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1

Nonsmooth nonnegative matrix factorization (nsNMF)

Pascual-Montano, A., Carazo, J.M., Kochi, K., Lehmann, D., Pascual-Marqui, R.D.

Journal:

IEEE Transactions on Pattern Analysis and Machine Intelligence

Year:

2006

Language:

english

File:

PDF, 3.87 MB

english, 2006

2

Genome-wide signatures of flowering adaptation to climate temperature: regional analyses in a highly diverse native range of Arabidopsis thaliana

Tabas-Madrid, Daniel, Méndez-Vigo, Belén, Arteaga, Noelia, Marcer, Arnald, Pascual-Montano, Alberto, Weigel, Detlef, Xavier Picó, F., Alonso-Blanco, Carlos

Journal:

Plant, Cell & Environment

Year:

2018

Language:

english

File:

PDF, 1.08 MB

english, 2018

3

Gene expression modular analysis: an overview from the data mining perspective

Alberto Pascual-Montano

Journal:

Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery

Year:

2011

Language:

english

File:

PDF, 707 KB

english, 2011

4

ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data

Abascal, F., Carmona-Saez, P., Carazo, J.-M., Pascual-Montano, A.

Journal:

Year:

2008

Language:

english

File:

PDF, 71 KB

english, 2008

5

[IEEE 2008 IEEE International Symposium on Circuits and Systems - ISCAS 2008 - Seattle, WA, USA (2008.05.18-2008.05.21)] 2008 IEEE International Symposium on Circuits and Systems - Non-negative matrix factorization in bioinformatics: Towards understanding biological processes

Pascual-Montano, Alberto

Year:

2008

Language:

english

File:

PDF, 125 KB

english, 2008

6

Smoothly distributed fuzzy c-means: a new self-organizing map

R.D. Pascual-Marqui, A.D. Pascual-Montano, K. Kochi, J.M. Carazo

Journal:

Pattern Recognition

Year:

2001

Language:

english

File:

PDF, 348 KB

english, 2001

7

Discovering semantic features in the literature: a foundation for building functional associations

Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, Jose M Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.29 MB

english, 2006

8

Host Response to the Attenuated Poxvirus Vector NYVAC: Upregulation of Apoptotic Genes and NF- B-Responsive Genes in Infected HeLa Cells

Guerra, S., Lopez-Fernandez, L. A., Pascual-Montano, A., Najera, J. L., Zaballos, A., Esteban, M.

Journal:

Journal of Virology

Year:

2006

Language:

english

File:

PDF, 686 KB

english, 2006

9

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures

Vazquez, M., Nogales-Cadenas, R., Arroyo, J., Botias, P., Garcia, R., Carazo, J. M., Tirado, F., Pascual-Montano, A., Carmona-Saez, P.

Journal:

Nucleic Acids Research

Year:

2010

Language:

english

File:

PDF, 1.13 MB

english, 2010

10

Improving miRNA-mRNA interaction predictions

Tabas-Madrid, Daniel, Muniategui, Ander, Sánchez-Caballero, Ignacio, Martínez-Herrera, Dannys Jorge, S Sorzano, Carlos Oscar, Rubio, Angel, Pascual-Montano, Alberto

Journal:

Year:

2014

Language:

english

File:

PDF, 1.68 MB

english, 2014

11

bioNMF: a versatile tool for non-negative matrix factorization in biology

Alberto Pascual-Montano, Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M Carazo, Roberto D Pascual-Marqui

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 706 KB

english, 2006

12

Cellular Gene Expression Survey of Vaccinia Virus Infection of Human HeLa Cells

Guerra, S., Lopez-Fernandez, L. A., Pascual-Montano, A., Munoz, M., Harshman, K., Esteban, M.

Journal:

Journal of Virology

Year:

2003

Language:

english

File:

PDF, 2.48 MB

english, 2003

13

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Medina, I., Carbonell, J., Pulido, L., Madeira, S. C., Goetz, S., Conesa, A., Tarraga, J., Pascual-Montano, A., Nogales-Cadenas, R., Santoyo, J., Garcia, F., Marba, M., Montaner, D., Dopazo, J.

Journal:

Nucleic Acids Research

Year:

2010

Language:

english

File:

PDF, 82 KB

english, 2010

14

555PASSOCIATION BETWEEN COLON CANCER MOLECULAR SUBTYPES OBTAINED BY EXPRESSION PROFILING AND BY MICRORNA (MIR) PROFILING

Perez-Villamil, B., Paz-Cabezas, M., Pascual-Montano, A., Fuentes, M., Sastre, J., Díaz-Rubio, E.

Journal:

Annals of Oncology

Year:

2014

File:

PDF, 60 KB

2014

15

GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics

Tabas-Madrid, D., Nogales-Cadenas, R., Pascual-Montano, A.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.41 MB

english, 2012

16

SENT: semantic features in text

Vazquez, M., Carmona-Saez, P., Nogales-Cadenas, R., Chagoyen, M., Tirado, F., Carazo, J. M., Pascual-Montano, A.

Journal:

Nucleic Acids Research

Year:

2009

Language:

english

File:

PDF, 938 KB

english, 2009

17

Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways

Manesia, Javed K., Xu, Zhuofei, Broekaert, Dorien, Boon, Ruben, van Vliet, Alex, Eelen, Guy, Vanwelden, Thomas, Stegen, Steve, Van Gastel, Nick, Pascual-Montano, Alberto, Fendt, Sarah-Maria, Carmeliet

Journal:

Stem Cell Research

Year:

2015

Language:

english

File:

PDF, 847 KB

english, 2015

18

Optimization problems in electron microscopy of single particles

C. O. S. Sorzano, R. Marabini, A. Pascual-Montano, S. H. W. Scheres, J. M. Carazo

Journal:

Annals of Operations Research

Year:

2006

Language:

english

File:

PDF, 772 KB

english, 2006

19

Microarray Analysis Reveals Characteristic Changes of Host Cell Gene Expression in Response to Attenuated Modified Vaccinia Virus Ankara Infection of Human HeLa Cells

Guerra, S., Lopez-Fernandez, L. A., Conde, R., Pascual-Montano, A., Harshman, K., Esteban, M.

Journal:

Journal of Virology

Year:

2004

Language:

english

File:

PDF, 1.37 MB

english, 2004

20

[IEEE 2011 11th International Conference on Intelligent Systems Design and Applications (ISDA) - Cordoba, Spain (2011.11.22-2011.11.24)] 2011 11th International Conference on Intelligent Systems Design and Applications - Biclustering and classification analysis in gene expression using Nonnegative Matrix Factorization on multi-GPU systems

Mejia-Roa, E., Garcia, C., Gomez, J. I., Prieto, M., Tirado, F., Nogales, R., Pascual-Montano, A.

Year:

2011

Language:

english

File:

PDF, 825 KB

english, 2011

21

Modeling Shape and Topology of Low-Resolution Density Maps of Biological Macromolecules

De-Alarcón, Pedro A., Pascual-Montano, Alberto, Gupta, Amarnath, Carazo, Jose M.

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 670 KB

english, 2002

22

The cyclic AMP receptor protein modulates quorum sensing, motility and multiple genes that affect intestinal colonization in Vibrio cholerae

Liang, W., Pascual-Montano, A., Silva, A. J., Benitez, J. A.

Journal:

Microbiology (Society for General Microbiology)

Year:

2007

Language:

english

File:

PDF, 278 KB

english, 2007

23

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

Javier A Velázquez-Muriel, Manuel Rueda, Isabel Cuesta, Alberto Pascual-Montano, Modesto Orozco, José-María Carazo

Journal:

BMC Structural Biology

Year:

2009

Language:

english

File:

PDF, 3.40 MB

english, 2009

24

Assessment of protein set coherence using functional annotations

Monica Chagoyen, Jose M Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 699 KB

english, 2008

25

XMIPP: a new generation of an open-source image processing package for electron microscopy

C.O.S. Sorzano, R. Marabini, J. Velázquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo, A. Pascual-Montano

Journal:

Journal of Structural Biology

Year:

2004

Language:

english

File:

PDF, 943 KB

english, 2004

26

Proteogenomics Dashboard for the Human Proteome Project

Tabas-Madrid, Daniel, Alves-Cruzeiro, Joao, Segura, Victor, Guruceaga, Elizabeth, Vialas, Vital, Prieto, Gorka, García, Carlos, Corrales, Fernando J., Albar, Juan Pablo, Pascual-Montano, Alberto

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 1.80 MB

english, 2015

27

A subpopulation of CD103 pos ICOS pos Treg cells occurs at high frequency in lymphopenic mice and represents a lymph node specific differentiation stage

Barthlott, Thomas, Bosch, Angela J. T., Berkemeier, Caroline, Nogales-Cadenas, Rubén, Jeker, Lukas T., Keller, Marcel P., Pascual-Montano, Alberto, Holländer, Georg A.

Journal:

European Journal of Immunology

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

28

[ACM Press the 14th International Conference - Uppsala, Sweden (2011.03.21-2011.03.24)] Proceedings of the 14th International Conference on Extending Database Technology - EDBT/ICDT '11 - Finding closed frequent item sets by intersecting transactions

Borgelt, Christian, Yang, Xiaoyuan, Nogales-Cadenas, Ruben, Carmona-Saez, Pedro, Pascual-Montano, Alberto

Year:

2011

Language:

english

File:

PDF, 921 KB

english, 2011

29

3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy

Nogales-Cadenas, R., Jonic, S., Tama, F., Arteni, A. A., Tabas-Madrid, D., Vazquez, M., Pascual-Montano, A., Sorzano, C. O. S.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 3.10 MB

english, 2013

30

[IEEE 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) - Stanford, CA, USA (08-11 Aug. 2005)] 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) - Two-way clustering of gene expression profiles by sparse matrix factorization

Pascual-Montano, A., Tirado, F., Carmona-Saez, P., Carazo, J.M., Pascual-Marqui, R.D.

Year:

2005

Language:

english

File:

PDF, 127 KB

english, 2005

31

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

Mejía-Roa, Edgardo, Tabas-Madrid, Daniel, Setoain, Javier, García, Carlos, Tirado, Francisco, Pascual-Montano, Alberto

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.57 MB

english, 2015

32

Moara: a Java library for extracting and normalizing gene and protein mentions

Mariana L Neves, José-María Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 3.15 MB

english, 2010

33

NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning

Setoain, Javier, Franch, Mònica, Martínez, Marta, Tabas-Madrid, Daniel, Sorzano, Carlos O. S., Bakker, Annette, Gonzalez-Couto, Eduardo, Elvira, Juan, Pascual-Montano, Alberto

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

34

Engene: the processing and exploratory analysis of gene expression data

Garcia de la Nava, J., Santaella, D. F., Alba, J. C., Carazo, J. M., Trelles, O., Pascual-Montano, A.

Journal:

Year:

2003

Language:

english

File:

PDF, 128 KB

english, 2003

35

Chromothripsis: Breakage-fusion-bridge over and over again

Oscar Sánchez Solorzano, Carlos, Pascual-Montano, Alberto, Sánchez de Diego, Ainhoa, Martínez-A, Carlos, H.M. van Wely, Karel

Journal:

Year:

2013

Language:

english

File:

PDF, 1.65 MB

english, 2013

36

Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs

Villarroya-Beltri, Carolina, Gutiérrez-Vázquez, Cristina, Sánchez-Cabo, Fátima, Pérez-Hernández, Daniel, Vázquez, Jesús, Martin-Cofreces, Noa, Martinez-Herrera, Dannys Jorge, Pascual-Montano, Alberto,

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 1.35 MB

english, 2013

37

Integrated analysis of gene expression by association rules discovery

Pedro Carmona-Saez, Monica Chagoyen, Andres Rodriguez, Oswaldo Trelles, Jose M Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.47 MB

english, 2006

38

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

Nogales-Cadenas, R., Carmona-Saez, P., Vazquez, M., Vicente, C., Yang, X., Tirado, F., Carazo, J. M., Pascual-Montano, A.

Journal:

Nucleic Acids Research

Year:

2009

Language:

english

File:

PDF, 2.68 MB

english, 2009

39

[IEEE Comput. Soc 16th International Conference on Pattern Recognition - Quebec City, Que., Canada (11-15 Aug. 2002)] Object recognition supported by user interaction for service robots - Modeling shape and topology of 3D images of biological specimens

De-Alarcon, P.A., Pascual-Montano, A.P., Gupta, A., Carazo, J.M.

Year:

2002

Language:

english

File:

PDF, 297 KB

english, 2002

40

Proteopathogen, a protein database for studying Candida albicans – host interaction

Vital Vialás, Rubén Nogales-Cadenas, César Nombela, Alberto Pascual-Montano, Concha Gil

Journal:

Year:

2009

Language:

english

File:

PDF, 222 KB

english, 2009

41

Biclustering of gene expression data by non-smooth non-negative matrix factorization

Pedro Carmona-Saez, Roberto D Pascual-Marqui, F Tirado, Jose M Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 625 KB

english, 2006

42

Quantitative self-organizing maps for clustering electron tomograms

A. Pascual-Montano, K.A. Taylor, H. Winkler, R.D. Pascual-Marqui, J.-M. Carazo

Journal:

Journal of Structural Biology

Year:

2002

Language:

english

File:

PDF, 387 KB

english, 2002

43

bioNMF: a web-based tool for nonnegative matrix factorization in biology

Mejia-Roa, E., Carmona-Saez, P., Nogales, R., Vicente, C., Vazquez, M., Yang, X. Y., Garcia, C., Tirado, F., Pascual-Montano, A.

Journal:

Nucleic Acids Research

Year:

2008

Language:

english

File:

PDF, 2.26 MB

english, 2008

44

Distinct Molecular Signature of Murine Fetal Liver and Adult Hematopoietic Stem Cells Identify Novel Regulators of Hematopoietic Stem Cell Function

Manesia, Javed K., Franch, Monica, Tabas-Madrid, Daniel, Nogales-Cadenas, Ruben, Vanwelden, Thomas, Van Den Bosch, Elisa, Xu, Zhuofei, Pascual-Montano, Alberto, Khurana, Satish, Verfaillie, Catherine

Journal:

Stem Cells and Development

Year:

2017

Language:

english

File:

PDF, 1.85 MB

english, 2017

45

A literature-based similarity metric for biological processes

Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, Jose M Carazo, Alberto Pascual-Montano

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 366 KB

english, 2006

46

A Novel Neural Network Technique for Analysis and Classification of EM Single-Particle Images

A Pascual-Montano, L.E Donate, M Valle, M Bárcena, R.D Pascual-Marqui, J.M Carazo

Journal:

Journal of Structural Biology

Year:

2001

Language:

english

File:

PDF, 529 KB

english, 2001

47

miRNA profiling during antigen-dependent T cell activation: A role for miR-132-3p

Gutiérrez-Vázquez, Cristina, Rodríguez-Galán, Ana, Fernández-Alfara, Marcos, Mittelbrunn, María, Sánchez-Cabo, Fátima, Martínez-Herrera, Dannys Jorge, Ramírez-Huesca, Marta, Pascual-Montano, Alberto,

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.39 MB

english, 2017

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