Slavica Jonic , Florence Tama , Florence Tama , A. A. Arteni, Daniel Tabas-Madrid, Miguel Vázquez , A. A. Arteni, Daniel Tabas-Madrid, Miguel Vázquez , Alberto D. Pascual-Montano, Carlos Oscar Sánchez Sorzano , Alberto D. Pascual-Montano, Carlos Oscar Sánchez Sorzano : :
 3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy. Nucleic Acids Res. 41(Webserver-Issue): 363-367 (2013)
- 2012
 [j22]Daniel Tabas-Madrid, Rubén Nogales-Cadenas, Alberto D. Pascual-Montano: [j22]Daniel Tabas-Madrid, Rubén Nogales-Cadenas, Alberto D. Pascual-Montano:
 GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Res. 40(Web-Server-Issue): 478-483 (2012)
- 2011
 [j21]Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn: [j21]Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn:
 Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. J. Biomed. Semant. 2(S-5): S11 (2011)
 [j20]Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor [j20]Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor , Christophe Roeder, Lawrence E. Hunter , Christophe Roeder, Lawrence E. Hunter , Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer , Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer , Makoto Miwa , Makoto Miwa , Sophia Ananiadou, Mariana L. Neves , Sophia Ananiadou, Mariana L. Neves , Alberto D. Pascual-Montano, Arzucan Özgür , Alberto D. Pascual-Montano, Arzucan Özgür , Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: , Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
 U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12: 481 (2011)
 [j19]Alberto D. Pascual-Montano: [j19]Alberto D. Pascual-Montano:
 Gene expression modular analysis: an overview from the data mining perspective. WIREs Data Mining Knowl. Discov. 1(5): 381-396 (2011)
- 2010
 [j18]Mariana L. Neves [j18]Mariana L. Neves , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 Moara: a Java library for extracting and normalizing gene and protein mentions. BMC Bioinform. 11: 157 (2010)
 [j17]Ignacio Medina [j17]Ignacio Medina , José Carbonell , José Carbonell , Luis Pulido, Sara C. Madeira , Luis Pulido, Sara C. Madeira , Stefan Götz , Stefan Götz , Ana Conesa , Ana Conesa , Joaquín Tárraga, Alberto D. Pascual-Montano, Rubén Nogales-Cadenas, Javier Santoyo , Joaquín Tárraga, Alberto D. Pascual-Montano, Rubén Nogales-Cadenas, Javier Santoyo , Francisco García-García , Francisco García-García , Martina Marbà, David Montaner , Martina Marbà, David Montaner , Joaquín Dopazo , Joaquín Dopazo : :
 Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 38(Web-Server-Issue): 210-213 (2010)
 [j16]Miguel Vázquez [j16]Miguel Vázquez , Rubén Nogales-Cadenas, Javier Arroyo , Rubén Nogales-Cadenas, Javier Arroyo , Pedro Botías , Pedro Botías , Raul García , Raul García , José María Carazo, Francisco Tirado , José María Carazo, Francisco Tirado , Alberto D. Pascual-Montano, Pedro Carmona-Saez , Alberto D. Pascual-Montano, Pedro Carmona-Saez : :
 MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Res. 38(Web-Server-Issue): 228-232 (2010)
- 2009
 [j15]Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez [j15]Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Res. 37(Database-Issue): 175-180 (2009)
 [j14]Miguel Vázquez [j14]Miguel Vázquez , Pedro Carmona-Saez , Pedro Carmona-Saez , Rubén Nogales-Cadenas, Monica Chagoyen , Rubén Nogales-Cadenas, Monica Chagoyen , Francisco Tirado , Francisco Tirado , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 SENT: semantic features in text. Nucleic Acids Res. 37(Web-Server-Issue): 153-159 (2009)
 [j13]Rubén Nogales-Cadenas, Pedro Carmona-Saez [j13]Rubén Nogales-Cadenas, Pedro Carmona-Saez , Miguel Vázquez , Miguel Vázquez , Cesar Vicente, Xiaoyuan Yang, Francisco Tirado , Cesar Vicente, Xiaoyuan Yang, Francisco Tirado , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Res. 37(Web-Server-Issue): 317-322 (2009)
- 2008
 [j12]Federico Abascal, Pedro Carmona-Saez [j12]Federico Abascal, Pedro Carmona-Saez , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. Bioinform. 24(9): 1208-1209 (2008)
 [j11]Monica Chagoyen [j11]Monica Chagoyen , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 Assessment of protein set coherence using functional annotations. BMC Bioinform. 9 (2008)
 [j10]Edgardo Mejía-Roa [j10]Edgardo Mejía-Roa , Pedro Carmona-Saez , Pedro Carmona-Saez , Rubén Nogales, Cesar Vicente, Miguel Vázquez , Rubén Nogales, Cesar Vicente, Miguel Vázquez , X. Y. Yang, Carlos García , X. Y. Yang, Carlos García , Francisco Tirado , Francisco Tirado , Alberto D. Pascual-Montano: , Alberto D. Pascual-Montano:
 bioNMF: a web-based tool for nonnegative matrix factorization in biology. Nucleic Acids Res. 36(Web-Server-Issue): 523-528 (2008)
- 2006
 [j9]Carlos Oscar Sánchez Sorzano [j9]Carlos Oscar Sánchez Sorzano , Roberto Marabini , Roberto Marabini , Alberto D. Pascual-Montano, Sjors H. W. Scheres , Alberto D. Pascual-Montano, Sjors H. W. Scheres , José María Carazo: , José María Carazo:
 Optimization problems in electron microscopy of single particles. Ann. Oper. Res. 148(1): 133-165 (2006)
 [j8]Monica Chagoyen [j8]Monica Chagoyen , Pedro Carmona-Saez , Pedro Carmona-Saez , Hagit Shatkay, José María Carazo, Alberto D. Pascual-Montano: , Hagit Shatkay, José María Carazo, Alberto D. Pascual-Montano:
 Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinform. 7: 41 (2006)
 [j7]Pedro Carmona-Saez [j7]Pedro Carmona-Saez , Monica Chagoyen , Monica Chagoyen , Andrés Rodríguez Moreno , Andrés Rodríguez Moreno , Oswaldo Trelles , Oswaldo Trelles , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 Integrated analysis of gene expression by association rules discovery. BMC Bioinform. 7: 54 (2006)
 [j6]Pedro Carmona-Saez [j6]Pedro Carmona-Saez , Roberto D. Pascual-Marqui , Roberto D. Pascual-Marqui , Francisco Tirado , Francisco Tirado , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 Biclustering of gene expression data by non-smooth non-negative matrix factorization. BMC Bioinform. 7: 78 (2006)
 [j5]Monica Chagoyen [j5]Monica Chagoyen , Pedro Carmona-Saez , Pedro Carmona-Saez , Concha Gil , Concha Gil , José María Carazo, Alberto D. Pascual-Montano: , José María Carazo, Alberto D. Pascual-Montano:
 A literature-based similarity metric for biological processes. BMC Bioinform. 7: 363 (2006)
 [j4]Alberto D. Pascual-Montano, Pedro Carmona-Saez [j4]Alberto D. Pascual-Montano, Pedro Carmona-Saez , Monica Chagoyen , Monica Chagoyen , Francisco Tirado , Francisco Tirado , José María Carazo, Roberto D. Pascual-Marqui , José María Carazo, Roberto D. Pascual-Marqui : :
 bioNMF: a versatile tool for non-negative matrix factorization in biology. BMC Bioinform. 7: 366 (2006)
 [j3]Alberto D. Pascual-Montano, José María Carazo, Kieko Kochi, Dietrich Lehmann, Roberto D. Pascual-Marqui [j3]Alberto D. Pascual-Montano, José María Carazo, Kieko Kochi, Dietrich Lehmann, Roberto D. Pascual-Marqui : :
 Nonsmooth Nonnegative Matrix Factorization (nsNMF). IEEE Trans. Pattern Anal. Mach. Intell. 28(3): 403-415 (2006)
- 2003
 [j2]Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles [j2]Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles , Alberto D. Pascual-Montano: , Alberto D. Pascual-Montano:
 Engene: the processing and exploratory analysis of gene expression data. Bioinform. 19(5): 657-658 (2003)
- 2001
 [j1]Roberto D. Pascual-Marqui, Alberto D. Pascual-Montano, Kieko Kochi, José María Carazo: [j1]Roberto D. Pascual-Marqui, Alberto D. Pascual-Montano, Kieko Kochi, José María Carazo:
 Smoothly distributed fuzzy c-means: a new self-organizing map. Pattern Recognit. 34(12): 2395-2402 (2001)
Conference and Workshop Papers
- 2011
 [c13]Christian Borgelt, Xiaoyuan Yang, Rubén Nogales-Cadenas, Pedro Carmona-Saez [c13]Christian Borgelt, Xiaoyuan Yang, Rubén Nogales-Cadenas, Pedro Carmona-Saez , Alberto D. Pascual-Montano: , Alberto D. Pascual-Montano:
 Finding closed frequent item sets by intersecting transactions. EDBT 2011: 367-376
 [c12]Edgardo Mejía-Roa [c12]Edgardo Mejía-Roa , Carlos García , Carlos García , José Ignacio Gómez , José Ignacio Gómez , Manuel Prieto , Manuel Prieto , Francisco Tirado , Francisco Tirado , Rubén Nogales, Alberto D. Pascual-Montano: , Rubén Nogales, Alberto D. Pascual-Montano:
 Biclustering and classification analysis in gene expression using Nonnegative Matrix Factorization on multi-GPU systems. ISDA 2011: 882-887
 [c11]Edgardo Mejía-Roa [c11]Edgardo Mejía-Roa , Carlos García , Carlos García , José Ignacio Gómez , José Ignacio Gómez , Manuel Prieto , Manuel Prieto , Christian Tenllado, Alberto D. Pascual-Montano, Francisco Tirado , Christian Tenllado, Alberto D. Pascual-Montano, Francisco Tirado : :
 Parallelism on the Nonnegative Matrix Factorization. PARCO 2011: 421-428
- 2010
 [c10]Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn: [c10]Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter T. Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René Witte, Jonas B. Laurila, Christopher J. O. Baker, Cheng-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Inés Furlong, Michael Rautschka, Mariana L. Neves, Alberto D. Pascual-Montano, Qi Wei, Nigel Collier, Md. Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga Llavori, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik M. van Mulligen, Jan A. Kors, Udo Hahn:
 Assessment of NER solutions against the first and second CALBC silver standard corpus. Semantic Mining in Biomedicine 2010
- 2009
 [c9]Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano: [c9]Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano:
 Extraction of biomedical events using case-based reasoning. BioNLP@HLT-NAACL (Shared Task) 2009: 68-76
- 2008
 [c8]Mariana L. Neves, Monica Chagoyen, José María Carazo, Alberto D. Pascual-Montano: [c8]Mariana L. Neves, Monica Chagoyen, José María Carazo, Alberto D. Pascual-Montano:
 CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem. BioNLP 2008: 108-109
 [c7]Alberto D. Pascual-Montano: [c7]Alberto D. Pascual-Montano:
 Non-negative matrix factorization in bioinformatics: Towards understanding biological processes. ISCAS 2008: 1332-1335
 [c6]Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano: [c6]Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano:
 Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library. BioLINK@ISMB/ECCB 2008: 71-80
 [c5]Miguel Vázquez [c5]Miguel Vázquez , Monica Chagoyen , Monica Chagoyen , Alberto D. Pascual-Montano: , Alberto D. Pascual-Montano:
 Named Entity Recognition and Normalization: A Domain-Specific Language Approach. IWPACBB 2008: 147-155
- 2005
 [c4]Alberto D. Pascual-Montano, Francisco Tirado [c4]Alberto D. Pascual-Montano, Francisco Tirado , Pedro Carmona-Saez , Pedro Carmona-Saez , José María Carazo, Roberto D. Pascual-Marqui , José María Carazo, Roberto D. Pascual-Marqui : :
 Two-way clustering of gene expression profiles by sparse matrix factorization. CSB Workshops 2005: 103-104
 [c3]Carlos García, Manuel Prieto, Alberto D. Pascual-Montano: [c3]Carlos García, Manuel Prieto, Alberto D. Pascual-Montano:
 A Speculative Parallel Algorithm for Self-Organizing Maps. PARCO 2005: 615-622
- 2002
 [c2]Pedro A. de Alarcón, Alberto D. Pascual-Montano, José María Carazo: [c2]Pedro A. de Alarcón, Alberto D. Pascual-Montano, José María Carazo:
 Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases. CIVR 2002: 225-234
 [c1]Pedro A. de Alarcón, Alberto D. Pascual-Montano, Amarnath Gupta, José María Carazo: [c1]Pedro A. de Alarcón, Alberto D. Pascual-Montano, Amarnath Gupta, José María Carazo:
 Modeling Shape and Topology of 3D Images of Biological Specimens. ICPR (1) 2002: 79-82
Informal and Other Publications
- 2014
 [i1]Carlos Oscar Sánchez Sorzano, Javier Vargas, Alberto Domingo Pascual-Montano: [i1]Carlos Oscar Sánchez Sorzano, Javier Vargas, Alberto Domingo Pascual-Montano:
 A survey of dimensionality reduction techniques. CoRR abs/1403.2877 (2014)
Coauthor Index

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