3-D electron microscopy and incomplete angular coverage: a restoration scheme based on projections onto convex sets. - José María Carazo (ICASSP, 1988)

Cluster validity based on the hard tendency of the fuzzy classification. - Francisco F. Rivera; Emilio L. Zapata; José María Carazo (Pattern Recognit. Lett., 1990)

Image template matching on hypercube SIMD computers. - Emilio L. Zapata; José Ignacio Benavides Benítez; Oscar G. Plata; Francisco F. Rivera; José María Carazo (Signal Process., 1990)

Image reconstruction on hypercube computers: Application to electron microscopy. - Emilio L. Zapata; Ignacio Benavides; Francisco F. Rivera; Javier D. Bruguera; Tomás F. Pena; José María Carazo (Signal Process., 1992)

Parallel algorithm for principal components based on Hotelling's iterative procedure. - José Carlos Cabaleiro; José María Carazo; Emilio L. Zapata (PDP, 1993)

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

3d Reconstruction Of Macromolecules On Multiprocessors. - Manuel Ujaldon; Rafael Asenjo; Emilio L. Zapata; José Carlos Cabaleiro; José María Carazo (PDP, 1994)

Prototype for a new distributed database of volume data obtained by 3D imaging. - Roberto Marabini; C. Vaquerizo; José-Jesús Fernández; José María Carazo; M. Ladjadj; O. Odesanya; J. Frank (VBC, 1994)

On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures. - Oswaldo Trelles-Salazar; Emilio L. Zapata; José María Carazo (Comput. Appl. Biosci., 1994)

Practical issues on invariant image averaging using the Bispectrum. - Roberto Marabini; José María Carazo (Signal Process., 1994)

An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data. - Oswaldo Trelles-Salazar; Emilio L. Zapata; Joaquín Dopazo; A. F. Coulson; José María Carazo (Comput. Appl. Biosci., 1995)

On a new computationally fast image invariant based on bispectral projections. - Roberto Marabini; José María Carazo (Pattern Recognit. Lett., 1996)

Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system. - Inmaculada García; J. Roca; Jose Rodrigo Sanjurjo; José María Carazo; Emilio L. Zapata (Signal Process., 1996)

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

A GA-optimized Neural Network for Classification of Biological Particles from Electron-Microscopy Images. - Juan Julián Merelo Guervós; Alberto Prieto; Federico Morán; Roberto Marabini; José María Carazo (IWANN, 1997)

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

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

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

New phylogenetic venues opened by a novel implementation of the DNAml algorithm. - Oswaldo Trelles; C. Ceron; Huaichun Wang; Joaquín Dopazo; José María Carazo (Bioinform., 1998)

Self-organizing tree growing network for classifying amino acids. - Huaichun Wang; Joaquín Dopazo; José María Carazo (Bioinform., 1998)

Automatic Classification of Biological Particles from Electron-microscopy Images Using Conventional and Genetic-algorithm Optimized Learning Vector Quantization. - Juan Julián Merelo Guervós; Alberto Prieto; Federico Morán; Roberto Marabini; José María Carazo (Neural Process. Lett., 1998)

Parallel Implementation of DNAml Program on Message-Passing Architectures. - C. Ceron; Joaquín Dopazo; Emilio L. Zapata; José María Carazo; Oswaldo Trelles (Parallel Comput., 1998)

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

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

Bayesian image restoration: Parallel implementation on a SGI origin multiprocessor. - José María Carazo; Ramon Doallo; J. M. Eiroa; Jose Rodrigo Sanjurjo (PARCO, 1999)

Organising multi-dimensional biological image information: the BioImage Database. - 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; et al. (Nucleic Acids Res., 1999)

Self-Organizing Networks for Mapping and Clustering Biological Macromolecules Images. - Alberto Pascual; Montserrat Barcéna; Juan Julián Merelo Guervós; José María Carazo (ANNIMAB, 2000)

Image processing approaches to biological three-dimensional electron microscopy. - Gabor T. Herman; Roberto Marabini; José María Carazo; Edgar Garduño; Robert M. Lewitt; Samuel Matej (Int. J. Imaging Syst. Technol., 2000)

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

Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases. - Pedro A. de Alarcón; Alberto D. Pascual-Montano; José María Carazo (CIVR, 2002)

Modeling Shape and Topology of 3D Images of Biological Specimens. - Pedro A. de Alarcón; Alberto D. Pascual-Montano; Amarnath Gupta; José María Carazo (ICPR (1), 2002)

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

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

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

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

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

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

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

Engene: the processing and exploratory analysis of gene expression data. - Jorge García de la Nava; Daniel Franco Santaella; Jesús Cuenca Alba; José María Carazo; Oswaldo Trelles; Alberto D. Pascual-Montano (Bioinform., 2003)

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

Designing and executing scientific workflows with a programmable integrator. - Monica Chagoyen; M. Erdem Kurul; Pedro A. de Alarcón; José María Carazo; Amarnath Gupta (Bioinform., 2004)

Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing. - José-Jesús Fernández; José María Carazo; Inmaculada García (J. Parallel Distributed Comput., 2004)

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

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

The Potential Of Grid Computing In Three-Dimensional Electron Microscopy. - Jose-Roman Bilbao-Castro; Roberto Marabini; José María Carazo; Inmaculada García; José-Jesús Fernández (Parallel Process. Lett., 2004)

3-D reconstruction of 2-D crystals in real space. - Roberto Marabini; Carlos Oscar Sánchez Sorzano; Samuel Matej; José-Jesús Fernández; José María Carazo; Gabor T. Herman (IEEE Trans. Image Process., 2004)

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

Two-way clustering of gene expression profiles by sparse matrix factorization. - Alberto D. Pascual-Montano; Francisco Tirado; Pedro Carmona-Saez; José María Carazo; Roberto D. Pascual-Marqui (CSB Workshops, 2005)

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

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

Mining association rules from biological databases. - Andrés Rodríguez Moreno; José María Carazo; Oswaldo Trelles-Salazar (J. Assoc. Inf. Sci. Technol., 2005)

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

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

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

Optimization problems in electron microscopy of single particles. - Carlos Oscar Sánchez Sorzano; Roberto Marabini; Alberto D. Pascual-Montano; Sjors H. W. Scheres; José María Carazo (Ann. Oper. Res., 2006)

Integrated analysis of gene expression by association rules discovery. - Pedro Carmona-Saez; Monica Chagoyen; Andrés Rodríguez Moreno; Oswaldo Trelles; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

Biclustering of gene expression data by non-smooth non-negative matrix factorization. - Pedro Carmona-Saez; Roberto D. Pascual-Marqui; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

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

Discovering semantic features in the literature: a foundation for building functional associations. - Monica Chagoyen; Pedro Carmona-Saez; Hagit Shatkay; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

bioNMF: a versatile tool for non-negative matrix factorization in biology. - Alberto D. Pascual-Montano; Pedro Carmona-Saez; Monica Chagoyen; Francisco Tirado; José María Carazo; Roberto D. Pascual-Marqui (BMC Bioinform., 2006)

Nonsmooth Nonnegative Matrix Factorization (nsNMF). - Alberto D. Pascual-Montano; José María Carazo; Kieko Kochi; Dietrich Lehmann; Roberto D. Pascual-Marqui (IEEE Trans. Pattern Anal. Mach. Intell., 2006)

Image processing and 3-D reconstruction in electron microscopy. - José-Jesús Fernández; Carlos Oscar Sánchez Sorzano; Roberto Marabini; José María Carazo (IEEE Signal Process. Mag., 2006)

Electron tomography of complex biological specimens on the Grid. - José-Jesús Fernández; Inmaculada García; José María Carazo; Roberto Marabini (Future Gener. Comput. Syst., 2007)

Parameter optimization in 3D reconstruction on a large scale grid. - Jose-Roman Bilbao-Castro; A. Merino; Inmaculada García; José María Carazo; José-Jesús Fernández (Parallel Comput., 2007)

CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem. - Mariana L. Neves; Monica Chagoyen; José María Carazo; Alberto D. Pascual-Montano (BioNLP, 2008)

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

Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library. - Mariana L. Neves; José María Carazo; Alberto D. Pascual-Montano (BioLINK@ISMB/ECCB, 2008)

ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. - Federico Abascal; Pedro Carmona-Saez; José María Carazo; Alberto D. Pascual-Montano (Bioinform., 2008)

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

Design and analysis of an object-oriented discrete-event simulation engine for ATM telecommunication networks. - Pablo Cortés 001; Jesús Muñuzuri; Luis Onieva; José María Carazo (Int. J. Simul. Process. Model., 2008)

Volumetric restrictions in single particle 3DEM reconstruction. - Carlos Oscar Sánchez Sorzano; Javier A. Velázquez-Muriel; Roberto Marabini; Gabor T. Herman; José María Carazo (Pattern Recognit., 2008)

Extraction of biomedical events using case-based reasoning. - Mariana L. Neves; José María Carazo; Alberto D. Pascual-Montano (BioNLP@HLT-NAACL (Shared Task), 2009)

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

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

CentrosomeDB: a human centrosomal proteins database. - Rubén Nogales-Cadenas; Federico Abascal; Javier Díez-Pérez; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. - Rubén Nogales-Cadenas; Pedro Carmona-Saez; Miguel Vázquez; Cesar Vicente; Xiaoyuan Yang 001; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

SENT: semantic features in text. - Miguel Vázquez; Pedro Carmona-Saez; Rubén Nogales-Cadenas; Monica Chagoyen; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

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

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. - Miguel Vázquez; Rubén Nogales-Cadenas; Javier Arroyo; Pedro Botías; Raul García; José María Carazo; Francisco Tirado; Alberto D. Pascual-Montano; Pedro Carmona-Saez (Nucleic Acids Res., 2010)

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

Integrating human and murine anatomical gene expression data for improved comparisons. - Natalia Jiménez-Lozano; Joan Segura; José Ramón Macías; Juanjo Vega; José María Carazo (Bioinform., 2012)

A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. - Vahid Abrishami; Airen Zaldívar-Peraza; José Miguel de la Rosa-Trevín; Javier Vargas 001; Joaquín Otón; Roberto Marabini; Yoel Shkolnisky; José María Carazo; Carlos Oscar Sánchez Sorzano (Bioinform., 2013)

An image processing approach to the simulation of electron microscopy volumes of atomic structures. - Carlos Oscar Sánchez Sorzano; Javier Vargas 001; Joaquín Otón; Vahid Abrishami; José Miguel de la Rosa-Trevín; S. del Riego; A. Fernandez-Alderete; C. Martinez-Rey; Roberto Marabini; José María Carazo (ICIP, 2014)

Outlier detection for single particle analysis in Electron Microscopy. - Carlos Oscar Sánchez Sorzano; Javier Vargas 001; José Miguel de la Rosa-Trevín; Airen Zaldívar-Peraza; Joaquín Otón; Vahid Abrishami; Ignacio Foche; Roberto Marabini; Gabriel Caffarena; José María Carazo (IWBBIO, 2014)

Efficient initial volume determination from electron microscopy images of single particles. - Javier Vargas 001; Ana-Lucia Álvarez-Cabrera; Roberto Marabini; José María Carazo; Carlos Oscar Sánchez Sorzano (Bioinform., 2014)

Using neighborhood cohesiveness to infer interactions between protein domains. - Joan Segura; Carlos Oscar Sánchez Sorzano; Jesús Cuenca Alba; Patrick Aloy; José María Carazo (Bioinform., 2015)

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures. - Joan Segura; Rubén Sánchez García; Marta Martínez; Jesús Cuenca Alba; Daniel Tabas-Madrid; Carlos Oscar Sánchez Sorzano; José María Carazo (Bioinform., 2017)

Challenges ahead Electron Microscopy for Structural Biology from the Image Processing point of view. - Carlos Oscar Sánchez Sorzano; José María Carazo (CoRR, 2017)

BIPSPI: a method for the prediction of partner-specific protein-protein interfaces. - Rubén Sánchez García; Carlos Oscar Sánchez Sorzano; José María Carazo; Joan Segura (Bioinform., 2019)

Validation of electron microscopy initial models via small angle X-ray scattering curves. - Amaya Jiménez; Slavica Jonic; Tomás Majtner; Joaquín Otón; Jose Luis Vilas; David Maluenda; Javier Mota; Erney Ramírez-Aportela; Marta Martínez; Yaiza Rancel; Joan Segura; Rubén Sánchez García; et al. (Bioinform., 2019)

3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations. - Joan Segura; Rubén Sánchez García; Carlos Oscar Sánchez Sorzano; José María Carazo (Bioinform., 2019)

A GPU acceleration of 3-D Fourier reconstruction in cryo-EM. - David Strelák; Carlos Oscar Sánchez Sorzano; José María Carazo; Jiri Filipovic (Int. J. High Perform. Comput. Appl., 2019)

Automatic local resolution-based sharpening of cryo-EM maps. - Erney Ramírez-Aportela; Jose Luis Vilas; Alisa Glukhova; Roberto Melero; Pablo Conesa; Marta Martínez; David Maluenda; Javier Mota; Amaya Jiménez; Javier Vargas 001; Roberto Marabini; Patrick M. Sexton; et al. (Bioinform., 2020)

Integration of Cryo-EM Model Building Software in Scipion. - Marta Martínez; A. Jiménez-Moreno; David Maluenda; Erney Ramírez-Aportela; Roberto Melero; Ana Cuervo; Pablo Conesa; Laura del Cano; Y. C. Fonseca; Rubén Sánchez García; David Strelák; J. J. Conesa; et al. (J. Chem. Inf. Model., 2020)

3DBionotes COVID-19 edition. - José Ramón Macías; Rubén Sánchez García; Pablo Conesa; Erney Ramírez-Aportela; Marta Martínez; Carlos Wert-Carvajal; Alberto M. Parra-Perez; Joan Segura Mora; Sam Horrell; Andrea Thorn; Carlos Oscar Sánchez Sorzano; José María Carazo (Bioinform., 2021)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

Umbrella Data Management Plans to Integrate FAIR Data: Lessons From the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. - Romain David 001; Audrey S. Richard; Claire Connellan; Katharina B. Lauer; Maria Luisa Chiusano; Carole A. Goble; Martin Houde; Isabel Kemmer; Antje Keppler; Philippe Lieutaud; Christian Ohmann; Maria Panagiotopoulou; et al. (Data Sci. J., 2023)

Fast Global Image Alignment Algorithm for CryoEM through Vector Compression. - Oier Lauzirika Zarrabeitia; E. Ramírez-Aportela; José María Carazo; Carlos Oscar Sánchez Sorzano (ISBI, 2024)