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Joaquín Dopazo

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Oligonucleotide Array Sequence Analysis

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Proteins

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TOP 3
Amparo Galan; David Montaner; Maria Eugenia Poo; Veronica Ruiz; Eva Sanchez; Ana Conesa; Patricia Diaz-Gimeno; Joaquín Dopazo; Diana Valbuena; Carlos Simon
Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development.
Luz García-Alonso; Ignacio Medina; Stefan Götz; Enrique Vidal; Roberto Alonso; Alicia Amadoz; Alejandro de María; Joaquín Dopazo
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments.
Fernando García-Alcalde; Stefan Götz; Thomas F Meyer; Konstantin Okonechnikov; Sonia Tarazona; José Carbonell; Luis M Cruz; Joaquín Dopazo; Ana Conesa
Qualimap: evaluating next-generation sequencing alignment data.

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All Publications

2013: Amparo Galan; David Montaner; Maria Eugenia Poo; Veronica Ruiz; Eva Sanchez; Ana Conesa; Patricia Diaz-Gimeno; Joaquín Dopazo; Diana Valbuena; Carlos Simon
Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development.
PloS one 2013;8(4):e62135.
2012: Luz García-Alonso; Ignacio Medina; Stefan Götz; Enrique Vidal; Roberto Alonso; Alicia Amadoz; Alejandro de María; Joaquín Dopazo
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments.
Nucleic acids research 2012;40(20):e158.
2012: Fernando García-Alcalde; Stefan Götz; Thomas F Meyer; Konstantin Okonechnikov; Sonia Tarazona; José Carbonell; Luis M Cruz; Joaquín Dopazo; Ana Conesa
Qualimap: evaluating next-generation sequencing alignment data.
Bioinformatics (Oxford, England) 2012;28(20):2678-9.
2012: Raquel Ma Fernández; Luz García-Alonso; Berta Luzón-Toro; Martina Marbà; Ignacio Medina; David Montaner; Rocío Núñez-Torres; Ana Torroglosa; Guillermo Antiñolo; Marta Bleda; Joaquín Dopazo; Ma Valle Enguix-Riego; Salud Borrego
Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease.
Orphanet journal of rare diseases 2012;7():103.
2012: Paula Fernandez; Francisco García-García; Sergio Gonzalez; Ruth Amelia Heinz; Esteban Hopp; Sebastian Moschen; Luis Aguirrezabal; David Blesa; Bernardo Jose Clavijo; Ana Conesa; Julio DiRienzo; Joaquín Dopazo; Guillermo Dosio; Lucila Peluffo; Dario Príncipi; Maximo Rivarola; Marcelo Soria; Norma Paniego
Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.
PloS one 2012;7(10):e45899.
2012: Iván Ventoso; Joaquín Dopazo; Alex Kochetov; David Montaner; Javier Santoyo
Extensive translatome remodeling during ER stress response in mammalian cells.
PloS one 2012;7(5):e35915.
2011: Sun Yung; Lyle Armstrong; Viviana Bisbal; Deborah Burks; Ana Conesa; Ian Dimmick; Joaquín Dopazo; Maria Ledran; Lamin Marenah; Pablo Menendez; David Montaner; Ruben Moreno; Inmaculada Moreno-Gimeno; Joanne Mountford; Iliana Paraskevopoulou; Pedro J Real; Mauro Santibanez-Koref; Nicholas J Slater; Majlinda Lako
Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells.
Human molecular genetics 2011;20(24):4932-46.
2011: Sonia Tarazona; Joaquín Dopazo; Alberto Ferrer; Fernando García-Alcalde; Ana Conesa
Differential expression in RNA-seq: a matter of depth.
Genome research 2011;21(12):2213-23.
2011: Jaime Huerta-Cepas; Martijn A Huynen; Joaquín Dopazo; Toni Gabaldón
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings in bioinformatics 2011;12(5):442-8.
2011: Rubén Sánchez; François Serra; Joaquín Tárraga; Salvador Capella-Gutíerrez; José Carbonell; Alejandro de María; Joaquín Dopazo; Toni Gabaldón; Jaime Huerta-Cepas; Ignacio Medina; Luis Pulido; Hernan Dopazo
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic acids research 2011;39(Web Server issue):W470-4.
2011: Greet De Baets; Javier Delgado Blanco; Joaquín Dopazo; Reumers Joke; Joost Schymkowitz; Frederic Rousseau
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins.
PLoS computational biology 2011;7(6):e1002090.
2011: Stefan Götz; Roland Arnold; Patricia Sebastián-León; Samuel Martín-Rodríguez; Patrick Tischler; Marc-André Jehl; Joaquín Dopazo; Thomas Rattei; Ana Conesa
B2G-FAR, a species-centered GO annotation repository.
Bioinformatics (Oxford, England) 2011;27(7):919-24.
2011: Eva Alloza; Fátima Al-Shahrour; Juan C Cigudosa; Joaquín Dopazo
A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression.
BMC medical genomics 2011;4():37.
2011: Pablo Minguez; Joaquín Dopazo
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties.
PloS one 2011;6(3):e17474.
2010: Maria José Nueda; Stefan Götz; Ignacio Medina; Joaquín Dopazo; Ana Conesa
Serial Expression Analysis: a web tool for the analysis of serial gene expression data.
Nucleic acids research 2010;38(Web Server issue):W239-45.
2010: Ignacio Medina; Stefan Götz; Luis Pulido; Sara C Madeira; Stefan Goetz; Ana Conesa; Joaquín Tárraga; Alberto Pascual-Montano; Ruben Nogales-Cadenas; Javier Santoyo; Francisco García; Martina Marbà; David Montaner; Joaquín Dopazo
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic acids research 2010;38(Web Server issue):W210-3.
2010: Arantxa Peña; Hanno Teeling; Jaime Huerta-Cepas; Fernando Santos; Pablo Yarza; Jocelyn Brito-Echeverría; Marianna Lucio; philippe schmitt-kopplin; Inmaculada Meseguer; Chantal Schenowitz; Carole Dossat; Valerie Barbe; Joaquín Dopazo; Ramon Rosselló-Mora; Margarete Schüler; Frank Oliver Glöckner; Rudolf Amann; Toni Gabaldón; Josefa Antón
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.
The ISME journal 2010;4(7):882-95.
2010: Núria Bonifaci; Bohdan Górski; Bartlomiej Masojć; Dominika Wokołorczyk; Anna Jakubowska; Tadeusz Dębniak; Antoni Berenguer; Jordi Serra Musach; Joan Brunet; Joaquín Dopazo; Steven A Narod; Jan Lubiński; Conxi Lázaro; Cezary Cybulski; Miguel Angel Pujana
Exploring the link between germline and somatic genetic alterations in breast carcinogenesis.
PloS one 2010;5(11):e14078.
2010: Fátima Al-Shahrour; Stefan Götz; Tomás Marqués-Bonet; Elodie Gazave; Arcadi Navarro; Joaquín Dopazo
Selection upon genome architecture: conservation of functional neighborhoods with changing genes.
PLoS computational biology 2010;6(10):e1000953.
2010: David Montaner; Joaquín Dopazo
Multidimensional gene set analysis of genomic data.
PloS one 2010;5(4):e10348.
2010: Jaime Huerta-Cepas; Joaquín Dopazo; Toni Gabaldón
ETE: a python Environment for Tree Exploration.
BMC bioinformatics 2010;11():24.
2010: Joaquín Dopazo
Functional profiling methods in cancer.
Methods in molecular biology (Clifton, N.J.) 2010;576():363-74.
2009: Pablo Minguez; Stefan Götz; David Montaner; Fátima Al-Shahrour; Joaquín Dopazo
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: David Montaner; Pablo Minguez; Fátima Al-Shahrour; Joaquín Dopazo
Gene set internal coherence in the context of functional profiling.
BMC genomics 2009;10():197.
2008: Ana Conesa; Rasmus Bro; Francisco García-García; José Manuel Prats; Stefan Götz; Karin Kjeldahl; David Montaner; Joaquín Dopazo
Direct functional assessment of the composite phenotype through multivariate projection strategies.
Genomics 2008;92(6):373-83.
2008: JOSE HORCAJADAS; Pablo Mínguez; Joaquín Dopazo; Francisco J Esteban; Francisco Domínguez; Linda C Giudice; Antonio Pellicer; Carlos Simón
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: Fátima Al-Shahrour; José Carbonell; Stefan Götz; Stefan Goetz; Ana Conesa; Joaquín Tárraga; Ignacio Medina; Eva Alloza; David Montaner; Joaquín Dopazo
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
Nucleic acids research 2008;36(Web Server issue):W341-6.
2008: Joaquín Tárraga; Ignacio Medina; Stefan Götz; Jaime Huerta-Cepas; Pablo Minguez; Eva Alloza; Fátima Al-Shahrour; Susana Vegas-Azcárate; Stefan Goetz; Pablo Escobar; Francisco Garcia-Garcia; Ana Conesa; David Montaner; Joaquín Dopazo
GEPAS, a web-based tool for microarray data analysis and interpretation.
Nucleic acids research 2008;36(Web Server issue):W308-14.
2008: Stefan Götz; Juan Miguel García-Gómez; Javier Terol; Tim Williams; Shivashankar H Nagaraj; María José Nueda; Montserrat Robles; Manuel Talón; Joaquín Dopazo; Ana Conesa
High-throughput functional annotation and data mining with the Blast2GO suite.
Nucleic acids research 2008;36(10):3420-35.
2008: Joan Valls; Mònica Grau; Xavier Sole; Pilar Hernández; David Montaner; Joaquín Dopazo; Miguel A Peinado; Gabriel Capellá; Victor Moreno; Miguel Angel Pujana
CLEAR-test: combining inference for differential expression and variability in microarray data analysis.
Journal of biomedical informatics 2008;41(1):33-45.
2008: Núria Bonifaci; Antoni Berenguer; Javier Díez; Oscar Reina; Ignacio Medina; Joaquín Dopazo; Víctor Moreno; Miguel Angel Pujana
Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes.
BMC medical genomics 2008;1():62.
2008: Joaquín Dopazo; Fátima Al-Shahrour
Expression and microarrays.
Methods in molecular biology (Clifton, N.J.) 2008;453():245-55.
2008: Reumers Joke; Lucía Conde; Ignacio Medina; Sebastian Maurer-Stroh; Joost Van Durme; Joaquín Dopazo; Frederic Rousseau; Joost Schymkowitz
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: Jaime Huerta-Cepas; Anibal Bueno; Joaquín Dopazo; Toni Gabaldón
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Nucleic acids research 2008;36(Database issue):D491-6.
2008: Emidio Capriotti; Leonardo Arbiza; Rita Casadio; Joaquín Dopazo; Hernan Dopazo; maricus MR
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.
2007: Pablo Minguez; Fátima Al-Shahrour; David Montaner; Joaquín Dopazo
Functional profiling of microarray experiments using text-mining derived bioentities.
Bioinformatics (Oxford, England) 2007;23(22):3098-9.
2007: Sergio Ruiz-Llorente; Cristina Montero-Conde; Roger L Milne; Christian M Moya; Arancha Cebrián; Rocío Letón; Alberto Cascón; Fátima Mercadillo; Iñigo Landa; Salud Borrego; Guiomar Pérez de Nanclares; Cristina Alvarez-Escolá; José Angel Díaz-Pérez; Angel Carracedo; Miguel Urioste; Anna González-Neira; Javier Benítez; Pilar Santisteban; Joaquín Dopazo; Bruce A J Ponder; Mercedes Robledo
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: maricus MR; Ursula Pieper; Mallur S Madhusudhan; Andrea Rossi; Narayanan Eswar; Fred P Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali
DBAli tools: mining the protein structure space.
Nucleic acids research 2007;35(Web Server issue):W393-7.
2007: Fátima Al-Shahrour; Pablo Minguez; Joaquín Tárraga; Ignacio Medina; Eva Alloza; David Montaner; Joaquín Dopazo
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: Lucía Conde; David Montaner; Jordi Burguet-Castell; Joaquín Tárraga; Ignacio Medina; Fátima Al-Shahrour; Joaquín Dopazo
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: Joaquín Tárraga; Ignacio Medina; Leonardo Arbiza; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernan Dopazo
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic acids research 2007;35(Web Server issue):W38-42.
2007: Ignacio Medina; David Montaner; Joaquín Tárraga; Joaquín Dopazo
Prophet, a web-based tool for class prediction using microarray data.
Bioinformatics (Oxford, England) 2007;23(3):390-1.
2007: Lucía Conde; David Montaner; Jordi Burguet-Castell; Joaquín Tárraga; Fátima Al-Shahrour; Joaquín Dopazo
Functional profiling and gene expression analysis of chromosomal copy number alterations.
Bioinformation 2007;1(10):432-5.
2007: Pilar Hernández; Jaime Huerta-Cepas; David Montaner; Fátima Al-Shahrour; Joan Valls; Laia Gómez; Gabriel Capellá; Joaquín Dopazo; Miguel Angel Pujana
Evidence for systems-level molecular mechanisms of tumorigenesis.
BMC genomics 2007;8():185.
2007: maricus MR; Andrea Rossi; Fátima Al-Shahrour; Fred P Davis; Ursula Pieper; Joaquín Dopazo; Andrej Sali
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
BMC bioinformatics 2007;8 Suppl 4():S4.
2007: Jaime Huerta-Cepas; Hernan Dopazo; Joaquín Dopazo; Toni Gabaldón
The human phylome.
Genome biology 2007;8(6):R109.
2007: Fátima Al-Shahrour; Leonardo Arbiza; Hernan Dopazo; Jaime Huerta-Cepas; Pablo Mínguez; David Montaner; Joaquín Dopazo
From genes to functional classes in the study of biological systems.
BMC bioinformatics 2007;8():114.
2006: Roger L Milne; Gloria Ribas; Anna González-Neira; Rainer Fagerholm; Antonio Salas; Emilio González; Joaquín Dopazo; Heli Nevanlinna; Mercedes Robledo; Javier Benítez
ERCC4 associated with breast cancer risk: a two-stage case-control study using high-throughput genotyping.
Cancer research 2006;66(19):9420-7.
2006: Lucía Conde; Juan M Vaquerizas; Hernan Dopazo; Leonardo Arbiza; Reumers Joke; Frederic Rousseau; Joost Schymkowitz; Joaquín Dopazo
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.
Nucleic acids research 2006;34(Web Server issue):W621-5.
2006: David Montaner; Joaquín Tárraga; Jaime Huerta-Cepas; Jordi Burguet; Juan M Vaquerizas; Lucía Conde; Pablo Minguez; Javier Vera; Sach Mukherjee; Joan Valls; Miguel Angel Pujana; Eva Alloza; Javier Herrero; Fátima Al-Shahrour; Joaquín Dopazo
Next station in microarray data analysis: GEPAS.
Nucleic acids research 2006;34(Web Server issue):W486-91.
2006: Fátima Al-Shahrour; Pablo Minguez; Joaquín Tárraga; David Montaner; Eva Alloza; Juan M Vaquerizas; Lucía Conde; christian blaschke; Javier Vera; Joaquín Dopazo
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
Nucleic acids research 2006;34(Web Server issue):W472-6.
2006: Joaquín Dopazo
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: Leonardo Arbiza; Serena Duchi; David Montaner; Jordi Burguet; David Pantoja-Uceda; Antonio Pineda-Lucena; Joaquín Dopazo; Hernan Dopazo
Selective pressures at a codon-level predict deleterious mutations in human disease genes.
Journal of molecular biology 2006;358(5):1390-404.
2006: Leonardo Arbiza; Joaquín Dopazo; Hernan Dopazo
Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
PLoS computational biology 2006;2(4):e38.
2006: Pablo Minguez; Fátima Al-Shahrour; Joaquín Dopazo
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: Joaquín Dopazo
Functional interpretation of microarray experiments.
Omics : a journal of integrative biology 2006;10(3):398-410.
2006: Francisco Azuaje; Fátima Al-Shahrour; Joaquín Dopazo
Ontology-driven approaches to analyzing data in functional genomics.
Methods in molecular biology (Clifton, N.J.) 2006;316():67-86.
2006: Josep Ramon Goñi; Juan M Vaquerizas; Joaquín Dopazo; Modesto Orozco
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.
BMC genomics 2006;7():63.
2005: Juan M Vaquerizas; Lucía Conde; Patricio Yankilevich; Amaya Cabezón; Pablo Minguez; Ramón Díaz-Uriarte; Fátima Al-Shahrour; Javier Herrero; Joaquín Dopazo
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.
Nucleic acids research 2005;33(Web Server issue):W616-20.
2005: Lucía Conde; Juan M Vaquerizas; Carles Ferrer-Costa; Xavier de la Cruz; Modesto Orozco; Joaquín Dopazo
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: Fátima Al-Shahrour; Pablo Minguez; Juan M Vaquerizas; Lucía Conde; Joaquín Dopazo
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: Fátima Al-Shahrour; Ramón Díaz-Uriarte; Joaquín Dopazo
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
Bioinformatics (Oxford, England) 2005;21(13):2988-93.
2005: Javier Santoyo; Juan M Vaquerizas; Joaquín Dopazo
Highly specific and accurate selection of siRNAs for high-throughput functional assays.
Bioinformatics (Oxford, England) 2005;21(8):1376-82.
2005: José Palacios; Emiliano Honrado; Ana Osorio; Alicia Cazorla; David Sarrió; Alicia Barroso; Sandra Rodríguez; Juan C Cigudosa; Orland Diez; Carmen Alonso; Enrique Lerma; Joaquín Dopazo; Carmen Rivas; Javier Benítez
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: Alberto Cascón; Sergio Ruiz-Llorente; Sandra Rodríguez-Perales; Emiliano Honrado; Angel Martínez-Ramírez; Rocío Letón; Cristina Montero-Conde; Javier Benítez; Joaquín Dopazo; Juan C Cigudosa; Mercedes Robledo
A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma.
Genes, chromosomes & cancer 2005;42(3):260-8.
2005: Sara Alvarez; Ramon Diaz-Uriarte; Ana Osorio; Alicia Barroso; Lorenzo Melchor; Maria Fe Paz; Emiliano Honrado; Raquel Rodríguez; Miguel Urioste; Laura Valle; Orland Díez; Juan C Cigudosa; Joaquín Dopazo; Manel Esteller; Javier Benitez
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: Hernan Dopazo; Joaquín Dopazo
Genome-scale evidence of the nematode-arthropod clade.
Genome biology 2005;6(5):R41.
2004: Juan M Vaquerizas; Joaquín Dopazo; Ramón Díaz-Uriarte
DNMAD: web-based diagnosis and normalization for microarray data.
Bioinformatics (Oxford, England) 2004;20(18):3656-8.
2004: Bárbara Meléndez; Ramón Díaz-Uriarte; Marta Cuadros; Angel Martínez-Ramírez; José Fernández-Piqueras; Ana Dopazo; Juan C Cigudosa; Carmen Rivas; Joaquín Dopazo; Beatriz Martínez-Delgado; Javier Benítez
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: Hernan Dopazo; Javier Santoyo; Joaquín Dopazo
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: Javier Herrero; Juan M Vaquerizas; Fátima Al-Shahrour; Lucía Conde; Alvaro Mateos; Javier Santoyo Ramón Díaz-Uriarte; Joaquín Dopazo
New challenges in gene expression data analysis and the extended GEPAS.
Nucleic acids research 2004;32(Web Server issue):W485-91.
2004: Lucía Conde; Juan M Vaquerizas; Javier Santoyo; Fátima Al-Shahrour; Sergio Ruiz-Llorente; Mercedes Robledo; Joaquín Dopazo
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: Fátima Al-Shahrour; Ramón Díaz-Uriarte; Joaquín Dopazo
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: Javier Herrero; Fátima Al-Shahrour; Ramón Díaz-Uriarte; Alvaro Mateos; Juan M Vaquerizas; Javier Santoyo; Joaquín Dopazo
GEPAS: A web-based resource for microarray gene expression data analysis.
Nucleic acids research 2003;31(13):3461-7.
2003: Maria J Martin; Javier Herrero; Alvaro Mateos; Joaquín Dopazo
Comparing bacterial genomes through conservation profiles.
Genome research 2003;13(5):991-8.
2003: Javier Herrero; Ramón Díaz-Uriarte; Joaquín Dopazo
Gene expression data preprocessing.
Bioinformatics (Oxford, England) 2003;19(5):655-6.
2003: Javier Herrero; Ramón Díaz-Uriarte; Joaquín Dopazo
An approach to inferring transcriptional regulation among genes from large-scale expression data.
Comparative and functional genomics 2003;4(1):148-54.
2002: Alvaro Mateos; Joaquín Dopazo; Ronald Jansen; Yuhai Tu; Mark Gerstein; Gustavo Stolovitzky
Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons.
Genome research 2002;12(11):1703-15.
2002: Lorraine Tracey; Raquel Villuendas; Pablo Ortiz; Ana Dopazo; Inmaculada Spiteri; Luis Lombardia; José L Rodríguez-Peralto; Jesús Fernández-Herrera; Almudena Hernández; Javier Fraga; Orlando Dominguez; Javier Herrero; Miguel A Alonso; Joaquín Dopazo; Miguel A Piris
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: Javier Tamames; Dominic Clark; Javier Herrero; Joaquín Dopazo; christian blaschke; José M Fernández; Juan C Oliveros; Carmen Galvez
Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction.
Journal of biotechnology 2002;98(2-3):269-83.
2002: Javier Herrero; Joaquín Dopazo
Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns.
Journal of proteome research 2002;1(5):467-70.
2001: Javier Herrero; Carmen Galvez; Joaquín Dopazo
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinformatics (Oxford, England) 2001;17(2):126-36.
2000: Juan C Oliveros; christian blaschke; Javier Herrero; Joaquín Dopazo; Carmen Galvez
Expression profiles and biological function.
Genome informatics. Workshop on Genome Informatics 2000;11():106-17.