José María Carazo

According to our database1, José María Carazo authored at least 84 papers between 1990 and 2017.

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Bibliography

2017
Challenges ahead Electron Microscopy for Structural Biology from the Image Processing point of view.
CoRR, 2017

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures.
Bioinformatics, 2017

2015
Using neighborhood cohesiveness to infer interactions between protein domains.
Bioinformatics, 2015

2014
Efficient initial volume determination from electron microscopy images of single particles.
Bioinformatics, 2014

An image processing approach to the simulation of electron microscopy volumes of atomic structures.
Proceedings of the 2014 IEEE International Conference on Image Processing, 2014

2013
A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs.
Bioinformatics, 2013

2012
Integrating human and murine anatomical gene expression data for improved comparisons.
Bioinformatics, 2012

Image processing for Cellular tomography using soft X-rays.
Proceedings of the 9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2012

2010
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures.
Nucleic Acids Research, 2010

Moara: a Java library for extracting and normalizing gene and protein mentions.
BMC Bioinformatics, 2010

2009
SENT: semantic features in text.
Nucleic Acids Research, 2009

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.
Nucleic Acids Research, 2009

CentrosomeDB: a human centrosomal proteins database.
Nucleic Acids Research, 2009

Marker-free image registration of electron tomography tilt-series.
BMC Bioinformatics, 2009

aGEM: an integrative system for analyzing spatial-temporal gene-expression information.
Bioinformatics, 2009

Extraction of biomedical events using case-based reasoning.
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, BioNLP@HLT-NAACL 2009, 2009

2008
Volumetric restrictions in single particle 3DEM reconstruction.
Pattern Recognition, 2008

Design and analysis of an object-oriented discrete-event simulation engine for ATM telecommunication networks.
IJSPM, 2008

Assessment of protein set coherence using functional annotations.
BMC Bioinformatics, 2008

ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data.
Bioinformatics, 2008

Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library.
Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008

Flexible image registration for the identification of best fitted protein models in 3D-EM maps.
Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008

CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem.
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, 2008

2007
Parameter optimization in 3D reconstruction on a large scale grid.
Parallel Computing, 2007

Electron tomography of complex biological specimens on the Grid.
Future Generation Comp. Syst., 2007

2006
Nonsmooth Nonnegative Matrix Factorization (nsNMF).
IEEE Trans. Pattern Anal. Mach. Intell., 2006

bioNMF: a versatile tool for non-negative matrix factorization in biology.
BMC Bioinformatics, 2006

Discovering semantic features in the literature: a foundation for building functional associations.
BMC Bioinformatics, 2006

A literature-based similarity metric for biological processes.
BMC Bioinformatics, 2006

Biclustering of gene expression data by non-smooth non-negative matrix factorization.
BMC Bioinformatics, 2006

Integrated analysis of gene expression by association rules discovery.
BMC Bioinformatics, 2006

Optimization problems in electron microscopy of single particles.
Annals OR, 2006

Molecular image registration using mutual information and differential evolution optimization.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006

Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization.
Proceedings of the Computer Vision Approaches to Medical Image Analysis, 2006

2005
Multiobjective algorithm parameter optimization using multivariate statistics in three-dimensional electron microscopy reconstruction.
Pattern Recognition, 2005

Mining association rules from biological databases.
JASIST, 2005

Fast maximum-likelihood refinement of electron microscopy images.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

Two-way clustering of gene expression profiles by sparse matrix factorization.
Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

Grid Computing in 3D-EM Image Processing Using Xmipp.
Proceedings of the 18th IEEE Symposium on Computer-Based Medical Systems (CBMS 2005), 2005

2004
3-D reconstruction of 2-D crystals in real space.
IEEE Trans. Image Processing, 2004

The Potential Of Grid Computing In Three-Dimensional Electron Microscopy.
Parallel Processing Letters, 2004

On the Suitability of Biological Structure Determination by Electron Microscopy to Grid Computing.
New Generation Comput., 2004

Biological Structure Determination by EM is Well Suited to Grid Computing.
New Generation Comput., 2004

Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing.
J. Parallel Distrib. Comput., 2004

Designing and executing scientific workflows with a programmable integrator.
Bioinformatics, 2004

Parallelization and Comparison of 3D Iterative Reconstruction Algorithms.
Proceedings of the 12th Euromicro Workshop on Parallel, 2004

2003
Engene: the processing and exploratory analysis of gene expression data.
Bioinformatics, 2003

Parallel iterative reconstruction methods for structure determination of biological specimens by electron microscopy.
Proceedings of the 2003 International Conference on Image Processing, 2003

Grid Computing in Structure Determination of Biological Specimens by Electron Microscope Tomography.
Proceedings of the Grid Computing, 2003

A Semantic Mediation Approach for Problems in Computational Molecular Biology.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002
Command-line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE).
Softw., Pract. Exper., 2002

High Performance Computing in Electron Microscope Tomography of Complex Biological Structures.
Proceedings of the High Performance Computing for Computational Science, 2002

3D reconstruction of 2D crystals from projections in real space.
Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging, 2002

Volumetric constraints in 3D tomography applied to electron microscopy.
Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging, 2002

Modeling Shape and Topology of 3D Images of Biological Specimens.
Proceedings of the 16th International Conference on Pattern Recognition, 2002

Spin Images and Neural Networks for Efficient Content-Based Retrieval in 3D Object Databases.
Proceedings of the Image and Video Retrieval, International Conference, 2002

2001
Smoothly distributed fuzzy c-means: a new self-organizing map.
Pattern Recognition, 2001

2000
Image processing approaches to biological three-dimensional electron microscopy.
Int. J. Imaging Systems and Technology, 2000

1999
Organising multi-dimensional biological image information: the BioImage Database.
Nucleic Acids Research, 1999

Bayesian image restoration: Parallel implementation on a SGI origin multiprocessor.
Proceedings of the Parallel Computing: Fundamentals & Applications, 1999

Application of the Fuzzy Kohonen Clustering Network to Biological Macromolecules Images Classification.
Proceedings of the Engineering Applications of Bio-Inspired Artificial Neural Networks, 1999

Improved Automatic Classification of Biological Particles from Electron-Microscopy Images Using Genetic Neural Nets.
Proceedings of the Engineering Applications of Bio-Inspired Artificial Neural Networks, 1999

1998
Parallel Implementation of DNAml Program on Message-Passing Architectures.
Parallel Computing, 1998

Automatic Classification of Biological Particles from Electron-microscopy Images Using Conventional and Genetic-algorithm Optimized Learning Vector Quantization.
Neural Processing Letters, 1998

Self-organizing tree growing network for classifying amino acids.
Bioinformatics, 1998

New phylogenetic venues opened by a novel implementation of the DNAml algorithm.
Bioinformatics, 1998

Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Bioinformatics, 1998

Biological sequence analysis on distributed-shared memory multiprocessors.
PDP, 1998

Biolmage, the database of biological microscopy data.
German Conference on Bioinformatics, 1998

1997
A GA-optimized Neural Network for Classification of Biological Particles from Electron-Microscopy Images.
Proceedings of the Biological and Artificial Computation: From Neuroscience to Technology, 1997

A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree.
Proceedings of the Biological and Artificial Computation: From Neuroscience to Technology, 1997

1996
Implementation and experimental evaluation of the constrained ART algorithm on a multicomputer system.
Signal Processing, 1996

On a new computationally fast image invariant based on bispectral projections.
Pattern Recognition Letters, 1996

1995
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, 1995

1994
Practical issues on invariant image averaging using the Bispectrum.
Signal Processing, 1994

On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures.
Computer Applications in the Biosciences, 1994

Prototype for a new distributed database of volume data obtained by 3D imaging.
Proceedings of the Visualization in Biomedical Computing 1994, 1994

3d Reconstruction Of Macromolecules On Multiprocessors.
Proceedings of the Second Euromicro Workshop on Parallel and Distributed Processing, 1994

Mapping Strategies for Sequential Sequence Comparison Algorithms on LAN-Based Message Passing Architectures.
Proceedings of the High-Performance Computing and Networking, 1994

1993
Parallel algorithm for principal components based on Hotelling's iterative procedure.
Proceedings of the 1993 Euromicro Workshop on Parallel and Distributed Processing, 1993

1992
Image reconstruction on hypercube computers: Application to electron microscopy.
Signal Processing, 1992

1990
Image template matching on hypercube SIMD computers.
Signal Processing, 1990

Cluster validity based on the hard tendency of the fuzzy classification.
Pattern Recognition Letters, 1990


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