Joaquín Dopazo
Orcid: 0000-0003-3318-120X
According to our database1,
Joaquín Dopazo
authored at least 117 papers
between 1988 and 2023.
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Bibliography
2023
Visualization of automatically combined disease maps and pathway diagrams for rare diseases.
Frontiers Bioinform., May, 2023
Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder.
Proceedings of the Computational Methods in Systems Biology, 2023
2022
Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data.
BioData Min., 2022
2021
A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.
PLoS Comput. Biol., 2021
Nucleic Acids Res., 2021
A comprehensive database for integrated analysis of omics data in autoimmune diseases.
BMC Bioinform., 2021
2020
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.
F1000Research, 2020
2019
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
BMC Bioinform., 2019
Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models.
BMC Bioinform., 2019
Briefings Bioinform., 2019
Briefings Bioinform., 2019
2018
Int. J. High Perform. Comput. Appl., 2018
2017
BMC Bioinform., 2017
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.
BMC Bioinform., 2017
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.
BMC Bioinform., 2017
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise.
Bioinform., 2017
2016
Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.
Nucleic Acids Res., 2016
BMC Bioinform., 2016
2015
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
PLoS Comput. Biol., 2015
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res., 2015
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.
Nucleic Acids Res., 2015
Nucleic Acids Res., 2015
A parallel and sensitive software tool for methylation analysis on multicore platforms.
Bioinform., 2015
Proceedings of the 2015 IEEE TrustCom/BigDataSE/ISPA, 2015
2014
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies.
Nucleic Acids Res., 2014
A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Nucleic Acids Res., 2014
BMC Syst. Biol., 2014
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Bioinform., 2014
Bioinform., 2014
2013
Nucleic Acids Res., 2013
Proceedings of the 20th European MPI Users's Group Meeting, 2013
2012
Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.
Nucleic Acids Res., 2012
CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.
Nucleic Acids Res., 2012
Nucleic Acids Res., 2012
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants.
Nucleic Acids Res., 2012
Int. J. Knowl. Discov. Bioinform., 2012
Int. J. Data Min. Bioinform., 2012
Proceedings of the Euro-Par 2012: Parallel Processing Workshops, 2012
2011
PLoS Comput. Biol., 2011
An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins.
PLoS Comput. Biol., 2011
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Res., 2011
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
Bioinform., 2011
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings Bioinform., 2011
Proceedings of the 30th International Conference of the Chilean Computer Science Society, 2011
2010
Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes.
PLoS Comput. Biol., 2010
Serial Expression Analysis: a web tool for the analysis of serial gene expression data.
Nucleic Acids Res., 2010
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic Acids Res., 2010
2009
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.
Nucleic Acids Res., 2009
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies.
Nucleic Acids Res., 2009
Papers on normalization, variable selection, classification or clustering of microarray data.
Bioinform., 2009
Artif. Intell. Medicine, 2009
2008
Nucleic Acids Res., 2008
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.
Nucleic Acids Res., 2008
Nucleic Acids Res., 2008
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
Nucleic Acids Res., 2008
CLEAR-test: Combining inference for differential expression and variability in microarray data analysis.
J. Biomed. Informatics, 2008
2007
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic Acids Res., 2007
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.
Nucleic Acids Res., 2007
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
Nucleic Acids Res., 2007
BMC Bioinform., 2007
BMC Bioinform., 2007
Functional profiling of microarray experiments using text-mining derived bioentities.
Bioinform., 2007
Bioinform., 2007
2006
Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome.
PLoS Comput. Biol., 2006
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.
Nucleic Acids Res., 2006
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
Nucleic Acids Res., 2006
2005
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Nucleic Acids Res., 2005
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.
Nucleic Acids Res., 2005
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
Nucleic Acids Res., 2005
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
Bioinform., 2005
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Bioinform., 2005
Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions.
Proceedings of the Data Analysis and Visualization in Genomics and Proteomics, 2005
Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges.
Proceedings of the Data Analysis and Visualization in Genomics and Proteomics, 2005
Proceedings of the Data Analysis and Visualization in Genomics and Proteomics, 2005
2004
Nucleic Acids Res., 2004
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.
Nucleic Acids Res., 2004
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
Bioinform., 2004
An Approach to the Modular Structure of Cancer.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004
Finding SNPs with Putative Phenotypic Effect at Transcriptional Level.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004
Infering Non-Neutral Evolution within the Context of a Growing Genomic Framework: Preliminary Results using Human-Chimp Proteomes.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004
Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships.
Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2004
2003
Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron.
J. VLSI Signal Process., 2003
Nucleic Acids Res., 2003
Using a Genetic Algorithm and a Perceptron for Feature Selection and Supervised Class Learning in DNA Microarray Data.
Artif. Intell. Rev., 2003
Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes.
Proceedings of the NNSP 2003, 2003
2002
Unsupervised reduction of the dimensionality followed by supervised learning with a perceptron improves the classification of conditions in DNA microarray gene expression data.
Proceedings of the 12th IEEE Workshop on Neural Networks for Signal Processing, 2002
Using Perceptrons for Supervised Classification of DNA Microarray Samples: Obtaining the Optimal Level of Information and Finding Differentially Expressed Genes.
Proceedings of the Artificial Neural Networks, 2002
2001
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinform., 2001
1998
Parallel Comput., 1998
Bioinform., 1998
1997
A new index to find regions showing an unexpected variability or conservation in sequence alignments.
Comput. Appl. Biosci., 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
1995
An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data.
Comput. Appl. Biosci., 1995
1993
Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches.
Comput. Appl. Biosci., 1993
Comput. Appl. Biosci., 1993
Comput. Appl. Biosci., 1993
1988
Reducing the effect of the data order in algorithms for constructing phylogenetic trees.
Comput. Appl. Biosci., 1988