José María Carazo

发表

Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, 2017 .

Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases

José María Carazo, Pedro A. de Alarcón, Alberto D. Pascual-Montano, 2002, CIVR.

Computational space reduction and parallelization of a new clustering approach for large groups of sequences

Miguel A. Andrade-Navarro, Alfonso Valencia, Emilio L. Zapata, 1998, Bioinform..

A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree

Joaquín Dopazo, José María Carazo, Huaichun Wang, 1997, IWANN.

Modulating the Expression of Disease Genes with RNA-Based Therapy

Francisco Tirado, José María Carazo, Alberto D. Pascual-Montano, 2006, BMC Bioinformatics.

Modeling shape and topology of 3D images of biological specimens

Amarnath Gupta, José María Carazo, Alberto D. Pascual-Montano, 2002, Object recognition supported by user interaction for service robots.

Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing

Inmaculada García, José María Carazo, José-Jesús Fernández, 2004, J. Parallel Distributed Comput..

3D reconstruction of 2D crystals from projections in real space

José María Carazo, Gabor T. Herman, Roberto Marabini, 2002, Proceedings IEEE International Symposium on Biomedical Imaging.

A variant to the “random approximation” of the reference-free alignment algorithm

José María Carazo, Monica Chagoyen, Luis Gerardo de la Fraga, 1996 .

Using neighborhood cohesiveness to infer interactions between protein domains

José María Carazo, Carlos Oscar Sánchez Sorzano, Patrick Aloy, 2015, Bioinform..

Efficient initial volume determination from electron microscopy images of single particles

José María Carazo, Roberto Marabini, Carlos Oscar Sánchez Sorzano, 2014, Bioinform..

Self-organizing tree growing network for classifying amino acids

Joaquín Dopazo, José María Carazo, Huaichun Wang, 1998 .

Fast maximum-likelihood refinement of electron microscopy images

José María Carazo, Sjors H. W. Scheres, Mikel Valle, 2005, ECCB/JBI.

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

Francisco Tirado, José María Carazo, Monica Chagoyen, 2006, BMC Bioinformatics.

Fringe pattern denoising by image dimensionality reduction

José María Carazo, Carlos Oscar S. Sorzano, J. C. Estrada, 2013 .

Image reconstruction on hypercube computers

Javier D. Bruguera, Francisco F. Rivera, Emilio L. Zapata, 1990, [1990 Proceedings] The Third Symposium on the Frontiers of Massively Parallel Computation.

Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system

Inmaculada García, Emilio L. Zapata, José María Carazo, 1996, Signal Process..

Image databases: What are they and what do they bring to microscopy

José María Carazo, Monica Chagoyen, P. A. De-Alarcon, 2003 .

Parallelization and comparison of 3D iterative reconstruction algorithms

José María Carazo, José-Jesús Fernández, Jose-Roman Bilbao-Castro, 2004, 12th Euromicro Conference on Parallel, Distributed and Network-Based Processing, 2004. Proceedings..

Fully Three-Dimensional Reconstruction in Electron Microscopy

José María Carazo, Gabor T. Herman, Roberto Marabini, 1999 .

Filtered back projection on shared-memory multiprocessors☆

Emilio L. Zapata, José María Carazo, J. I. Benavides, 1990 .

On the suitability of Biological structure determination by electron microscopy to Grid Computing

José María Carazo, Roberto Marabini, José-Jesús Fernández, 2005, New Generation Computing.

Design and analysis of an object-oriented discrete-event simulation engine for ATM telecommunication networks

José María Carazo, Pablo Cortés, Jesús Muñuzuri, 2008, Int. J. Simul. Process. Model..

Marker-free image registration of electron tomography tilt-series

José María Carazo, Reiner Hegerl, Carlos Oscar Sánchez Sorzano, 2009, BMC Bioinformatics.

Prototype for a new distributed database of volume data obtained by 3D imaging

José María Carazo, Roberto Marabini, José-Jesús Fernández, 1994, Other Conferences.

CentrosomeDB: a human centrosomal proteins database

José María Carazo, Alberto D. Pascual-Montano, Rubén Nogales-Cadenas, 2008, Nucleic Acids Res..

Self-Organizing Networks for Mapping and Clustering Biological Macromolecules Images

Juan Julián Merelo Guervós, José María Carazo, Alberto Pascual, 2000, ANNIMAB.

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

José María Carazo, Alberto D. Pascual-Montano, Roberto D. Pascual-Marqui, 2001, Pattern Recognit..

Measurement of local resolution in electron tomography

José María Carazo, Roberto Marabini, José Luis Vilas, 2019, Journal of structural biology: X.

Flexible image registration for the identification of best fitted protein models in 3D-EM maps

María J. Ledesma-Carbayo, Andrés Santos, José María Carazo, 2008, 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

Biological structure determination by EM is well suited to grid computing

José María Carazo, Roberto Marabini, José-Jesús Fernández, 2009, New Generation Computing.

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

José María Carazo, Carlos Oscar Sánchez Sorzano, Joan Segura, 2017, Bioinform..

Challenges ahead Electron Microscopy for Structural Biology from the Image Processing point of view pdf

José María Carazo, Carlos Oscar Sánchez Sorzano, J. Carazo, 2017, ArXiv.

A literature-based similarity metric for biological processes

José María Carazo, Monica Chagoyen, Alberto D. Pascual-Montano, 2006, BMC Bioinformatics.

On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures

Emilio L. Zapata, José María Carazo, Oswaldo Trelles, 1994, Comput. Appl. Biosci..

Nonsmooth nonnegative matrix factorization (nsNMF)

Dietrich Lehmann, José María Carazo, Alberto D. Pascual-Montano, 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.

Biological sequence analysis on distributed-shared memory multiprocessors

Emilio L. Zapata, José María Carazo, Luis Gerardo de la Fraga, 1998, Proceedings of the Sixth Euromicro Workshop on Parallel and Distributed Processing - PDP '98 -.

Biolmage, the database of biological microscopy data

David M. Shotton, José María Carazo, Ernst H. K. Stelzer, 1998, German Conference on Bioinformatics.

Mapping Strategies for Sequential Sequence Comparison Algorithms on LAN-Based Message Passing Architectures

Emilio L. Zapata, José María Carazo, Oswaldo Trelles, 1994, HPCN.

Image processing approaches to biological three-dimensional electron microscopy

Robert M. Lewitt, José María Carazo, Edgar Garduño, 2000, Int. J. Imaging Syst. Technol..

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

Francisco Tirado, José María Carazo, Alberto D. Pascual-Montano, 2009, Nucleic Acids Res..

Assessment of protein set coherence using functional annotations

José María Carazo, Monica Chagoyen, Alberto D. Pascual-Montano, 2008, BMC Bioinformatics.

SENT: semantic features in text

Francisco Tirado, José María Carazo, Monica Chagoyen, 2009, Nucleic Acids Res..

A semantic mediation approach for problems in computational molecular biology

Simone Santini, Bertram Ludäscher, M. Erdem Kurul, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Image processing for Cellular tomography using soft X-rays

José María Carazo, Roberto Marabini, Gabriel Caffarena, 2012, 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI).

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

Hagit Shatkay, José María Carazo, Monica Chagoyen, 2006, BMC Bioinformatics.

3-D reconstruction of 2-D crystals in real space

José María Carazo, Gabor T. Herman, Roberto Marabini, 2004, IEEE Transactions on Image Processing.

aGEM: an integrative system for analyzing spatial-temporal gene-expression information

José María Carazo, Natalia Jiménez-Lozano, Joan Segura, 2009, Bioinform..

Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library

Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano, 2009, BioLINK@ISMB/ECCB.

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

José María Carazo, Alberto D. Pascual-Montano, Pedro Carmona-Saez, 2008, Bioinform..

Mining Low-level Similarity Signals from Sequence Databases

José María Carazo, Oswaldo Trelles, Antonio J. Pérez-Pulido, 2007 .

Integration of Cryo-EM Model Building Software in Scipion

José María Carazo, Roberto Melero, Roberto Marabini, 2020, J. Chem. Inf. Model..

Parallel Implementation of DNAml Program on Message-Passing Architectures

Joaquín Dopazo, Emilio L. Zapata, José María Carazo, 1998, Parallel Comput..

BIPSPI: a method for the prediction of partner-specific protein–protein interfaces

José María Carazo, Carlos Oscar Sánchez Sorzano, Joan Segura, 2018, Bioinform..

Application of the Fuzzy Kohonen Clustering Network to Biological Macromolecules Images Classification

Juan Julián Merelo Guervós, José María Carazo, Alberto Pascual, 1999, IWANN.

Cluster validity based on the hard tendency of the fuzzy classification

Francisco F. Rivera, Emilio L. Zapata, José María Carazo, 1990, Pattern Recognit. Lett..

The Potential Of Grid Computing In Three-Dimensional Electron Microscopy

Inmaculada García, José María Carazo, Roberto Marabini, 2004, Parallel Process. Lett..

Electron tomography of complex biological specimens on the Grid

Inmaculada García, José María Carazo, Roberto Marabini, 2007, Future Gener. Comput. Syst..

3d Reconstruction Of Macromolecules On Multiprocessors

Rafael Asenjo, Emilio L. Zapata, Manuel Ujaldon, 1994, Proceedings. Second Euromicro Workshop on Parallel and Distributed Processing.

Multiobjective algorithm parameter optimization using multivariate statistics in three-dimensional electron microscopy reconstruction

José María Carazo, Gabor T. Herman, Roberto Marabini, 2005, Pattern Recognit..

Automatic local resolution-based sharpening of cryo-EM maps

José María Carazo, Roberto Melero, Roberto Marabini, 2020, Bioinform..

Alignment of direct detection device micrographs using a robust Optical Flow approach.

Xueming Li, José María Carazo, Roberto Marabini, 2015, Journal of structural biology.

Designing and executing scientific workflows with a programmable integrator

M. Erdem Kurul, Amarnath Gupta, José María Carazo, 2004, Bioinform..

MicrographCleaner: a python package for cryo-EM micrograph cleaning using deep learning

José María Carazo, Carlos Oscar S. Sorzano, Joan Segura, 2019, bioRxiv.

Automatic local resolution-based sharpening of cryo-EM maps

José María Carazo, Roberto Melero, Roberto Marabini, 2018, bioRxiv.

3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations

José María Carazo, Carlos Oscar Sánchez Sorzano, Joan Segura, 2019, Bioinform..

Bayesian image restoration: Parallel implementation on a SGI origin multiprocessor

José María Carazo, Ramón Doallo, Jose Rodrigo Sanjurjo, 1999, PARCO.

Integrating human and murine anatomical gene expression data for improved comparisons

José María Carazo, Natalia Jiménez-Lozano, Joan Segura, 2012, Bioinform..

A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs

Yoel Shkolnisky, Vahid Abrishami, José María Carazo, 2013, Bioinform..

An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data

Joaquín Dopazo, Emilio L. Zapata, José María Carazo, 1995, Comput. Appl. Biosci..

Organising multi-dimensional biological image information: the BioImage Database

David M. Shotton, Patricia Rodriguez-Tomé, José María Carazo, 1999, Nucleic Acids Res..

A GA-optimized Neural Network for Classification of Biological Particles from Electron-Microscopy Images

Juan Julián Merelo Guervós, Alberto Prieto, Federico Morán, 1997, IWANN.

Mining association rules from biological databases

José María Carazo, Oswaldo Trelles, Andrés Rodríguez Moreno, 2005, J. Assoc. Inf. Sci. Technol..

Volumetric restrictions in single particle 3DEM reconstruction

José María Carazo, Gabor T. Herman, Roberto Marabini, 2008, Pattern Recognit..

Improved Automatic Classification of Biological Particles from Electron-Microscopy Images Using Genetic Neural Nets

Juan Julián Merelo Guervós, Pedro Ángel Castillo Valdivieso, Víctor Manuel Rivas Santos, 1999, IWANN.

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, 1998, Neural Processing Letters.

Accessing information on the conformational flexibility of molecular machines.

José María Carazo, J. Carazo, 2004, Structure.

Two-way clustering of gene expression profiles by sparse matrix factorization

Francisco Tirado, José María Carazo, Alberto D. Pascual-Montano, 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

Molecular image registration using mutual information and differential evolution optimization

María J. Ledesma-Carbayo, Andrés Santos, José María Carazo, 2006, 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro, 2006..

Mining association rules from biological databases: Research Articles

José María Carazo, Oswaldo Trelles, Andrés Rodríguez, 2005 .

Storing, reporting and comparing proteomics experiments using the miape generator tool

José María Carazo, Salvador Martínez-Bartolomé, J. Alberto Medina-Aunon, 2009 .

High Performance Computing in Electron Microscope Tomography of Complex Biological Structures

Albert F. Lawrence, Inmaculada García, Mark H. Ellisman, 2002, VECPAR.

A GPU acceleration of 3-D Fourier reconstruction in cryo-EM

José María Carazo, Carlos Oscar Sánchez Sorzano, Jiri Filipovic, 2019, Int. J. High Perform. Comput. Appl..

New phylogenetic venues opened by a novel implementation of the DNAml algorithm

Joaquín Dopazo, José María Carazo, Oswaldo Trelles, 1998, Bioinform..

Extraction of biomedical events using case-based reasoning

Mariana L. Neves, José María Carazo, Alberto D. Pascual-Montano, 2009, BioNLP@HLT-NAACL.

Parallel iterative reconstruction methods for structure determination of biological specimens by electron microscopy

Inmaculada García, José María Carazo, José-Jesús Fernández, 2003, Proceedings 2003 International Conference on Image Processing (Cat. No.03CH37429).

Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy.

José María Carazo, Roberto Marabini, J Vargas, 2013, Methods in molecular biology.

Image template matching on hypercube SIMD computers

Francisco F. Rivera, Emilio L. Zapata, José Ignacio Benavides Benítez, 1990, Signal Process..

West-Life: A Virtual Research Environment for structural biology

Andrea Giachetti, Chris Morris, Daniel Kouřil, 2019, Journal of structural biology: X.

BMC Bioinformatics BioMed Central Methodology article Integrated analysis of gene expression by association rules discovery

José María Carazo, Monica Chagoyen, Alberto D. Pascual-Montano, 2022 .

Grid computing in 3D-EM image processing using Xmipp

José María Carazo, Carlos Oscar Sánchez Sorzano, Sjors H. W. Scheres, 2005, 18th IEEE Symposium on Computer-Based Medical Systems (CBMS'05).

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

José María Carazo, Jiří Filipovič, David Střelák, 2020, Electronics.

Efficient functional bioinformatics tools: towards understanding biological processes

José María Carazo, Alberto Pascual-Montano, J. Carazo, 2010 .

Engene: the processing and exploratory analysis of gene expression data

José María Carazo, Alberto D. Pascual-Montano, Oswaldo Trelles, 2003, Bioinform..

An image processing approach to the simulation of electron microscopy volumes of atomic structures

José María Carazo, Roberto Marabini, Carlos Oscar Sánchez Sorzano, 2014, 2014 IEEE International Conference on Image Processing (ICIP).

CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem

Mariana L. Neves, José María Carazo, Monica Chagoyen, 2008, BioNLP.

A fast iterative convolution weighting approach for gridding-based direct Fourier three-dimensional reconstruction with correction for the contrast transfer function.

José María Carazo, Roberto Marabini, Javier Vargas, 2015, Ultramicroscopy.

Parameter optimization in 3D reconstruction on a large scale grid

Inmaculada García, José María Carazo, José-Jesús Fernández, 2007, Parallel Comput..

Optimization problems in electron microscopy of single particles

José María Carazo, Roberto Marabini, Alberto D. Pascual-Montano, 2006, Ann. Oper. Res..

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.

José María Carazo, Roberto Melero, Roberto Marabini, 2018, Structure.

Grid Computing in Structure Determination of Biological Specimens by Electron Microscope Tomography

José María Carazo, Roberto Marabini, José-Jesús Fernández, 2003, European Across Grids Conference.

Command‐line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE)

José María Carazo, Oswaldo Trelles, Carlos Oscar Sánchez Sorzano, 2002, Softw. Pract. Exp..

Volumetric constraints in 3D tomography applied to electron microscopy

José María Carazo, Gabor T. Herman, Roberto Marabini, 2002, Proceedings IEEE International Symposium on Biomedical Imaging.

Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization

Carlos Ortiz-de-Solorzano, Jan Kybic, José María Carazo, 2006, CVAMIA.

PARALLEL ALGORITHMS FOR PATTERN RECOGNITION

E. L. Zapata, Francisco F. Rivera, José María Carazo, 1992 .

Multidimensional fast Fourier transform into SIMD hypercubes

Emilio L. Zapata, José María Carazo, I. Benavides, 1990 .

Validation of electron microscopy initial models via small angle X-ray scattering curves

José María Carazo, Roberto Melero, Roberto Marabini, 2019, Bioinform..

Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM

José María Carazo, Javier A. Velázquez-Muriel, 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

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

Francisco Tirado, José María Carazo, Alberto D. Pascual-Montano, 2010, Nucleic Acids Res..

Functional Classification of Genes Using Non-Negative Independent Component Analysis

José María Carazo, Hugo Fernandes, Monica Chagoyen, 2008 .

On a new computationally fast image invariant based on bispectral projections

José María Carazo, Roberto Marabini, J. Carazo, 1996, Pattern Recognit. Lett..

Image reconstruction on hypercube computers: Application to electron microscopy

Tomás F. Pena, Javier D. Bruguera, Francisco F. Rivera, 1992, Signal Process..

Author Correction: Self-assembly and regulation of protein cages from pre-organised coiled-coil modules

Fabio Lapenta, Jana Aupič, José María Carazo, 2021, Nature communications.

Information recovery in missing angular data cases: an approach by the convex projections method in three dimensions

José María Carazo, J. Carazo, J. Carrascosa, 1987 .

Practical issues on invariant image averaging using the Bispectrum

José María Carazo, Roberto Marabini, 1994, Signal Process..

Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra

José María Carazo, Carlos Oscar S Sorzano, J. Carazo, 2009, BMC Structural Biology.

Image processing for electron microscopy single-particle analysis using XMIPP

José María Carazo, Roberto Marabini, Carlos O S Sorzano, 2008, Nature Protocols.

Study of the direct Fourier method for the three‐dimensional reconstruction of objects in the case of a missing angular data range

José María Carazo, Antonio Santisteban, J. Carazo, 1986 .

Fast and accurate conversion of atomic models into electron density maps

José María Carazo, Roberto Marabini, Javier Vargas, 2015 .

Interchanging Geometry Conventions in 3DEM: Mathematical Context for the Development of Standards

José María Carazo, Roberto Marabini, Javier Vargas, 2014 .

Structural basis for the cooperative assembly of large T antigen on the origin of replication.

José María Carazo, Mikel Valle, Ellen Fanning, 2006, Journal of molecular biology.

Discrete Tomography in Electron Microscopy

José María Carazo, Roberto Marabini, Rasmus R. Schröder, 1999 .

Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.

José María Carazo, L. E. Donate, J. Carazo, 2006, Journal of molecular biology.

Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo

Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, 2017, Nature Biotechnology.

Modeling experimental image formation for likelihood-based classification of electron microscopy data.

José María Carazo, Sjors H W Scheres, P. Eggermont, 2007, Structure.

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

José María Carazo, Alberto D. Pascual-Montano, M. Neves, 2010, BMC Bioinformatics.

Confidence limits for resolution estimation in image averaging by random subsampling

José María Carazo, Luis Gerardo de la Fraga, J. Dopazo, 1995 .