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ORCIDAlberto D. Pascual-Montano
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Journal Articles
- 2015
[j26]Edgardo Mejía-Roa
, Daniel Tabas-Madrid, Javier Setoain, Carlos García, Francisco Tirado, 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, Daniel Tabas-Madrid, Carlos Oscar Sánchez Sorzano, Annette Bakker, 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:
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, Florence Tama, A. A. Arteni, Daniel Tabas-Madrid, Miguel Vázquez, 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:
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:
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, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, 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:
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12: 481 (2011) - [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, 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, 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, Martina Marbà, David Montaner, 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, Rubén Nogales-Cadenas, Javier Arroyo, Pedro Botías, Raul García, José María Carazo, Francisco Tirado, 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, 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, Pedro Carmona-Saez, Rubén Nogales-Cadenas, Monica Chagoyen, Francisco Tirado, 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, Miguel Vázquez, Cesar Vicente, Xiaoyuan Yang, Francisco Tirado, 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, 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, José María Carazo, Alberto D. Pascual-Montano:
Assessment of protein set coherence using functional annotations. BMC Bioinform. 9 (2008) - [j10]Edgardo Mejía-Roa, Pedro Carmona-Saez, Rubén Nogales, Cesar Vicente, Miguel Vázquez, X. Y. Yang, Carlos García, Francisco Tirado, 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, Roberto Marabini, Alberto D. Pascual-Montano, Sjors H. W. Scheres, José María Carazo:
Optimization problems in electron microscopy of single particles. Ann. Oper. Res. 148(1): 133-165 (2006) - [j8]Monica Chagoyen, Pedro Carmona-Saez, 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, Monica Chagoyen, Andrés Rodríguez Moreno, Oswaldo Trelles, 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, Roberto D. Pascual-Marqui, Francisco Tirado, 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, Pedro Carmona-Saez, Concha Gil, 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, Monica Chagoyen, Francisco Tirado, 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:
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, 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:
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, Alberto D. Pascual-Montano:
Finding closed frequent item sets by intersecting transactions. EDBT 2011: 367-376 - [c12]Edgardo Mejía-Roa, Carlos García, José Ignacio Gómez, Manuel Prieto, Francisco Tirado, 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, Carlos García, José Ignacio Gómez, Manuel Prieto, 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:
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:
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:
CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem. BioNLP 2008: 108-109 - [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:
Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library. BioLINK@ISMB/ECCB 2008: 71-80 - [c5]Miguel Vázquez, Monica Chagoyen, 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, Pedro Carmona-Saez, 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:
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:
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:
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:
A survey of dimensionality reduction techniques. CoRR abs/1403.2877 (2014)
Coauthor Index
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