Selected Publications:
2012:
- GeneCodis3: a non-redundant and
modular enrichment analysis tool for functional genomics.Tabas-Madrid D,
Nogales-Cadenas R, Pascual-Montano A.
Nucleic Acids Res. 2012 May 9
[Medline] [Online version] - Quantification
of miRNA-mRNA interactions. Ander Muniategui; Rubén
Nogales-Cadenas;
Miguél Vázquez; Xabier L. Aranguren; Xabier Agirre;
Aernout Luttun;
Felipe Prosper; Alberto Pascual-Montano; Angel Rubio PLoS One. 2012;7(2):e30766. Epub 2012 Feb 14.
[Medline][Online version]
2011:
- U-Compare
Bio-Event Meta-Service: Compatible BioNLP Event Extraction Services.
Yoshinobu Kano, Jari Björne, Filip Ginter, Ekaterina Buyko, Udo
Hahn,
Kevin 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
Neves, Alberto Pascual-Montano,
Arzucan Özgür, Dragomir R Radev, Sebastian Riedel, Rune
Sætre, Hong-Woo
Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii. BMC Bioinformatics. 2011 Dec 18;12(1):481
[Medline] [Online version] - Functional
Analysis beyond Enrichment: Non-Redundant Reciprocal Linkage of Genes
and Biological Terms. Celia Fontanillo, Ruben Nogales-Cadenas, Alberto
Pascual-Montano and Javier De Las Rivas. 2011. PLoS ONE 6 (9) p. e24289
[Medline] [Online version] - Dietrich
Rebholz-Schuhmann, Antonio J Yepes, Chen Li, Senay Kafkas, Ian Lewin,
Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena
Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, René
Witte,
Jonas B Laurila, Christopher JO Baker, Cheng-Ju Kuo, Simone Clematide,
Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo
Hara, Laura I
Furlong, Michael Rautschka, Mariana L Neves, Alberto Pascual-Montano,
Qi Wei, Nigel Collier, Md FM Chowdhury, Alberto Lavelli, Rafael
Berlanga, Roser Morante, Vincent Van Asch, Walter Daelemans,
José L
Marina, Erik van Mulligen, Jan Kors and Udo Hahn. Assessment of NER
solutions against the first and second CALBC Silver Standard Corpus. Journal of Biomedical Semantics 2011,
2(Suppl 5):S11.
[Medline] [Online version] - A. Pascual-Montano.
Gene
classification, gene expression data processing and exploratory data
analysis. Wiley
Interdisciplinary Reviews Data Mining and Knowledge Discovery. Apr 04 2011. DOI: 10.1002/widm.29
[Online version] - A. Pascual-Montano,
JM Carazo.
Efficient functional bioinformatics tools: towards understanding
biological processes. EMBnet.news.
2011. Vol 16. No. 1 pp. 31-38
[Online version]
2010:
- MARQ:
an online tool to mine GEO for experiments with
similar or opposite gene expression signatures. Miguel
Vazquez,
Ruben Nogales-Cadenas, Javier Arroyo, Pedro Botías,
Raul García, Jose M. Carazo, Francisco Tirado, Alberto
Pascual-Montano
and Pedro Carmona-Saez. Nucleic
Acids Research 2010. Jul 1;38 Suppl:W228-32. Epub 2010 May 31
[Medline] [Online version] - Ignacio;
Carbonell, Jose; Pulido, Luis; Madeira, Sara; Gtz, Stefan; Conesa, Ana;
Tarraga, Joaqun; Pascual-Montano,
Alberto; Nogales-Cadenas,
Ruben; Santoyo-Lopez, Javier;
Garcia-Garcia, Francisco; Marba, Martina; Montaner, David; Dopazo,
Joaquin. Babelomics: an integrative platform for the analysis of
transcriptomics, proteomics and genomic data with advanced functional
profiling. Nucleic
Acids Research 2010. Jul 1;38 Suppl:W210-3. Epub 2010 May 16.
[Medline] [Online version] - Mariana
Lara Neves, Jose Maria Carazo and Alberto
Pascual-Montano.
Extracting and normalizing gene/protein
mentions with the flexible and trainable Moara Java library. Lecture Notes on
Bioinformatics. 2010,
Volume 6004/2010, 71-80
[Online version] - Mariana
Lara Neves, Jose Maria Carazo and Alberto
Pascual-Montano. Moara:
a Java library for extracting and
normalizing gene and protein mentions. BMC Bioinformatics. 2010
Mar 26;11:157.
[Medline] [Online version]
2009:
- Vital
Vialas, Ruben Nogales-Cadenas, Cesar Nombela, Alberto
Pascual-Montano and Concha
Gil. Proteopathogen, a protein
database for
studying Candida albicans–host interaction. Proteomics 2009;
doi:
10.1002/pmic.200900023.
[Medline] [Online version] - Ruben Nogales-Cadenas,
Pedro Carmona-Saez,
Miguel Vazquez, Cesar Vicente, Xiaoyuan Yang, Francisco Tirado, Jose M.
Carazo and Alberto
Pascual-Montano.
GeneCodis: interpreting
gene lists
through enrichment analysis and integration of diverse
biological
information. Nucleic
Acids Research 2009; doi: 10.1093/nar/gkp416
[Medline] [On-line version]
- Miguel
Vazquez, Ruben Nogales-Cadenas, Monica Chagoyen, Pedro Carmona-Saez and
Alberto
Pascual-Montano.
SENT: Semantic Features in Text. Nucleic
Acids Research 2009; doi: 10.1093/nar/gkp392
[Medline] [On-line version] - Javier
A Velázquez-Muriel, Manuel Rueda, Isabel Cuesta, Alberto Pascual-Montano,
Modesto
Orozco and José-María Carazo. Comparison
of molecular dynamics and superfamily spaces of protein domain
deformation. BMC Structural Biology
2009, 9:6 (17 February 2009)
[Medline] [On-line version]
2008:
- Nogales-Cadenas, R.,
Abascal, F.,
Díez-Pérez, J., Carazo, JM, Pascual-Montano,
A. CentrosomeDB: A Human
Centrosomal
Proteins Database.
Nucleic Acids
Research 2008; doi: 10.1093/nar/gkn815
[Medline] [On-line version] - Monica
Chagoyen, Jose M. Carazo and Alberto
Pascual-Montano. Assessment
of protein set coherence using
functional annotations. BMC
Bioinformatics 2008, 9:444
[Medline] [On-line version]
- Mejía-Roa, E., Carmona-Saez,
P., Nogales, R., Vicente, C., Vázquez, M., Yang, XY.,
García, C.,
Tirado, F., Pascual-Montano,
A..
bioNMF: A web-based tool for
Non-negative Matrix Factorization in biology. Nucleic Acid Research.
2008. Nucleic Acids Research
2008; doi: 10.1093/nar/gkn335
[Medline] [On-line version]
- F. Abascal, P. Carmona-Saez, JM Carazo and A.
Pascual-Montano.
ChIPCodis:
Mining complex regulatory systems in yeast by concurrent
enrichment analysis of Chip-on-chip data. Bioinformatics. 2008.May 1;24(9):1208-1209
[Medline] [On-line version]
- MA. Anton, D. Gorostiaga, E. Guruceaga, V.
Segura, P.
Carmona-Saez, A. Pascual-Montano,
R. Pio, LM. Montuenga, A. Rubio. SPACE: an algorithm to predict and
quantify alternatively spliced isoforms using microarrays. Genome Biology.2008,
9:R46
[Medline] [On-line version]
Go to 2007 and older publications...
Publications in peer-reviewed international conferences
- Christian Borgelt, Xiaoyuan Yang, Ruben Nogales-Cadenas, Pedro Carmona-Saez, and Alberto Pascual-Montano. Finding Closed Frequent Item Sets by Intersecting Transactions. Proc. 14th Int. Conf. on Extending Database Technology (EDBT 2011, Uppsala, Sweden), Accepted, to appear in 2011.
- Rebholz-Schuhmann D, Jimeno A, Li C, Kafkas S, Lewin I, van
Mulligen E, Kang N, Buyko E, Beisswanger E, Hornbostel K, Corbett P,
Milward D, Kouznetsov A, Witte R, Laurila J B, Baker C J, Kuo C-J,
Clematide S, Rinaldi F, Farkas R, Móra G, Hara K, Furlong L,
Rautschka M, Neves M L, Pascual-Montano A, Wei Q, Collier N, Chowdhury
F M, Lavelli A, Berlanga R, Morante R, Van Asch V, Daelemans W, Kors J
and Hahn U. Assessment of NER solutions against the first and second
CALBC Silver Standard Corpus, Fourth International Symposium on
Semantic Mining in Biomedicine (SMBM'10), 25th-26th October 2010,
European Bioinformatics Institute, Hinxton, Cambridgeshire, United
Kingdom.
[PDF] - Miguel Vázquez, Rubén Nogales, Pedro Carmona,
Alberto Pascual and Juan Pavón. Rbbt: A Framework for Fast
Bioinformatics Development with Ruby. Advances in
Bioinformatics. Advances in Soft Computing, 2010, Volume 74/2010,
201-208, DOI: 10.1007/978-3-642-13214-8_26
[On-line version] - Vazquez, M; Chagoyen, M; Pascual-Montano, A. Named Entity
Recognition and Normalization: A Domain-Specific Language Approach. 2nd
International Workshop on Practical Applications of Computational
Biology and Bioinformatics (IWPACBB 08). Volume: 49 Pages:
147-155 Published: 2009
[On-line version] - L.N. Ciuffo, et. al. on behalf of the EELA-2 project. Biomedical applications in the EELA-2 project. NETTAB 2009. Ninth Annual Workshop Network Tools and Applications in Biology.
- Mariana Neves, José-María Carazo and Alberto
Pascual-Montano. Extraction of biomedical events using case-based
reasoning. BioNLP 2009.
[PDF] - M.L. Neves, J.M. Carazo and A. Pascual-Montano. Moara Project: A Flexible and Trainable Java Library for the Gene/Protein Recognition and Normalization Tasks. The Annual Meeting of The ISMB BioLINK Special Interest Group on Text Data Mining. In Association with ISMB 2009.
- M. Vazquez, M. Chagoyen and A. Pascual-Montano. SENT: Semantics Features in Text. BioLINK SIG: Linking Literature, Information and Knowledge for Biology. The Annual Meeting of The ISMB BioLINK Special Interest Group on Text Data Mining. In Association with ISMB 2008.
- A. Pascual-Montano. Non-negative matrix factorization in bioinformatics:towards understanding biological processes. Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS 2008). pp. 1332-1335
- R. Nogales, E. Mejía, C. Vicente, E. Montes, A. Delgado, F.J. Pérez Griffo, F. Tirado, A. Pascual-Montano. GENECODIS-Grid: An online grid-based tool to predict functional information in gene lists. Proceedings of the Third Conference of the EELA Project.2007 pp. 167-174
- Chagoyen, M., Fernandes, H., Carazo, J.M. and Pascual-Montano, A.
(2008) Functional classification of genes using non-negative
independent component analysis. In Bonilla, L.L., Moscoso, M., Platero,
G. and Vega, J.M. (eds), Progress in Industrial Mathematics at Ecmi
2006. 571-575.
[On-line version] - García, C., Prieto, M. and Pascual-Montano, A.. A speculative parallel algorithm for Self-organizing Maps. 2005. Proceedings of Parallel Computing. pp. 615-622
- Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, Jose M.
Carazo, Alberto Pascual-Montano. Can literature analysis reveal
similarities among cellular processes? The Joint BioLINK and 9th
Bio-Ontologies Meeting. ISMB 2006
[On-line version] - Alberto Pascual-Montano, Pedro Carmona-Sáez, Roberto D.
Pascual-Marqui, Francisco Tirado and José María Carazo.
Two-way clustering of gene expression profiles by sparse matrix
factorization. IEEE Computational Systems Bioinformatics Conference.
2005. pp. 103-104.
[On-line version]