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Joaquín Dopazo

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Oligonucleotide Array Sequence Analysis

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Genes & Molecular Sequences

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TOP 3
Dopazo Joaquín
Functional profiling methods in cancer.
Minguez Pablo; Götz Stefan; Montaner David; Al-Shahrour Fatima; Dopazo Joaquin
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.
Montaner David; Minguez Pablo; Al-Shahrour Fátima; Dopazo Joaquín
Gene set internal coherence in the context of functional profiling.

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All Publications

2010: Dopazo Joaquín
Functional profiling methods in cancer.
Methods in molecular biology (Clifton, N.J.) 2010;576():363-74.
2009: Minguez Pablo; Götz Stefan; Montaner David; Al-Shahrour Fatima; Dopazo Joaquin
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.
Nucleic acids research 2009;37(Web Server issue):W109-14.
2009: Montaner David; Minguez Pablo; Al-Shahrour Fátima; Dopazo Joaquín
Gene set internal coherence in the context of functional profiling.
BMC genomics 2009;10():197.
2008: Conesa Ana; Bro Rasmus; García-García Francisco; Prats José Manuel; Götz Stefan; Kjeldahl Karin; Montaner David; Dopazo Joaquín
Direct functional assessment of the composite phenotype through multivariate projection strategies.
Genomics 2008;92(6):373-83.
2008: Horcajadas José A; Mínguez Pablo; Dopazo Joaquín; Esteban Francisco J; Domínguez Francisco; Giudice Linda C; Pellicer Antonio; Simón Carlos
Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications.
The Journal of clinical endocrinology and metabolism 2008;93(11):4500-10.
2008: Al-Shahrour Fátima; Carbonell José; Minguez Pablo; Goetz Stefan; Conesa Ana; Tárraga Joaquín; Medina Ignacio; Alloza Eva; Montaner David; Dopazo Joaquín
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
Nucleic acids research 2008;36(Web Server issue):W341-6.
2008: Tárraga Joaquín; Medina Ignacio; Carbonell José; Huerta-Cepas Jaime; Minguez Pablo; Alloza Eva; Al-Shahrour Fátima; Vegas-Azcárate Susana; Goetz Stefan; Escobar Pablo; Garcia-Garcia Francisco; Conesa Ana; Montaner David; Dopazo Joaquín
GEPAS, a web-based tool for microarray data analysis and interpretation.
Nucleic acids research 2008;36(Web Server issue):W308-14.
2008: Götz Stefan; García-Gómez Juan Miguel; Terol Javier; Williams Tim D; Nagaraj Shivashankar H; Nueda María José; Robles Montserrat; Talón Manuel; Dopazo Joaquín; Conesa Ana
High-throughput functional annotation and data mining with the Blast2GO suite.
Nucleic acids research 2008;36(10):3420-35.
2008: Valls Joan; Grau Mònica; Solé Xavier; Hernández Pilar; Montaner David; Dopazo Joaquín; Peinado Miguel A; Capellá Gabriel; Moreno Víctor; Pujana Miguel Angel
CLEAR-test: combining inference for differential expression and variability in microarray data analysis.
Journal of biomedical informatics 2008;41(1):33-45.
2008: Reumers Joke; Conde Lucia; Medina Ignacio; Maurer-Stroh Sebastian; Van Durme Joost; Dopazo Joaquin; Rousseau Frederic; Schymkowitz Joost
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.
Nucleic acids research 2008;36(Database issue):D825-9.
2008: Huerta-Cepas Jaime; Bueno Anibal; Dopazo Joaquín; Gabaldón Toni
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Nucleic acids research 2008;36(Database issue):D491-6.
2008: Capriotti Emidio; Arbiza Leonardo; Casadio Rita; Dopazo Joaquín; Dopazo Hernán; Marti-Renom Marc A
Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans.
Human mutation 2008;29(1):198-204.
2008: Bonifaci Núria; Berenguer Antoni; Díez Javier; Reina Oscar; Medina Ignacio; Dopazo Joaquín; Moreno Víctor; Pujana Miguel Angel
Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes.
BMC medical genomics 2008;1():62.
2008: Dopazo Joaquín; Al-Shahrour Fátima
Expression and microarrays.
Methods in molecular biology (Clifton, N.J.) 2008;453():245-55.
2007: Minguez Pablo; Al-Shahrour Fátima; Montaner David; Dopazo Joaquín
Functional profiling of microarray experiments using text-mining derived bioentities.
Bioinformatics (Oxford, England) 2007;23(22):3098-9.
2007: Ruiz-Llorente Sergio; Montero-Conde Cristina; Milne Roger L; Moya Christian M; Cebrián Arancha; Letón Rocío; Cascón Alberto; Mercadillo Fátima; Landa Iñigo; Borrego Salud; Pérez de Nanclares Guiomar; Alvarez-Escolá Cristina; Díaz-Pérez José Angel; Carracedo Angel; Urioste Miguel; González-Neira Anna; Benítez Javier; Santisteban Pilar; Dopazo Joaquín; Ponder Bruce A; Robledo Mercedes;
Association study of 69 genes in the ret pathway identifies low-penetrance loci in sporadic medullary thyroid carcinoma.
Cancer research 2007;67(19):9561-7.
2007: Marti-Renom Marc A; Pieper Ursula; Madhusudhan M S; Rossi Andrea; Eswar Narayanan; Davis Fred P; Al-Shahrour Fátima; Dopazo Joaquín; Sali Andrej
DBAli tools: mining the protein structure space.
Nucleic acids research 2007;35(Web Server issue):W393-7.
2007: Al-Shahrour Fátima; Minguez Pablo; Tárraga Joaquín; Medina Ignacio; Alloza Eva; Montaner David; Dopazo Joaquín
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
Nucleic acids research 2007;35(Web Server issue):W91-6.
2007: Conde Lucía; Montaner David; Burguet-Castell Jordi; Tárraga Joaquín; Medina Ignacio; Al-Shahrour Fátima; Dopazo Joaquín
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.
Nucleic acids research 2007;35(Web Server issue):W81-5.
2007: Tárraga Joaquín; Medina Ignacio; Arbiza Leonardo; Huerta-Cepas Jaime; Gabaldón Toni; Dopazo Joaquín; Dopazo Hernán
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic acids research 2007;35(Web Server issue):W38-42.
2007: Medina Ignacio; Montaner David; Tárraga Joaquín; Dopazo Joaquín
Prophet, a web-based tool for class prediction using microarray data.
Bioinformatics (Oxford, England) 2007;23(3):390-1.
2007: Conde Lucía; Montaner David; Burguet-Castell Jordi; Tárraga Joaquín; Al-Shahrour Fátima; Dopazo Joaquín
Functional profiling and gene expression analysis of chromosomal copy number alterations.
Bioinformation 2007;1(10):432-5.
2007: Hernández Pilar; Huerta-Cepas Jaime; Montaner David; Al-Shahrour Fátima; Valls Joan; Gómez Laia; Capellá Gabriel; Dopazo Joaquín; Pujana Miguel Angel
Evidence for systems-level molecular mechanisms of tumorigenesis.
BMC genomics 2007;8():185.
2007: Marti-Renom Marc A; Rossi Andrea; Al-Shahrour Fátima; Davis Fred P; Pieper Ursula; Dopazo Joaquín; Sali Andrej
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC bioinformatics 2007;8 Suppl 4():S4.
2007: Huerta-Cepas Jaime; Dopazo Hernán; Dopazo Joaquín; Gabaldón Toni
The human phylome.
Genome biology 2007;8(6):R109.
2007: Al-Shahrour Fátima; Arbiza Leonardo; Dopazo Hernán; Huerta-Cepas Jaime; Mínguez Pablo; Montaner David; Dopazo Joaquín
From genes to functional classes in the study of biological systems.
BMC bioinformatics 2007;8():114.
2006: Milne Roger Laughlin; Ribas Gloria; González-Neira Anna; Fagerholm Rainer; Salas Antonio; González Emilio; Dopazo Joaquín; Nevanlinna Heli; Robledo Mercedes; Benítez Javier
ERCC4 associated with breast cancer risk: a two-stage case-control study using high-throughput genotyping.
Cancer research 2006;66(19):9420-7.
2006: Conde Lucía; Vaquerizas Juan M; Dopazo Hernán; Arbiza Leonardo; Reumers Joke; Rousseau Frederic; Schymkowitz Joost; Dopazo Joaquín
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.
Nucleic acids research 2006;34(Web Server issue):W621-5.
2006: Montaner David; Tárraga Joaquín; Huerta-Cepas Jaime; Burguet Jordi; Vaquerizas Juan M; Conde Lucía; Minguez Pablo; Vera Javier; Mukherjee Sach; Valls Joan; Pujana Miguel A G; Alloza Eva; Herrero Javier; Al-Shahrour Fátima; Dopazo Joaquín
Next station in microarray data analysis: GEPAS.
Nucleic acids research 2006;34(Web Server issue):W486-91.
2006: Al-Shahrour Fátima; Minguez Pablo; Tárraga Joaquín; Montaner David; Alloza Eva; Vaquerizas Juan M; Conde Lucía; Blaschke Christian; Vera Javier; Dopazo Joaquín
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
Nucleic acids research 2006;34(Web Server issue):W472-6.
2006: Dopazo Joaquín
Bioinformatics and cancer: an essential alliance.
Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico 2006;8(6):409-15.
2006: Arbiza Leonardo; Duchi Serena; Montaner David; Burguet Jordi; Pantoja-Uceda David; Pineda-Lucena Antonio; Dopazo Joaquín; Dopazo Hernán
Selective pressures at a codon-level predict deleterious mutations in human disease genes.
Journal of molecular biology 2006;358(5):1390-404.
2006: Arbiza Leonardo; Dopazo Joaquín; Dopazo Hernán
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
PLoS computational biology 2006;2(4):e38.
2006: Minguez Pablo; Al-Shahrour Fátima; Dopazo Joaquín
A function-centric approach to the biological interpretation of microarray time-series.
Genome informatics. International Conference on Genome Informatics 2006;17(2):57-66.
2006: Dopazo Joaquín
Functional interpretation of microarray experiments.
Omics : a journal of integrative biology 2006;10(3):398-410.
2006: Azuaje Francisco; Al-Shahrour Fatima; Dopazo Joaquin
Ontology-driven approaches to analyzing data in functional genomics.
Methods in molecular biology (Clifton, N.J.) 2006;316():67-86.
2006: Goñi Josep Ramon; Vaquerizas Juan Manuel; Dopazo Joaquin; Orozco Modesto
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.
BMC genomics 2006;7():63.
2005: Vaquerizas Juan M; Conde Lucía; Yankilevich Patricio; Cabezón Amaya; Minguez Pablo; Díaz-Uriarte Ramón; Al-Shahrour Fátima; Herrero Javier; Dopazo Joaquín
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Nucleic acids research 2005;33(Web Server issue):W616-20.
2005: Conde Lucía; Vaquerizas Juan M; Ferrer-Costa Carles; de la Cruz Xavier; Orozco Modesto; Dopazo Joaquín
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes.
Nucleic acids research 2005;33(Web Server issue):W501-5.
2005: Al-Shahrour Fátima; Minguez Pablo; Vaquerizas Juan M; Conde Lucía; Dopazo Joaquín
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
Nucleic acids research 2005;33(Web Server issue):W460-4.
2005: Al-Shahrour Fátima; Díaz-Uriarte Ramón; Dopazo Joaquín
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Bioinformatics (Oxford, England) 2005;21(13):2988-93.
2005: Santoyo Javier; Vaquerizas Juan M; Dopazo Joaquín
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
Bioinformatics (Oxford, England) 2005;21(8):1376-82.
2005: Palacios José; Honrado Emiliano; Osorio Ana; Cazorla Alicia; Sarrió David; Barroso Alicia; Rodríguez Sandra; Cigudosa Juan C; Diez Orland; Alonso Carmen; Lerma Enrique; Dopazo Joaquín; Rivas Carmen; Benítez Javier
Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers.
Breast cancer research and treatment 2005;90(1):5-14.
2005: Cascón Alberto; Ruiz-Llorente Sergio; Rodríguez-Perales Sandra; Honrado Emiliano; Martínez-Ramírez Angel; Letón Rocío; Montero-Conde Cristina; Benítez Javier; Dopazo Joaquín; Cigudosa Juan C; Robledo Mercedes
A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma.
Genes, chromosomes & cancer 2005;42(3):260-8.
2005: Alvarez Sara; Diaz-Uriarte Ramon; Osorio Ana; Barroso Alicia; Melchor Lorenzo; Paz Maria Fe; Honrado Emiliano; Rodríguez Raquel; Urioste Miguel; Valle Laura; Díez Orland; Cigudosa Juan Cruz; Dopazo Joaquin; Esteller Manel; Benitez Javier
A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation.
Clinical cancer research : an official journal of the American Association for Cancer Research 2005;11(3):1146-53.
2005: Dopazo Hernán; Dopazo Joaquín
Genome-scale evidence of the nematode-arthropod clade.
Genome biology 2005;6(5):R41.
2004: Meléndez Bárbara; Díaz-Uriarte Ramón; Cuadros Marta; Martínez-Ramírez Angel; Fernández-Piqueras José; Dopazo Ana; Cigudosa Juan-Cruz; Rivas Carmen; Dopazo Joaquín; Martínez-Delgado Beatriz; Benítez Javier
Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization.
Genes, chromosomes & cancer 2004;41(4):353-65.
2004: Vaquerizas Juan M; Dopazo Joaquín; Díaz-Uriarte Ramón
DNMAD: web-based diagnosis and normalization for microarray data.
Bioinformatics (Oxford, England) 2004;20(18):3656-8.
2004: Dopazo Hernán; Santoyo Javier; Dopazo Joaquín
Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i116-21.
2004: Herrero Javier; Vaquerizas Juan M; Al-Shahrour Fátima; Conde Lucía; Mateos Alvaro; Díaz-Uriarte Javier Santoyo Ramón; Dopazo Joaquín
New challenges in gene expression data analysis and the extended GEPAS.
Nucleic acids research 2004;32(Web Server issue):W485-91.
2004: Conde Lucía; Vaquerizas Juan M; Santoyo Javier; Al-Shahrour Fátima; Ruiz-Llorente Sergio; Robledo Mercedes; Dopazo Joaquín
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.
Nucleic acids research 2004;32(Web Server issue):W242-8.
2004: Al-Shahrour Fátima; Díaz-Uriarte Ramón; Dopazo Joaquín
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.
Bioinformatics (Oxford, England) 2004;20(4):578-80.
2003: Herrero Javier; Al-Shahrour Fátima; Díaz-Uriarte Ramón; Mateos Alvaro; Vaquerizas Juan M; Santoyo Javier; Dopazo Joaquín
GEPAS: A web-based resource for microarray gene expression data analysis.
Nucleic acids research 2003;31(13):3461-7.
2003: Martin Maria J; Herrero Javier; Mateos Alvaro; Dopazo Joaquin
Comparing bacterial genomes through conservation profiles.
Genome research 2003;13(5):991-8.
2003: Herrero J; Díaz-Uriarte R; Dopazo J
Gene expression data preprocessing.
Bioinformatics (Oxford, England) 2003;19(5):655-6.
2003: Herrero Javier; Díaz-Uriarte Ramón; Dopazo Joaquín
An approach to inferring transcriptional regulation among genes from large-scale expression data.
Comparative and functional genomics 2003;4(1):148-54.
2002: Mateos Alvaro; Dopazo Joaquín; Jansen Ronald; Tu Yuhai; Gerstein Mark; Stolovitzky Gustavo
Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons.
Genome research 2002;12(11):1703-15.
2002: Tracey Lorraine; Villuendas Raquel; Ortiz Pablo; Dopazo Ana; Spiteri Inmaculada; Lombardia Luis; Rodríguez-Peralto Jose L; Fernández-Herrera Jesús; Hernández Almudena; Fraga Javier; Dominguez Orlando; Herrero Javier; Alonso Miguel A; Dopazo Joaquin; Piris Miguel A
Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma.
The American journal of pathology 2002;161(5):1825-37.
2002: Herrero Javier; Dopazo Joaquín
Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns.
Journal of proteome research 2002;1(5):467-70.
2002: Tamames Javier; Clark Dominic; Herrero Javier; Dopazo Joaquín; Blaschke Christian; Fernández José M; Oliveros Juan C; Valencia Alfonso
Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction.
Journal of biotechnology 2002;98(2-3):269-83.
2001: Herrero J; Valencia A; Dopazo J
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinformatics (Oxford, England) 2001;17(2):126-36.
2000: Oliveros J C; Blaschke C; Herrero J; Dopazo J; Valencia A
Expression profiles and biological function.
Genome informatics. Workshop on Genome Informatics 2000;11():106-17.

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Joaquín Dopazo

Research Profile (preview)

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Phenomena

Chemicals & Drugs

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Genes & Molecular Sequences

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Publications

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