José María Carazo

Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, José María Carazo: Integrating human and murine anatomical gene expression data for improved comparisons. Bioinformatics 28(3): 397-402 (2012)

Carlos Oscar Sánchez Sorzano, Joaquín Oton, Jesús Cuenca Alba, Airen Zaldivar-Perez, Gabriel Caffarena, Javier Sanchez-Jimenez, Cédric Messaoudi, Sergio Marco, Roberto Marabini, José María Carazo: Image processing for Cellular tomography using soft X-rays. ISBI 2012: 1322

Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano: Moara: a Java library for extracting and normalizing gene and protein mentions. BMC Bioinformatics 11: 157 (2010)

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 Research 38(Web-Server-Issue): 228-232 (2010)

Natalia Jiménez-Lozano, Joan Segura, José Ramón Macías, Juanjo Vega, José María Carazo: aGEM: an integrative system for analyzing spatial-temporal gene-expression information. Bioinformatics 25(19): 2566-2572 (2009)

Carlos Oscar Sánchez Sorzano, Cédric Messaoudi, Matthias Eibauer, Jose-Roman Bilbao-Castro, Reiner Hegerl, S. Nickell, Sergio Marco, José María Carazo: Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 10 (2009)

Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez, José María Carazo, Alberto D. Pascual-Montano: CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Research 37(Database-Issue): 175-180 (2009)

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 Research 37(Web-Server-Issue): 153-159 (2009)

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 Research 37(Web-Server-Issue): 317-322 (2009)

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. Bioinformatics 24(9): 1208-1209 (2008)

Monica Chagoyen, José María Carazo, Alberto D. Pascual-Montano: Assessment of protein set coherence using functional annotations. BMC Bioinformatics 9 (2008)

Carlos Oscar Sánchez Sorzano, Javier A. Velázquez-Muriel, Roberto Marabini, Gabor T. Herman, José María Carazo: Volumetric restrictions in single particle 3DEM reconstruction. Pattern Recognition 41(2): 616-626 (2008)

Laura Fernandez-de-Manuel, María J. Ledesma-Carbayo, Julian Atienza-Herrero, Carlos Oscar Sánchez Sorzano, José María Carazo, Andrés Santos: Flexible image registration for the identification of best fitted protein models in 3D-EM maps. ISBI 2008: 983-986

José-Jesús Fernández, Inmaculada García, José María Carazo, Roberto Marabini: Electron tomography of complex biological specimens on the Grid. Future Generation Comp. Syst. 23(3): 435-446 (2007)

Jose-Roman Bilbao-Castro, A. Merino, Inmaculada García, José María Carazo, José-Jesús Fernández: Parameter optimization in 3D reconstruction on a large scale grid. Parallel Computing 33(4-5): 250-263 (2007)

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. Annals OR 148(1): 133-165 (2006)

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 Bioinformatics 7: 41 (2006)

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 Bioinformatics 7: 54 (2006)

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 Bioinformatics 7: 78 (2006)

Monica Chagoyen, Pedro Carmona-Saez, Concha Gil, José María Carazo, Alberto D. Pascual-Montano: A literature-based similarity metric for biological processes. BMC Bioinformatics 7: 363 (2006)

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 Bioinformatics 7: 366 (2006)

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)

Ignacio Arganda-Carreras, Carlos Oscar Sánchez Sorzano, Roberto Marabini, José María Carazo, Carlos Ortiz-de-Solorzano, Jan Kybic: Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization. CVAMIA 2006: 85-95

Bartosz Telenczuk, María J. Ledesma-Carbayo, Javier A. Velázquez-Muriel, Carlos Oscar Sánchez Sorzano, José María Carazo, Andrés Santos: Molecular image registration using mutual information and differential evolution optimization. ISBI 2006: 844-847

Andrés Rodríguez Moreno, José María Carazo, Oswaldo Trelles-Salazar: Mining association rules from biological databases. JASIST 56(5): 493-504 (2005)

Carlos Oscar Sánchez Sorzano, Roberto Marabini, Gabor T. Herman, José María Carazo: Multiobjective algorithm parameter optimization using multivariate statistics in three-dimensional electron microscopy reconstruction. Pattern Recognition 38(12): 2587-2601 (2005)

Sjors H. W. Scheres, A. J. Merino, Carlos Oscar Sánchez Sorzano, José María Carazo: Grid Computing in 3D-EM Image Processing Using Xmipp. CBMS 2005: 561-563

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

Javier A. Velázquez-Muriel, José María Carazo: Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM. CSB Workshops 2005: 209-210

Sjors H. W. Scheres, Mikel Valle, José María Carazo: Fast maximum-likelihood refinement of electron microscopy images. ECCB/JBI 2005: 244

Monica Chagoyen, M. Erdem Kurul, Pedro A. de Alarcón, José María Carazo, Amarnath Gupta: Designing and executing scientific workflows with a programmable integrator. Bioinformatics 20(13): 2092-2100 (2004)

José-Jesús Fernández, José María Carazo, Inmaculada García: Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing. J. Parallel Distrib. Comput. 64(2): 285-300 (2004)

José-Jesús Fernández, Jose-Roman Bilbao-Castro, Roberto Marabini, José María Carazo, Inmaculada García: Biological Structure Determination by EM is Well Suited to Grid Computing. New Generation Comput. 22(2): 187-188 (2004)

José-Jesús Fernández, Jose-Roman Bilbao-Castro, Roberto Marabini, José María Carazo, Inmaculada García: On the Suitability of Biological Structure Determination by Electron Microscopy to Grid Computing. New Generation Comput. 23(1): 101-112 (2004)

Jose-Roman Bilbao-Castro, Roberto Marabini, José María Carazo, Inmaculada García, José-Jesús Fernández: The Potential Of Grid Computing In Three-Dimensional Electron Microscopy. Parallel Processing Letters 14(2): 151-162 (2004)

Roberto Marabini, Carlos Oscar Sánchez Sorzano, Samuel Matej, José-Jesús Fernández, José María Carazo, Gabor T. Herman: 3-D reconstruction of 2-D crystals in real space. IEEE Transactions on Image Processing 13(4): 549-561 (2004)

Jose-Roman Bilbao-Castro, José María Carazo, José-Jesús Fernández, Inmaculada García: Parallelization and Comparison of 3D Iterative Reconstruction Algorithms. PDP 2004: 96-102

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. Bioinformatics 19(5): 657-658 (2003)

Monica Chagoyen, M. Erdem Kurul, Pedro A. de Alarcón, Simone Santini, Bertram Ludäscher, José María Carazo, Amarnath Gupta: A Semantic Mediation Approach for Problems in Computational Molecular Biology. CSB 2003: 386-387

José-Jesús Fernández, Jose-Roman Bilbao-Castro, Roberto Marabini, José María Carazo, Inmaculada García: Grid Computing in Structure Determination of Biological Specimens by Electron Microscope Tomography. European Across Grids Conference 2003: 171-181

Jose-Roman Bilbao-Castro, José María Carazo, Inmaculada García, José-Jesús Fernández: Parallel iterative reconstruction methods for structure determination of biological specimens by electron microscopy. ICIP (1) 2003: 565-568

Carlos Oscar Sánchez Sorzano, José María Carazo, Oswaldo Trelles: Command-line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE). Softw., Pract. Exper. 32(9): 873-887 (2002)

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

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

Roberto Marabini, Gabor T. Herman, Carlos Oscar Sánchez Sorzano, José María Carazo: Volumetric constraints in 3D tomography applied to electron microscopy. ISBI 2002: 641-644

Roberto Marabini, Gabor T. Herman, Carlos Oscar Sánchez Sorzano, José María Carazo, José-Jesús Fernández, Samuel Matej: 3D reconstruction of 2D crystals from projections in real space. ISBI 2002: 689-692

José-Jesús Fernández, Albert F. Lawrence, Javier Roca Piera, Inmaculada García, Mark H. Ellisman, José María Carazo: High Performance Computing in Electron Microscope Tomography of Complex Biological Structures. VECPAR 2002: 166-180

Roberto D. Pascual-Marqui, Alberto D. Pascual-Montano, Kieko Kochi, José María Carazo: Smoothly distributed fuzzy c-means: a new self-organizing map. Pattern Recognition 34(12): 2395-2402 (2001)

Gabor T. Herman, Roberto Marabini, José María Carazo, Edgar Garduño, Robert M. Lewitt, Samuel Matej: Image processing approaches to biological three-dimensional electron microscopy. Int. J. Imaging Systems and Technology 11(1): 12-29 (2000)

José María Carazo, Ernst H. K. Stelzer, A. Engel, I. Fita, C. Henn, J. Machtynger, P. McNeil, David M. Shotton, Monica Chagoyen, Pedro A. de Alarcón, R. Fritsch, J. B. Heymann, S. Kalko, J. J. Pittet, Patricia Rodriguez-Tomé, Thomas Boudier: Organising multi-dimensional biological image information: the BioImage Database. Nucleic Acids Research 27(1): 280-283 (1999)

Alberto Pascual, Montserrat Barcéna, Juan J. Merelo Guervós, José María Carazo: Application of the Fuzzy Kohonen Clustering Network to Biological Macromolecules Images Classification. IWANN (2) 1999: 331-340

Juan J. Merelo Guervós, Víctor Manuel Rivas Santos, Gustavo Romero, Pedro A. Castillo Valdivieso, Alberto Pascual, José María Carazo: Improved Automatic Classification of Biological Particles from Electron-Microscopy Images Using Genetic Neural Nets. IWANN (2) 1999: 373-382

Huaichun Wang, Joaquín Dopazo, José María Carazo: Self-organizing tree growing network for classifying amino acids. Bioinformatics 14(4): 376-377 (1998)

Oswaldo Trelles, Miguel A. Andrade, Alfonso Valencia, Emilio L. Zapata, José María Carazo: Computational space reduction and parallelization of a new clustering approach for large groups of sequences. Bioinformatics 14(5): 439-451 (1998)

Oswaldo Trelles, C. Ceron, Huaichun Wang, Joaquín Dopazo, José María Carazo: New phylogenetic venues opened by a novel implementation of the DNAml algorithm. Bioinformatics 14(6): 544-545 (1998)

Juan J. Merelo Guervós, Alberto Prieto, Federico Morán, Roberto Marabini, José María Carazo: Automatic Classification of Biological Particles from Electron-microscopy Images Using Conventional and Genetic-algorithm Optimized Learning Vector Quantization. Neural Processing Letters 8(1): 55-65 (1998)

C. Ceron, Joaquín Dopazo, Emilio L. Zapata, José María Carazo, Oswaldo Trelles: Parallel Implementation of DNAml Program on Message-Passing Architectures. Parallel Computing 24(5-6): 701-716 (1998)

S. Lindek, R. Fritsch, Ernst H. K. Stelzer, José María Carazo, A. Engel, I. Fita, C. Henn, P. McNeil, David M. Shotton, J. Machtynger: Biolmage, the database of biological microscopy data. German Conference on Bioinformatics 1998

Andrés Rodríguez Moreno, Luis Gerardo de la Fraga, Emilio L. Zapata, José María Carazo, Oswaldo Trelles: Biological sequence analysis on distributed-shared memory multiprocessors. PDP 1998: 20-26

Joaquín Dopazo, Huaichun Wang, José María Carazo: A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree. IWANN 1997: 932-941

Juan J. Merelo Guervós, Alberto Prieto, Federico Morán, Roberto Marabini, José María Carazo: A GA-optimized Neural Network for Classification of Biological Particles from Electron-Microscopy Images. IWANN 1997: 1174-1182

Roberto Marabini, José María Carazo: On a new computationally fast image invariant based on bispectral projections. Pattern Recognition Letters 17(9): 959-967 (1996)

Oswaldo Trelles-Salazar, Emilio L. Zapata, Joaquín Dopazo, A. F. Coulson, José María Carazo: An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data. Computer Applications in the Biosciences 11(3): 301-308 (1995)

Oswaldo Trelles-Salazar, Emilio L. Zapata, José María Carazo: On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures. Computer Applications in the Biosciences 10(5): 509-511 (1994)

Oswaldo Trelles-Salazar, Emilio L. Zapata, José María Carazo: Mapping Strategies for Sequential Sequence Comparison Algorithms on LAN-Based Message Passing Architectures. HPCN 1994: 197-202

Francisco F. Rivera, Emilio L. Zapata, José María Carazo: Cluster validity based on the hard tendency of the fuzzy classification. Pattern Recognition Letters 11(1): 7-12 (1990)