Joaquín Dopazo

According to our database1, Joaquín Dopazo
  • authored at least 102 papers between 1988 and 2017.
  • has a "Dijkstra number"2 of four.



In proceedings 
PhD thesis 




A new parallel pipeline for DNA methylation analysis of long reads datasets.
BMC Bioinformatics, 2017

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.
BMC Bioinformatics, 2017

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.
BMC Bioinformatics, 2017

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise.
Bioinformatics, 2017

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.
Nucleic Acids Research, 2016

HPG pore: an efficient and scalable framework for nanopore sequencing data.
BMC Bioinformatics, 2016

Web-based network analysis and visualization using CellMaps.
Bioinformatics, 2016

Integrated gene set analysis for microRNA studies.
Bioinformatics, 2016

Concurrent and Accurate Short Read Mapping on Multicore Processors.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.
PLoS Computational Biology, 2015

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Research, 2015

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.
Nucleic Acids Research, 2015

Babelomics 5.0: functional interpretation for new generations of genomic data.
Nucleic Acids Research, 2015

A parallel and sensitive software tool for methylation analysis on multicore platforms.
Bioinformatics, 2015

Scalable RNA Sequencing on Clusters of Multicore Processors.
Proceedings of the 2015 IEEE TrustCom/BigDataSE/ISPA, 2015

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies.
Nucleic Acids Research, 2014

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Nucleic Acids Research, 2014

Understanding disease mechanisms with models of signaling pathway activities.
BMC Systems Biology, 2014

Pathway network inference from gene expression data.
BMC Systems Biology, 2014

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Bioinformatics, 2014

ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing.
Bioinformatics, 2014

Inferring the functional effect of gene expression changes in signaling pathways.
Nucleic Acids Research, 2013

Genome Maps, a new generation genome browser.
Nucleic Acids Research, 2013

Concurrent and Accurate RNA Sequencing on Multicore Platforms
CoRR, 2013

A dynamic pipeline for RNA sequencing on multicore processors.
Proceedings of the 20th European MPI Users's Group Meeting, 2013

Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform.
IEEE/ACM Trans. Comput. Biology 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 Research, 2012

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.
Nucleic Acids Research, 2012

Inferring the regulatory network behind a gene expression experiment.
Nucleic Acids Research, 2012

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants.
Nucleic Acids Research, 2012

Protein Interactions for Functional Genomics.
IJKDB, 2012

Select Your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs.
IJDMB, 2012

Qualimap: evaluating next-generation sequencing alignment data.
Bioinformatics, 2012

Multicore and Cloud-Based Solutions for Genomic Variant Analysis.
Proceedings of the Euro-Par 2012: Parallel Processing Workshops, 2012

Natural Selection on Functional Modules, a Genome-Wide Analysis.
PLoS Computational Biology, 2011

An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins.
PLoS Computational Biology, 2011

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Research, 2011

B2G-FAR, a species-centered GO annotation repository.
Bioinformatics, 2011

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
Bioinformatics, 2011

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings in Bioinformatics, 2011

Using Papers Citations for Selecting the Best Genomic Databases.
Proceedings of the 30th International Conference of the Chilean Computer Science Society, 2011

Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes.
PLoS Computational Biology, 2010

Serial Expression Analysis: a web tool for the analysis of serial gene expression data.
Nucleic Acids Research, 2010

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic Acids Research, 2010

ETE: a python Environment for Tree Exploration.
BMC Bioinformatics, 2010

SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.
Nucleic Acids Research, 2009

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies.
Nucleic Acids Research, 2009

Functional assessment of time course microarray data.
BMC Bioinformatics, 2009

Papers on normalization, variable selection, classification or clustering of microarray data.
Bioinformatics, 2009

Formulating and testing hypotheses in functional genomics.
Artificial Intelligence in Medicine, 2009

GEPAS, a web-based tool for microarray data analysis and interpretation.
Nucleic Acids Research, 2008

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.
Nucleic Acids Research, 2008

PhylomeDB: a database for genome-wide collections of gene phylogenies.
Nucleic Acids Research, 2008

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
Nucleic Acids Research, 2008

CLEAR-test: Combining inference for differential expression and variability in microarray data analysis.
Journal of Biomedical Informatics, 2008

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic Acids Research, 2007

DBAli tools: mining the protein structure space.
Nucleic Acids Research, 2007

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.
Nucleic Acids Research, 2007

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
Nucleic Acids Research, 2007

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC Bioinformatics, 2007

From genes to functional classes in the study of biological systems.
BMC Bioinformatics, 2007

Functional profiling of microarray experiments using text-mining derived bioentities.
Bioinformatics, 2007

Prophet, a web-based tool for class prediction using microarray data.
Bioinformatics, 2007

Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome.
PLoS Computational Biology, 2006

Next station in microarray data analysis: GEPAS.
Nucleic Acids Research, 2006

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.
Nucleic Acids Research, 2006

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
Nucleic Acids Research, 2006

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Nucleic Acids Research, 2005

HCAD, closing the gap between breakpoints and genes.
Nucleic Acids Research, 2005

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.
Nucleic Acids Research, 2005

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
Nucleic Acids Research, 2005

Highly specific and accurate selection of siRNAs for high-throughput functional assays.
Bioinformatics, 2005

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Bioinformatics, 2005

New challenges in gene expression data analysis and the extended GEPAS.
Nucleic Acids Research, 2004

PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.
Nucleic Acids Research, 2004

DNMAD: web-based diagnosis and normalization for microarray data.
Bioinformatics, 2004

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
Bioinformatics, 2004

Highly Specific and Accurate Selection of siRNAs for High-Throughput Functional Assays.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

An Approach to the Modular Structure of Cancer.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

New Challenges in Gene Expression Data Analysis and the Extended GEPAS.
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

Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron.
VLSI Signal Processing, 2003

GEPAS: a web-based resource for microarray gene expression data analysis.
Nucleic Acids Research, 2003

Gene expression data preprocessing.
Bioinformatics, 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

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

A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinformatics, 2001

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

A new index to find regions showing an unexpected variability or conservation in sequence alignments.
Computer Applications in the Biosciences, 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

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

Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches.
Computer Applications in the Biosciences, 1993

Quantitative characterization of antigens using monoclonal antibody reactivities.
Computer Applications in the Biosciences, 1993

Design of primers for PCR amplification of highly variable genomes.
Computer Applications in the Biosciences, 1993

Reducing the effect of the data order in algorithms for constructing phylogenetic trees.
Computer Applications in the Biosciences, 1988