J. Dopazo

发表

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

David P. Kreil, Todd M. Smith, Thomas M. Blomquist, 2014, Nature Biotechnology.

Highly sensitive and ultrafast read mapping for RNA-seq analysis

E. S. Quintana-Ortí, E. S. Quintana‐Ortí, J. Dopazo, 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

Evidence for systems-level molecular mechanisms of tumorigenesis

J. Dopazo, M. Pujana, Pilar Hernández, 2007, BMC Genomics.

HGVA: the Human Genome Variation Archive

Joaquín Dopazo, Marta Bleda, Joaquín Tárraga, 2017, Nucleic Acids Res..

267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation

Josephine T. Daub, J. P. Florido, Javier Santoyo-Lopez, 2016, Molecular biology and evolution.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Kevin C. Dorff, Aaron M. Smalter, Stephen C. Harris, 2010, Nature Biotechnology.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

David P. Kreil, Steven P. Lund, Paweł P. Łabaj, 2014, Nature Communications.

Differential expression in RNA-seq: a matter of depth.

A. Conesa, J. Dopazo, Sonia Tarazona, 2011, Genome research.

Selective pressures at a codon-level predict deleterious mutations in human disease genes.

Joaquín Dopazo, David Montaner, Leonardo Arbiza, 2006, Journal of molecular biology.

Differential Lipid Partitioning Between Adipocytes and Tissue Macrophages Modulates Macrophage Lipotoxicity and M2/M1 Polarization in Obese Mice

David Montaner, Nuria Barbarroja, Matej Orešič, 2011, Diabetes.

Phylogenetic Reconstruction Using an Unsupervised Growing Neural Network That Adopts the Topology of a Phylogenetic Tree

J. Dopazo, J. Carazo, 1997, Journal of Molecular Evolution.

Comparing bacterial genomes through conservation profiles.

Maria J Martin, Javier Herrero, Joaquin Dopazo, 2003, Genome research.

protein sequences Self-organizing tree-growing network for the classification of

J. Dopazo, J. Carazo, H. C. Wang, 2002 .

Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns.

Joaquín Dopazo, Javier Herrero, J. Dopazo, 2002, Journal of proteome research.

Methods and approaches in the analysis of gene expression data.

J. Dopazo, F. Falciani, I. Dragoni, 2001, Journal of immunological methods.

Expression profiles and biological function.

C. Blaschke, J. Dopazo, A. Valencia, 2000, Genome informatics. Workshop on Genome Informatics.

Self‐organizing tree‐growing network for the classification of protein sequences

Joaquin Dopazo, J. Dopazo, J. Carazo, 1998, Protein science : a publication of the Protein Society.

Signaling Pathway Activities Improve Prognosis for Breast Cancer

Marta R. Hidalgo, Jean-Philippe Vert, J. Dopazo, 2017, bioRxiv.

The role of the interactome in the maintenance of deleterious variability in human populations

Joaquin Dopazo, Guillermo Antiñolo, Javier Santoyo-Lopez, 2014, Molecular systems biology.

Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas

Cristina Y. González, Ignacio Medina, Marta Bleda, 2015, BMC Medical Genomics.

Functional genomics and networks: new approaches in the extraction of complex gene modules

J. Dopazo, Pablo Minguez, P. Minguez, 2010, Expert review of proteomics.

Assessing the Biological Significance of Gene Expression Signatures and Co-Expression Modules by Studying Their Network Properties

J. Dopazo, Pablo Minguez, P. Minguez, 2011, PloS one.

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

J. Dopazo, A. Amadoz, M. Hidalgo, 2016, bioRxiv.

Using mechanistic models for the clinical interpretation of complex genomic variation

Marta R. Hidalgo, J. Dopazo, M. Hidalgo, 2019, Scientific Reports.

University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite

M. Robles, A. Conesa, J. Dopazo, 2022 .

The Activation of the Sox2 RR2 Pluripotency Transcriptional Reporter in Human Breast Cancer Cell Lines is Dynamic and Labels Cells with Higher Tumorigenic Potential

J. Dopazo, F. García-García, J. Menéndez, 2014, Front. Oncol..

Assessing differential expression measurements by highly parallel pyrosequencing and DNA microarrays: a comparative study.

A. Casamayor, J. Dopazo, M. Álvarez-Tejado, 2013, Omics : a journal of integrative biology.

Gene expression analysis of chromosomal regions with gain or loss of genetic material detected by comparative genomic hybridization

A. Dopazo, J. Cigudosa, J. Benítez, 2004, Genes, chromosomes & cancer.

A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression

J. Cigudosa, J. Dopazo, F. Al-Shahrour, 2011, BMC Medical Genomics.

Functional interpretation of microarray experiments.

J. Dopazo, 2006, Omics : a journal of integrative biology.

Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments

J. Dopazo, I. Medina, A. Amadoz, 2012, Nucleic acids research.

Multidimensional Gene Set Analysis of Genomic Data

J. Dopazo, D. Montaner, 2010, PloS one.

Direct functional assessment of the composite phenotype through multivariate projection strategies.

R. Bro, A. Conesa, J. Dopazo, 2008, Genomics.

Gene set internal coherence in the context of functional profiling

J. Dopazo, D. Montaner, F. Al-Shahrour, 2009, BMC Genomics.

Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons.

M. Gerstein, Y. Tu, R. Jansen, 2002, Genome research.

Large deletions in the 5'-untranslated region of foot-and-mouth disease virus of serotype C.

E. Domingo, J. Dopazo, C. Escarmís, 1995, Virus research.

SNP and haplotype mapping for genetic analysis in the rat

E. Birney, R. Guigó, M. Bihoreau, 2008, Nature Genetics.

The human phylome

J. Dopazo, J. Huerta-Cepas, T. Gabaldón, 2007, Genome Biology.

Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

C. Erten, J. Dopazo, 2017, BMC Systems Biology.

Genome-scale evidence of the nematode-arthropod clade

J. Dopazo, H. Dopazo, 2005, Genome Biology.

Initial Genomics of the Human Nucleolus

A. Conesa, Javier Santoyo-Lopez, J. Dopazo, 2010, PLoS genetics.

Variable selection for multifactorial genomic data

A. Conesa, J. Dopazo, Sonia Tarazona, 2012 .

Use of estimated evolutionary strength at the codon level improves the prediction of disease‐related protein mutations in humans

E. Capriotti, M. Martí-Renom, R. Casadio, 2008, Human mutation.

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.

C. Nislow, A. Conesa, J. Dopazo, 2014, Fungal genetics and biology : FG & B.

Genomics of the origin and evolution of Citrus

J. Dopazo, D. Rokhsar, M. Talón, 2018, Nature.

Genomics and transcriptomics in drug discovery.

J. Dopazo, 2014, Drug discovery today.

Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation

J. Dopazo, F. García-García, S. Beltran, 2017, Human mutation.

Mutation Screening of Multiple Genes in Spanish Patients with Autosomal Recessive Retinitis Pigmentosa by Targeted Resequencing

J. Dopazo, S. Borrego, G. Antiñolo, 2011, PloS one.

Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium

D. Blesa, A. Conesa, J. Dopazo, 2010, Stem cells.

Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis

S. Puig, J. Dopazo, M. del Río, 2016, Oncotarget.

NOIseq: a RNA-seq differential expression method robust for sequencing depth biases

Joaquín Dopazo, Ana Conesa, Sonia Tarazona, 2012 .

Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity

Francisco Salavert, Alicia Amadoz, Joaquin Dopazo, 2015, Scientific Reports.

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

C. Furlanello, Giuseppe Jurman, T. Nikolskaya, 2010, The Pharmacogenomics Journal.

PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level

Joaquín Dopazo, Fátima Al-Shahrour, Juan M. Vaquerizas, 2004, Nucleic Acids Res..

ERCC4 associated with breast cancer risk: a two-stage case-control study using high-throughput genotyping.

Joaquín Dopazo, Heli Nevanlinna, Rainer Fagerholm, 2006, Cancer research.

Bioinformatics a nd c ancer: an e ssential a lliance

J. Dopazo, 2006 .

Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp. citri

A. Conesa, J. Dopazo, F. Gmitter, 2011, BMC Plant Biology.

Interpretable machine learning analysis of functional metagenomic profiles improves colorectal cancer prediction and reveals basic molecular mechanisms.

J. Dopazo, M. Peña-Chilet, Carlos Loucera, 2020 .

Genetic evolution and tropism of transmissible gastroenteritis coronaviruses

Joaquín Dopazo, J. Dopazo, F. Gebauer, 1992, Virology.

DNA methylation epigenotypes in breast cancer molecular subtypes

M. Fraga, J. Dopazo, D. Montaner, 2010, Breast Cancer Research.

CENTRAL NERVOUS SYSTEM GENES TO THE DEVELOPMENT OF THE ENTERIC NERVOUS SYSTEM

Berta, Aravinda, Rutger, 2016 .

Design of primers for PCR amplification of highly variable genomes

Joaquín Dopazo, A. Rodriguez, J. C. Saiz, 1993, Comput. Appl. Biosci..

A method for determining the position and size of optimal sequence regions for phylogenetic analysis

J. Dopazo, F. González-Candelas, F. Sobrino, 1995, Journal of Molecular Evolution.

Molecular epidemiology of foot-and-mouth disease virus type O.

J. Dopazo, J. Saiz, F. Sobrino, 1993, The Journal of general virology.

Gene encoding capsid protein VP1 of foot-and-mouth disease virus: a quasispecies model of molecular evolution.

A. Moya, E. Domingo, J. Dopazo, 1988, Proceedings of the National Academy of Sciences of the United States of America.

Primer design for specific diagnosis by PCR of highly variable RNA viruses: typing of foot-and-mouth disease virus.

J. Dopazo, J. Saiz, F. Sobrino, 1992, Virology.

A procedure for detecting selection in highly variable viral genomes: evidence of positive selection in antigenic regions of capsid protein VP1 of foot-and-mouth disease virus.

J. Dopazo, F. Sobrino, J. Nunez, 1998, Journal of virological methods.

RT-PCR in foot-and-mouth.

J. Dopazo, F. Sobrino, J. Nunez, 1998, The Veterinary quarterly.

A RT-PCR assay for the differential diagnosis of vesicular viral diseases of swine.

J. Dopazo, F. Sobrino, J. Nunez, 1998, Journal of virological methods.

Highly Specific and Accurate Selection of siRNAs for High-Throughput Functional Assays

Joaquín Dopazo, Juan M. Vaquerizas, Javier Santoyo, 2005, Spanish Bioinformatics Conference.

The pan-cancer pathological regulatory landscape

Joaquín Dopazo, Marta Bleda, Matias M. Falco, 2016, Scientific Reports.

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape.

Marta R. Hidalgo, J. Dopazo, M. Pujana, 2018, Cancer research.

15 THE USE OF GO TERMS TO UNDERSTAND THE BIOLOGICAL SIGNIFICANCE OF MICROARRAY DIFFERENTIAL GENE EXPRESSION DATA

Joaquín Dopazo, Ramón Díaz-Uriarte, Fátima Al-Shahrour, 2003 .

Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape

Marta R. Hidalgo, J. Dopazo, M. Hidalgo, 2020, NAR cancer.

Mechanistic models of signaling pathways deconvolute the functional landscape of glioblastoma at single cell resolution

Marta R. Hidalgo, J. Dopazo, M. Hidalgo, 2019, bioRxiv.

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples

J. Dopazo, Carlos Loucera, C. S. Casimiro-Soriguer, 2018, bioRxiv.

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples

J. P. Florido, J. Dopazo, Carlos Loucera, 2018, bioRxiv.

10th Anniversary of the European Association for Predictive, Preventive and Personalised (3P) Medicine - EPMA World Congress Supplement 2020

Rostyslav V Bubnov, R. Kučera, Tomáš Svoboda, 2020, EPMA Journal.

Exploring the Link between Germline and Somatic Genetic Alterations in Breast Carcinogenesis

J. Dopazo, A. Berenguer, M. Pujana, 2010, PloS one.

Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers

J. Cigudosa, J. Benítez, J. Dopazo, 2005, Breast Cancer Research and Treatment.

Permanent Cardiac Sarcomere Changes in a Rabbit Model of Intrauterine Growth Restriction

J. Dopazo, B. Bijnens, F. García-García, 2014, PloS one.

Intrauterine growth restriction is associated with cardiac ultrastructural and gene expression changes related to the energetic metabolism in a rabbit model.

J. Dopazo, B. Bijnens, F. García-García, 2013, American journal of physiology. Heart and circulatory physiology.

Intrauterine growth restriction is associated with cardiac ultrastructural and 1 gene expression changes related to the energetic metabolism in a rabbit model ” 2 3

J. Dopazo, B. Bijnens, F. García-García, 2013 .

Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction.

Joaquín Dopazo, Christian Blaschke, Javier Herrero, 2002, Journal of biotechnology.

Concurrent and Accurate Short Read Mapping on Multicore Platforms

E. S. Quintana‐Ortí, J. Dopazo, I. Medina, 2013 .

Phylogenetic Analysis of Viroid and Viroid-Like Satellite RNAs from Plants: A Reassessment

Joaquín Dopazo, Santiago F. Elena, Andrés Moya, 2001, Journal of Molecular Evolution.

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Rubén Sánchez, Joaquín Dopazo, Ignacio Medina, 2011, Nucleic Acids Res..

Sequences of isopenicillin N synthetase genes suggest horizontal gene transfer from prokaryotes to eukaryotes

A. Moya, J. Dopazo, D. Ramón, 1990, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Analysis of Normal-Tumour Tissue Interaction in Tumours: Prediction of Prostate Cancer Features from the Molecular Profile of Adjacent Normal Cells

M. Vannucci, J. Dopazo, F. Al-Shahrour, 2011, PloS one.

Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development

J. Dopazo, Rajiv Kumar, J. López-Guerrero, 2021, Cancers.

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.)

J. Dopazo, N. Paniego, A. Fernie, 2017, Plant Molecular Biology.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Dmitri D. Pervouchine, Pedro G. Ferreira, Marta R. Hidalgo, 2018, Nature Communications.

Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups

I. Benet, J. Garcia-conde, M. Terol, 2009, Leukemia & lymphoma.

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

A. Conesa, J. Dopazo, J. Calvete, 2011, BMC Genomics.

Comparative gene expression study of the vestibular organ of the Igf1 deficient mouse using whole-transcript arrays

J. Dopazo, C. Avendaño, I. Varela-Nieto, 2015, Hearing Research.

Immune Cell Associations with Cancer Risk

A. Antoniou, T. Mak, J. Dopazo, 2020, iScience.

Title: Genomics and transcriptomics in drug discovery

J. Dopazo, 2013 .

Exome Sequencing Reveals Novel and Recurrent Mutations with Clinical Significance in Inherited Retinal Dystrophies

J. Dopazo, Alicia Vela-Boza, C. Méndez-Vidal, 2014, PloS one.

Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease

P. Sham, S. Cherny, J. Dopazo, 2015, Scientific Reports.

Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray

Bernardo J. Clavijo, D. Blesa, A. Conesa, 2012, PloS one.

Mutational oncogenic signatures on structurally resolved protein interacting interfaces

J. Dopazo, Luz Garcia-Alonso, 2015, bioRxiv.

Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel

J. Dopazo, C. Méndez-Vidal, S. Borrego, 2016, Scientific Reports.

Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree

J. Dopazo, Alicia Vela-Boza, C. Méndez-Vidal, 2014, BMC Genetics.

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

Marta R. Hidalgo, J. Dopazo, M. Pujana, 2018, npj Systems Biology and Applications.

A function-centric approach to the biological interpretation of microarray time-series.

J. Dopazo, F. Al-Shahrour, Pablo Minguez, 2006, Genome informatics. International Conference on Genome Informatics.

Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications.

L. Giudice, J. Dopazo, C. Simón, 2008, The Journal of clinical endocrinology and metabolism.

Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet–Biedl family

Javier Santoyo-Lopez, J. Dopazo, Alicia Vela-Boza, 2013, Molecular genetics & genomic medicine.

Mechanistic modeling of the SARS-CoV-2 disease map

Marta R. Hidalgo, J. Dopazo, C. Çubuk, 2020, BioData Mining.

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome

Marta R. Hidalgo, J. Dopazo, A. Amadoz, 2018, Biology Direct.

Chronic subordination stress selectively downregulates the insulin signaling pathway in liver and skeletal muscle but not in adipose tissue of male mice

J. Dopazo, A. Vidal-Puig, S. Carobbio, 2016, Stress.

Detailed stratified GWAS analysis for severe COVID-19 in four European populations

Francisco J. Medrano, S. Brunak, V. Moreno, 2022, Human molecular genetics.

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Hiroaki Kitano, Egon L. Willighagen, Olaf Wolkenhauer, 2020, Scientific Data.

Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations.

J. Dopazo, F. García-García, M. Cortón, 2015, Human molecular genetics.

Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments

J. Dopazo, C. Çubuk, M. Peña-Chilet, 2020, Cells.

Fixation of mutations at the VP1 gene of foot-and-mouth disease virus. Can quasispecies define a transient molecular clock?

A. Moya, E. Domingo, J. Dopazo, 1991, Gene.

The protease MT1‐MMP drives a combinatorial proteolytic program in activated endothelial cells

J. Dopazo, D. Montaner, J. Arribas, 2012, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

DB100705 797..809

J. Dopazo, D. Montaner, N. Barbarroja, 2011 .

Novel genes detected by transcriptional profiling from whole-blood cells in patients with early onset of acute coronary syndrome.

J. Dopazo, Á. Carracedo, F. García-García, 2013, Clinica chimica acta; international journal of clinical chemistry.

IL1β Induces Mesenchymal Stem Cells Migration and Leucocyte Chemotaxis Through NF-κB

J. Dopazo, F. García-García, I. Cerrada, 2012, Stem Cell Reviews and Reports.

Identification of overexpressed genes in frequently gained/amplified chromosome regions in multiple myeloma.

Borja Saez, Reiner Siebert, Sara Alvarez, 2006, Haematologica.

Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus.

Fatima Al-Shahrour, Esteban Ballestar, Reiner Siebert, 2010, Genome research.

Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain)

Jose L. Fernandez-Rueda, J. Dopazo, C. S. Casimiro-Soriguer, 2021, Viruses.

Protein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus

J. Dopazo, M. González-Escribano, J. García-Lozano, 2022, Scientific Reports.

Incidence and Prevalence of Children's Diffuse Lung Disease in Spain.

J. Dopazo, M. Griese, M. Fernández-Cancio, 2021, Archivos de bronconeumologia.

Therapeutic targets for olive pollen allergy defined by gene markers modulated by Ole e 1-derived peptides.

J. Dopazo, D. Montaner, M. Mata, 2015, Molecular immunology.

The EGR2 gene is involved in axonal Charcot−Marie−Tooth disease

J. Dopazo, R. Sivera, C. Espinós, 2015, European journal of neurology.

Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa

J. Dopazo, F. García-García, M. Cortón, 2016, Scientific Reports.

Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma.

A. Dopazo, M. Piris, J. Dopazo, 2002, The American journal of pathology.

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

J. Dopazo, I. Medina, J. Tárraga, 2007, Nucleic Acids Res..

Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy.

J. Dopazo, F. García-García, S. Pascual-Pascual, 2016, The Journal of molecular diagnostics : JMD.

Mutations in the MORC2 gene cause axonal Charcot-Marie-Tooth disease.

J. Dopazo, S. Pascual-Pascual, R. Sivera, 2016, Brain : a journal of neurology.

Mutations in the MORC 2 gene cause axonal Charcot – Marie – Tooth disease

J. Dopazo, S. Pascual-Pascual, R. Sivera, 2015 .

GGPS1 Mutation and Atypical Femoral Fractures with Bisphosphonates.

J. Abril, A. Díez-Pérez, J. Dopazo, 2017, The New England journal of medicine.

Endoglin and MMP14 Contribute to Ewing Sarcoma Spreading by Modulation of Cell–Matrix Interactions

E. Álava, J. Dopazo, A. Amaral, 2022, International journal of molecular sciences.

Antigenic structure of the human respiratory syncytial virus G glycoprotein and relevance of hypermutation events for the generation of antigenic variants.

J. Dopazo, J. Melero, I. Martínez, 1997, The Journal of general virology.

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

C. Auffray, H. Kitano, M. Gillespie, 2020, Scientific Data.

Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer‐prone genodermatoses

S. Puig, J. Dopazo, S. Llames, 2019, The British journal of dermatology.

Re‐evaluation casts doubt on the pathogenicity of homozygous USH2A p.C759F

J. Dopazo, J. Millán, C. Méndez-Vidal, 2015, American journal of medical genetics. Part A.

Integrating prior knowledge in neural network methods to reduce the dimensions of single-cell RNA-Seq Data

Isabel A. Nepomuceno-Chamorro, J. Dopazo, C. Loucera, 2020 .

Models of cell signalling uncover molecular mechanisms of high-risk neuroblastoma and predict outcome

J. Dopazo, A. Amadoz, C. Çubuk, 2017 .

Estimates by computer simulation of genetic distances from comparisons of RNAse A mismatch cleavage patterns.

J. Dopazo, F. Sobrino, C. López-Galíndez, 1993, Journal of virological methods.

Differential gene-expression analysis defines a molecular pattern related to olive pollen allergy.

J. Dopazo, D. Montaner, M. Mata, 2013, Journal of biological regulators and homeostatic agents.

Comparative study of the genetic variability in thymidine kinase and glycoprotein B genes of herpes simplex viruses by the RNase A mismatch cleavage method.

J. Dopazo, E. Tabarés, M. Santana, 1995, Virus research.

Pazopanib for treatment of advanced malignant and dedifferentiated solitary fibrous tumour: a multicentre, single-arm, phase 2 trial.

J. Blay, J. Dopazo, A. Italiano, 2019, The Lancet. Oncology.

Pazopanib for treatment of typical solitary fibrous tumours: a multicentre, single-arm, phase 2 trial.

J. Blay, J. Dopazo, E. de Álava, 2020, The Lancet. Oncology.

A New Overgrowth Syndrome is due to Mutations in RNF125

J. Dopazo, D. Montaner, E. López-Granados, 2014, Human mutation.

The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid

J. Dopazo, N. Paniego, Sergio Gonzalez, 2018, Microbial genomics.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Benjamin M. Gyori, John A. Bachman, Sara Sadat Aghamiri, 2022, bioRxiv.

COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Benjamin M. Gyori, John A. Bachman, Sara Sadat Aghamiri, 2021, Molecular systems biology.

New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations

M. Nöthen, S. Brunak, V. Moreno, 2021, medRxiv.

Progress in pharmacogenetics: consortiums and new strategies

Joaquín Dopazo, Munir Pirmohamed, Gérard Siest, 2016, Drug metabolism and personalized therapy.

Genetic Variability and Antigenic Diversity of Foot-and-Mouth Disease Virus

A. Moya, E. Domingo, J. Dopazo, 1990 .

Immunogenicity of non-structural proteins of foot-and-mouth disease virus: differences between infected and vaccinated swine

J. Dopazo, J. Saiz, F. Sobrino, 2005, Archives of Virology.

A new parallel pipeline for DNA methylation analysis of long reads datasets

J. Dopazo, J. Tárraga, J. Orduña, 2017, BMC Bioinformatics.

Fast inexact mapping using advanced tree exploration on backward search methods

J. Dopazo, I. Medina, J. Tárraga, 2015, BMC Bioinformatics.

Deciphering Genomic Heterogeneity and the Internal Composition of Tumour Activities through a Hierarchical Factorisation Model

J. Dopazo, D. Conesa, J. Carbonell-Caballero, 2021, Mathematics.

GEPAS, a web-based tool for microarray data analysis and interpretation

Joaquín Dopazo, Ignacio Medina, Stefan Götz, 2008, Nucleic Acids Res..

Next station in microarray data analysis: GEPAS

Joaquín Dopazo, Joaquín Tárraga, Javier Herrero, 2006, Nucleic Acids Res..

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2005, Nucleic Acids Res..

Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses.

J. Dopazo, F. Sobrino, E. Carrillo, 2001, Veterinary research.

Two Novel Mutations in the BCKDK (Branched‐Chain Keto‐Acid Dehydrogenase Kinase) Gene Are Responsible for a Neurobehavioral Deficit in Two Pediatric Unrelated Patients

Joaquín Dopazo, Rosa Navarrete, Anna López-Sala, 2014, Human mutation.

Two novel mutations in the BCKDK gene ( branched-chain keto-acid dehydrogenase kinase ) are responsible of a neurobehavioral deficit in two pediatric unrelated patients

Joaquín Dopazo, Joana, Rafael Artuch, 2014 .

A map of human microRNA variation uncovers unexpectedly high levels of variability

Joaquín Dopazo, Ignacio Medina, Eva Alloza, 2012, Genome Medicine.

Objective review of de novo stand‐alone error correction methods for NGS data

Ignacio Blanquer, Joaquín Dopazo, Andy S. Alic, 2016 .

Qualimap: evaluating next-generation sequencing alignment data

Joaquín Dopazo, Stefan Götz, Sonia Tarazona, 2012, Bioinform..

Babelomics 5.0: functional interpretation for new generations of genomic data

Rosa D. Hernansaiz-Ballesteros, Marta Bleda, Francisco Salavert, 2015, Nucleic Acids Res..

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

Joaquín Dopazo, Ramón Díaz-Uriarte, Fátima Al-Shahrour, 2004, Bioinform..

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions

Modesto Orozco, Juan M. Vaquerizas, Joaquin Dopazo, 2006, BMC Genomics.

Early Transcriptional Defense Responses in Arabidopsis Cell Suspension Culture under High-Light Conditions1[C][W][OA]

J. Revuelta, J. Dopazo, F. García-García, 2011, Plant Physiology.

Capturing the biological impact of CDKN2A and MC1R genes as an early predisposing event in melanoma and non melanoma skin cancer

S. Puig, J. Dopazo, M. del Río, 2013, Oncotarget.

The CD36, CLA-1 (CD36L1), and LIMPII (CD36L2) gene family: cellular distribution, chromosomal location, and genetic evolution.

J. Dopazo, M. Vega, D. Calvo, 1995, Genomics.

Discovering potential interactions between rare diseases and COVID-19 by combining mechanistic models of viral infection with statistical modeling

J. Dopazo, M. Peña-Chilet, C. Loucera, 2022, Human molecular genetics.

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

J R Ecker, M. Esteller, J. Dopazo, 2016, Translational psychiatry.

FM19G11, a New Hypoxia-inducible Factor (HIF) Modulator, Affects Stem Cell Differentiation Status*

J. Dopazo, D. Montaner, M. Stojkovic, 2009, The Journal of Biological Chemistry.

Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species

Joaquín Dopazo, Hernán Dopazo, Javier Santoyo, 2004, ISMB/ECCB.

A comprehensive database for integrated analysis of omics data in autoimmune diseases

J. Dopazo, J. Saez-Rodriguez, F. Al-Shahrour, 2021, BMC Bioinform..

A comprehensive and centralized database for exploring omics data in Autoimmune Diseases

J. Dopazo, J. Saez-Rodriguez, F. Al-Shahrour, 2020, bioRxiv.

Bioinformatics and cancer: an essential alliance

Joaquín Dopazo, J. Dopazo, 2006, Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico.

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes

Joaquín Dopazo, Modesto Orozco, Xavier de la Cruz, 2005, Nucleic Acids Res..

Implementing Personalized Medicine in COVID-19 in Andalusia: An Opportunity to Transform the Healthcare System

J. Dopazo, J. López-Miranda, J. Padillo, 2021, Journal of personalized medicine.

Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

P. Sham, P. Tam, A. Chakravarti, 2017, Genome Biology.

Title Whole exome sequencing coupled with unbiased functionalanalysis reveals new Hirschsprung disease genes

P. Sham, P. Tam, A. Chakravarti, 2017 .

Phylogenetic analysis of the thiolase family. Implications for the evolutionary origin of peroxisomes

J. Pérez-Ortín, J. Dopazo, J. C. Igual, 1992, Journal of Molecular Evolution.

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)

Jonathan M. Mudge, Jennifer Harrow, Roderic Guigó, 2016, Nature Communications.

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

Joaquín Dopazo, Jaime Huerta-Cepas, Martijn A. Huynen, 2011, Briefings Bioinform..

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Pedro G. Ferreira, Marta R. Hidalgo, R. Guigó, 2018, Nature Communications.

A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified coat protein gene

J. Dopazo, B. Blanco-Urgoiti, F. Ponz, 2005, Archives of Virology.

Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach

Joaquin Dopazo, J. Dopazo, 1994, Journal of Molecular Evolution.

Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA

J. Dopazo, M. Aranda, A. Fraile, 2014, Journal of Molecular Evolution.

Molecular epidemiology of HIV-1 in Madrid.

J. Dopazo, M. J. Martin, I. Nájera, 1994, Virus research.

Evolutionary relationships among bean common mosaic virus strains and closely related potyviruses.

J. Dopazo, M. Sáiz, J. Romero, 1994, Virus research.

Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographic structuring of nuclear gene pools.

J. Dopazo, P. Vera, N. Paniego, 2021, Annals of botany.

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data

Carlos Loucera, Pelin Gundogdu, Inmaculada Alamo-Alvarez, 2021, BioData Mining.

Salinibacter ruber: genomics and biogeography

R. Amann, F. Glöckner, J. Dopazo, 2005 .

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.)

J. Dopazo, N. Paniego, A. Fernie, 2017, Plant Molecular Biology.

Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower.

J. Dopazo, N. Paniego, A. Fernie, 2016, Plant biotechnology journal.

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

J. Dopazo, M. Peña-Chilet, C. Loucera, 2019, bioRxiv.

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

Francisco Salavert, Cankut Cubuk, Alicia Amadoz, 2016, bioRxiv.

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

Joaquín Dopazo, Joost J. J. van Durme, Joost Schymkowitz, 2011, Nucleic Acids Res..

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Joaquín Dopazo, Ignacio Medina, Stefan Götz, 2010, Nucleic Acids Res..

From genes to functional classes in the study of biological systems

Joaquín Dopazo, Fátima Al-Shahrour, David Montaner, 2007, BMC Bioinformatics.

Dysfunctional mitochondrial fission impairs cell reprogramming

J. Dopazo, F. García-García, Josema Torres, 2016, Cell cycle.

Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa

Francisco J. López-Domingo, Joaquin Dopazo, Salud Borrego, 2013, Molecular vision.

A hierarchical unsupervised growing neural network for clustering gene expression patterns

Alfonso Valencia, Joaquín Dopazo, Javier Herrero, 2001, Bioinform..

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

Joaquín Dopazo, Ignacio Medina, Joaquín Tárraga, 2007, Nucleic Acids Res..

Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development

A. Conesa, J. Dopazo, D. Montaner, 2013, PloS one.

Functional Genomics of 5- to 8-Cell Stage Human Embryos by Blastomere Single-Cell cDNA Analysis

J. Dopazo, D. Montaner, D. Valbuena, 2010, PloS one.

A map of human microRNA variation uncovers unexpectedly high levels of variability

J. Dopazo, I. Medina, J. Jimenez-Almazan, 2012, Genome Medicine.

From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance

J. Dopazo, J. Lepe, Pedro Martinez, 2021, bioRxiv.

Multicore and Cloud-Based Solutions for Genomic Variant Analysis

Cristina Y. González, Marta Bleda, Francisco Salavert, 2012, Euro-Par Workshops.

Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response

J. Dopazo, S. Llames, M. del Río, 2020, Genes.

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

Marta R. Hidalgo, J. Dopazo, M. Pujana, 2018, bioRxiv.

Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response.

M. Cascante, J. Dopazo, G. Capellá, 2013, Carcinogenesis.

Maslinic Acid-Enriched Diet Decreases Intestinal Tumorigenesis in ApcMin/+ Mice through Transcriptomic and Metabolomic Reprogramming

Fernando J. Reyes-Zurita, M. Cascante, U. Günther, 2013, PloS one.

Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass

A. Dopazo, J. Dopazo, F. García-García, 2011, BMC Medical Genomics.

Natural Selection on Functional Modules, a Genome-Wide Analysis

Joaquín Dopazo, François Serra, Leonardo Arbiza, 2011, PLoS Comput. Biol..

Association study of 69 genes in the ret pathway identifies low-penetrance loci in sporadic medullary thyroid carcinoma.

Joaquín Dopazo, Roger L Milne, Angel Carracedo, 2007, Cancer research.

The Use of Go Terms to Understand the Biological Significance of Microarray Differential Gene Expression Data

Fatima Al-Shahrour, Joaquín Dopazo, Ramón Díaz-Uriarte, 2004 .

An Approach to Inferring Transcriptional Regulation Among Genes From Large-Scale Expression Data

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2003, Comparative and functional genomics.

Exome Sequencing Reveals Novel and Recurrent Mutations with Clinical Significance in Inherited Retinal

J. Dopazo, Alicia Vela-Boza, S. Borrego, 2014 .

Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome

Joaquín Dopazo, Leonardo Arbiza, Hernán Dopazo, 2006, PLoS Comput. Biol..

A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma

J. Cigudosa, J. Benítez, J. Dopazo, 2005, Genes, chromosomes & cancer.

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models

Carlos Loucera, Marina Esteban-Medina, Joaquín Dopazo, 2019, BMC Bioinformatics.

A comparison of mechanistic signaling pathway activity analysis methods

Joaquín Dopazo, José Carbonell, Alicia Amadoz, 2018, Briefings Bioinform..

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

Joaquín Dopazo, Adam Godzik, Thomas Hrabe, 2015, PLoS Comput. Biol..

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

Joaquín Dopazo, Ignacio Medina, Joaquín Tárraga, 2009, Nucleic Acids Res..

Extensive Translatome Remodeling during ER Stress Response in Mammalian Cells

J. Dopazo, D. Montaner, A. Kochetov, 2012, PloS one.

Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient

M. Esteller, J. Dopazo, I. Medina, 2012, Epigenetics.

Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation

J. Dopazo, M. Talón, J. Terol, 2015, BMC Genomics.

Reporting guidelines for human microbiome research: the STORMS checklist

Chris I. Hunter, Jennifer M. Fettweis, F. Bushman, 2021, Nature Medicine.

Expression and microarrays.

Joaquín Dopazo, Fátima Al-Shahrour, J. Dopazo, 2008, Methods in molecular biology.

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer

J. Dopazo, M. Peña-Chilet, C. S. Casimiro-Soriguer, 2022, Scientific Reports.

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer

Carlos Loucera, Joaquin Dopazo, Carlos S Casimiro-Soriguer, 2021, Scientific Reports.

A computer program for the design of PCR primers for diagnosis of highly variable genomes.

J. Dopazo, F. Sobrino, J Dopazo, 1993, Journal of virological methods.

Integrated gene set analysis for microRNA studies

Joaquín Dopazo, David Montaner, Francisco García-García, 2014, Bioinform..

Integrated gene set analysis for microRNA studies

J. Dopazo, D. Montaner, F. García-García, 2014, Bioinform..

Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information

J. Dopazo, D. Montaner, E. Lerma, 2008, Oncogene.

Data Analysis and Visualization in Genomics and Proteomics

Joaquín Dopazo, Francisco Azuaje, F. Azuaje, 2005 .

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways

J. Dopazo, M. Peña-Chilet, M. Calzado, 2021, PLoS Comput. Biol..

A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition.

M. Esteller, I. Gut, J. Dopazo, 2014, Cancer research.

HCAD, closing the gap between breakpoints and genes

Alfonso Valencia, Joaquín Dopazo, Robert Hoffmann, 2004, Nucleic Acids Res..

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

Hiroaki Kitano, Xiaoming Hu, Marina Esteban-Medina, 2020, bioRxiv.

Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes

Arcadi Navarro, Joaquín Dopazo, Fátima Al-Shahrour, 2010, PLoS Comput. Biol..

Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies

A. Carrió, J. Dopazo, B. Rodríguez-Santiago, 2019, Journal of Medical Genetics.

Pathway network inference from gene expression data

Joaquín Dopazo, Stefan Götz, Ignacio Ponzoni, 2014, BMC Systems Biology.

3 Data and Predictive Model Integration : An Overview of Key Concepts , Problems and Solutions

Haiying Wang, F. Azuaje, J. Dopazo, 2006 .

The modular network structure of the mutational landscape of Acute Myeloid Leukemia

J. Dopazo, Luz Garcia-Alonso, E. Barragán, 2018, PloS one.

The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations

J. Dopazo, J. Jimenez-Almazan, Luz Garcia-Alonso, 2016, PloS one.

The transcriptomics of an experimentally evolved plant-virus interaction

S. Elena, J. Dopazo, F. García-García, 2016, Scientific Reports.

Analysis pipeline for the detection of mutations causative of rare diseases on whole exome sequencing data

Francisco J. Lopez, Luis M. Cruz, J. Dopazo, 2013 .

Orchestrating and sharing large multimodal data for transparent and reproducible research

B. Haibe-Kains, W. Tong, Susanna-Assunta Sansone, 2020, Nature Communications.

Serum metabolomic profiling facilitates the non-invasive identification of metabolic biomarkers associated with the onset and progression of non-small cell lung cancer

J. Dopazo, F. García-García, A. Pineda-Lucena, 2016, Oncotarget.

ETE: a python Environment for Tree Exploration

Joaquín Dopazo, Toni Gabaldón, Jaime Huerta-Cepas, 2010, BMC Bioinformatics.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

Joaquín Dopazo, Christian Blaschke, Joaquín Tárraga, 2006, Nucleic Acids Res..

FM19G11, a new HIF modulator, affects stem cell differentiation status

Miodrag, J. Dopazo, D. Montaner, 2009 .

Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes

J. Dopazo, I. Medina, A. Berenguer, 2008, BMC Medical Genomics.

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus

J. Dopazo, M. Talón, J. Terol, 2015, Molecular biology and evolution.

Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua

Arvind Y. M. Sundaram, J. Dopazo, V. Kiron, 2012, BMC Evolutionary Biology.

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

Joaquín Dopazo, Ana Conesa, Fernando García-Alcalde, 2010, Bioinform..

Prediction of human population responses to toxic compounds by a collaborative competition

Karsten M. Borgwardt, Ana L. Teixeira, Eleni G. Christodoulou, 2015, Nature Biotechnology.

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling

Joaquín Dopazo, Ignacio Medina, Joaquín Tárraga, 2007, Nucleic Acids Res..

Precision medicine needs pioneering clinical bioinformaticians

Alfonso Valencia, Joaquín Dopazo, Juan C. Cigudosa, 2019, Briefings Bioinform..

Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data

Marta R. Hidalgo, J. Dopazo, C. Çubuk, 2021, Computational and structural biotechnology journal.

Predictive Value of MRP-1 in Localized High-Risk Soft Tissue Sarcomas: A Translational Research Associated to ISG-STS 1001 Randomized Phase III Trial

J. Blay, J. Dopazo, J. Coindre, 2021, Molecular Cancer Therapeutics.

Gene expression data preprocessing

Joaquín Dopazo, Javier Herrero, Ramón Díaz-Uriarte, 2003, Bioinform..

Molecular Genetics in the Next Generation Sequencing Era

J. Dopazo, 2021, Mitochondrial Diseases.

A framework for genomic sequencing on clusters of multicore and manycore processors

Joaquín Dopazo, Enrique S. Quintana-Ortí, Ignacio Medina, 2018, Int. J. High Perform. Comput. Appl..

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array

Ignacio Blanquer, Joaquín Dopazo, Ignacio Medina, 2014, Bioinform..

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

Joaquín Dopazo, Peer Bork, Jaime Huerta-Cepas, 2014, Nucleic Acids Res..

Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype

M. Esteller, J. Dopazo, J. Armstrong, 2016, Human Genetics.

Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival

J. Dopazo, J. Rodríguez-Baño, J. Lepe, 2022, medRxiv.

GEPAS: a web-based resource for microarray gene expression data analysis

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2003, Nucleic Acids Res..

Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA.

S. Elena, A. Moya, J. Dopazo, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Microarray Data Processing and Analysis

Joaquín Dopazo, J. Dopazo, 2002 .

Combined Genetic and High-Throughput Strategies for Molecular Diagnosis of Inherited Retinal Dystrophies

Joaquín Dopazo, Roser Gonzàlez-Duarte, Gemma Marfany, 2014, PloS one.

Evolution of the capsid protein genes of foot-and-mouth disease virus: antigenic variation without accumulation of amino acid substitutions over six decades

Miguel Ángel Martínez, E. Domingo, J. Dopazo, 1992, Journal of virology.

Family-based genome-wide association study in Patagonia confirms the association of the DMD locus and cleft lip and palate.

J. Dopazo, D. Montaner, M. A. Moreira, 2015, European journal of oral sciences.

SMN1 copy‐number and sequence variant analysis from next‐generation sequencing data

J. Dopazo, Daniel López-López, Ángel Alonso, 2020, bioRxiv.

Potato virus Y group C isolates are a homogeneous pathotype but two different genetic strains.

J. Dopazo, B. Blanco-Urgoiti, F. Ponz, 1998, The Journal of general virology.

SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks

Joaquín Dopazo, Stefan Götz, Fátima Al-Shahrour, 2009, Nucleic Acids Res..

Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia

Jose L. Fernandez-Rueda, J. Dopazo, J. Lepe, 2023, International journal of molecular sciences.

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A. Martí-Renom, Joaquín Dopazo, Ursula Pieper, 2007, BMC Bioinformatics.

Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases

Joaquín Dopazo, Ignacio Medina, Joost J. J. van Durme, 2007, Nucleic Acids Res..

A crowdsourcing database for the copy-number variation of the Spanish population

Jose L. Fernandez-Rueda, Luis Antonio Castaño, J. Dopazo, 2023, Human Genomics.

Evolutionary pattern of human respiratory syncytial virus (subgroup A): cocirculating lineages and correlation of genetic and antigenic changes in the G glycoprotein

J. Dopazo, B. García-Barreno, I. Martínez, 1994, Journal of virology.

Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma.

A. Dopazo, M. Piris, J. Dopazo, 2002, The American journal of pathology.

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

Marta Bleda, Francisco Salavert, Joaquín Dopazo, 2012, Nucleic Acids Res..

PhylomeDB: a database for genome-wide collections of gene phylogenies

Joaquín Dopazo, Jaime Huerta-Cepas, Toni Gabaldón, 2007, Nucleic Acids Res..

Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships

Olivier Bodenreider, Haiying Wang, Francisco Azuaje, 2004, 2004 Symposium on Computational Intelligence in Bioinformatics and Computational Biology.

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies

Francisco Salavert, Joaquín Dopazo, Ignacio Medina, 2014, Nucleic Acids Res..

Association of a single nucleotide polymorphism in ubxn6 gene with long term non progression phenotype in hiv-positive individuals.

M. Lathrop, J. Dopazo, F. García-García, 2020, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism

J. Dopazo, C. Pineda, C. Çubuk, 2021, Molecular Medicine.

Genetic characterization of populations of a de novo arisen sugar beet pest, aubeonymus mariaefranciscae (coleoptera, curculionidae), by RAPD analysis

J. Dopazo, A. Taberner, P. Castanera, 1997, Journal of Molecular Evolution.

F. Ayala, J. Dopazo, A. Rzhetsky, 1996, Genetics.

Differential Features between Chronic Skin Inflammatory Diseases Revealed in Skin-Humanized Psoriasis and Atopic Dermatitis Mouse Models.

J. Dopazo, M. del Río, F. Larcher, 2015, The Journal of investigative dermatology.

CLEAR-test: Combining inference for differential expression and variability in microarray data analysis

Joaquín Dopazo, David Montaner, Pilar Hernández, 2008, J. Biomed. Informatics.

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome

Marta R. Hidalgo, J. Dopazo, A. Amadoz, 2018, Biology Direct.

A DNA damage repair gene‐associated signature predicts responses of patients with advanced soft‐tissue sarcoma to treatment with trabectedin

J. Dopazo, J. Martín-Broto, C. Romagosa, 2021, Molecular oncology.

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.

Ana Osorio, Javier Benitez, Ramon Diaz-Uriarte, 2005, Clinical cancer research : an official journal of the American Association for Cancer Research.

Functional signatures identified in B-cell non-Hodgkin lymphoma profiles

E. Kimby, D. Pisano, M. Piris, 2009, Leukemia & lymphoma.

A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification That Adopts the Topology of a Phylogenetic Tree

Joaquín Dopazo, José María Carazo, Huaichun Wang, 1997, IWANN.

Nivolumab and sunitinib combination in advanced soft tissue sarcomas: a multicenter, single-arm, phase Ib/II trial

J. Dopazo, E. de Álava, J. Martín-Broto, 2020, Journal for ImmunoTherapy of Cancer.

Polystyrene nanoplastics affect transcriptomic and epigenomic signatures of human fibroblasts and derived induced pluripotent stem cells: Implications for human health.

J. Dopazo, M. Stojkovic, K. Stankovic, 2022, Environmental pollution.

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau, 2006, Nucleic Acids Res..

A Mechanistic Model for Genome-Scale Estimations of Metabolic Activity

Marta R. Hidalgo, J. Dopazo, A. Amadoz, 2021 .

Using mechanistic models for the clinical interpretation of complex genomic variation

Marta R. Hidalgo, J. Dopazo, M. Peña-Chilet, 2019, Scientific Reports.

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models

Francisco Salavert, Joaquín Dopazo, Ignacio Medina, 2016, Nucleic Acids Res..

Understanding disease mechanisms with models of signaling pathway activities

Joaquín Dopazo, Francisco Salavert, David Montaner, 2014, BMC Systems Biology.

Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system development

J. Dopazo, S. Borrego, G. Antiñolo, 2021, Clinical Epigenetics.

Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells.

Joaquín Dopazo, David Montaner, Ana Conesa, 2011, Human molecular genetics.

discordance in systemic lupus erythematosus Changes in the pattern of DNA methylation associate with twin Material Supplemental

R. Siebert, M. Fraga, E. Ballestar, 2009 .

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Amir K. Foroushani, Yuanfang Guan, Jaewoo Kang, 2019, Nature Communications.

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Alexander R. Pico, Benjamin M. Gyori, John A. Bachman, 2021, Molecular systems biology.

Role of CPI-17 in restoring skin homoeostasis in cutaneous field of cancerization: effects of topical application of a film-forming medical device containing photolyase and UV filters

J. Malvehy, S. Puig, J. Dopazo, 2013, Experimental Dermatology.

Mammosphere Formation in Breast Carcinoma Cell Lines Depends upon Expression of E-cadherin

J. Dopazo, F. García-García, J. Menéndez, 2013, PloS one.

Mutation Spectrum of EYS in Spanish Patients with Autosomal Recessive Retinitis Pigmentosa

Joaquín Dopazo, Javier Santoyo, Montserrat Baiget, 2010, Human mutation.

Supplementary File 12

A. N. Gur'yanov, Giuseppe Jurman, Tieliu Shi, 2010 .

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

Thomas M. Keane, Victoria Dominguez Del Angel, Irina M. Armean, 2020, F1000Research.

Evolutionary analysis of the picornavirus family

J. Dopazo, M. Rodrigo, 1995, Journal of Molecular Evolution.

Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types

J. Dopazo, F. García-García, J. Bernal, 2015, Cerebral cortex.

IL1β Induces Mesenchymal Stem Cells Migration and Leucocyte Chemotaxis Through NF-κB

J. Dopazo, F. García-García, I. Cerrada, 2012, Stem Cell Reviews and Reports.

myKaryoView: A Light-Weight Client for Visualization of Genomic Data

Rafael C. Jimenez, Gustavo A. Salazar, Manuel Corpas, 2011, PloS one.

From Genomics to Microevolution and Ecology: The Case of Salinibacter ruber

R. Amann, H. Teeling, F. Glöckner, 2011 .

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

Frank Oliver Glöckner, Joaquín Dopazo, Jaime Huerta-Cepas, 2010, The ISME Journal.

New Challenges in Gene Expression Data Analysis and the Extended GEPAS

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2004, Spanish Bioinformatics Conference.

Phylogenetic relationships of european strains of porcine reproductive and respiratory syndrome virus (PRRSV) inferred from DNA sequences of putative ORF-5 and ORF-7 genes.

J. Dopazo, R. Zardoya, C. Prieto, 1996, Virus research.

Transdifferentiation of MALME-3 M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis

A. Conesa, J. Dopazo, C. Simón, 2015 .

Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis

A. Conesa, J. Dopazo, C. Simón, 2012, SpringerPlus.

Molecular interactions between sugar beet and Polymyxa betae during its life cycle

A. Conesa, J. Dopazo, A. Legrève, 2014 .

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

Joaquín Dopazo, Patricio Moreno, Bernardo J. Clavijo, 2017, BMC Bioinformatics.

La evaluación de impacto en protección de datos en los proyectos de investigación

J. Dopazo, F. J. García-León, R. Villegas-Portero, 2020 .

CSVS, a crowdsourcing database of the Spanish population genetic variability

Carlos Loucera, Joaquín Dopazo, Aurora Pujol, 2020, Nucleic Acids Res..

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources

Francisco J. Lopez, A. Rendon, J. Dopazo, 2019, BMC Bioinformatics.

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information

Joaquín Dopazo, Ramón Díaz-Uriarte, Fátima Al-Shahrour, 2005, Bioinform..

Molecular characterization of human immunodeficiency virus type 1 isolates from Venezuela.

E. Domingo, J. Dopazo, M. Quiñones-Mateu, 1995, AIDS research and human retroviruses.

From genes to functional classes in the study of biological systems

J. Dopazo, J. Huerta-Cepas, D. Montaner, 2007, BMC bioinformatics.

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments

Joaquín Dopazo, Fátima Al-Shahrour, Pablo Minguez, 2005, Nucleic Acids Res..

Protein Interactions for Functional Genomics

Joaquín Dopazo, Pablo Minguez, J. Dopazo, 2012, Int. J. Knowl. Discov. Bioinform..

An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins

Joaquín Dopazo, Javier Delgado Blanco, Joost Schymkowitz, 2011, PLoS Comput. Biol..

BRCA1 Alternative splicing landscape in breast tissue samples

J. Dopazo, F. García-García, J. García-Saenz, 2015, BMC Cancer.

Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria.

Joaquín Dopazo, Frederic Tort, Paz Briones, 2013, Molecular genetics and metabolism.

Deregulation of key signaling pathways involved in oocyte maturation in FMR1 premutation carriers with Fragile X-associated primary ovarian insufficiency.

X. Estivill, J. Dopazo, F. García-García, 2015, Gene.

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

Alfonso Valencia, Philippe Bardou, Arcadi Navarro, 2008, Briefings in bioinformatics.

A Comprehensive Analysis of 21 Actionable Pharmacogenes in the Spanish Population: From Genetic Characterisation to Clinical Impact

J. Dopazo, A. González-Neira, G. Pita, 2023, Pharmaceutics.

Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches

Joaquín Dopazo, Enrique Silvestre, Ana Taberner, 1993, Comput. Appl. Biosci..

Title Exome sequencing reveals a high genetic heterogeneity onfamilial Hirschsprung disease

P. Sham, S. Cherny, J. Dopazo, 2015 .

Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli.

Fátima Al-Shahrour, Joaquin Dopazo, J. Dopazo, 2009, Microbiology.

Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity

J. Dopazo, M. Aouadi, A. Vidal-Puig, 2019, bioRxiv.

DNMAD: web-based diagnosis and normalization for microarray data

Joaquín Dopazo, Ramón Díaz-Uriarte, Juan M. Vaquerizas, 2004, Bioinform..

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

Joaquín Dopazo, Ignacio Medina, Stefan Götz, 2008, Nucleic Acids Res..

Genome analysis Advance Access publication February 18, 2011 B2G-FAR, a species-centered GO annotation repository

Joaquín Dopazo, Thomas Rattei, Ana Conesa, 2022 .

Confidence limits for resolution estimation in image averaging by random subsampling

José María Carazo, Luis Gerardo de la Fraga, J. Dopazo, 1995 .

Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging

J. Dopazo, M. Vinaixa, M. Scheibye-Knudsen, 2023, Communications Biology.

Using a Genetic Algorithm and a Perceptron for Feature Selection and Supervised Class Learning in DNA Microarray Data

Joaquín Dopazo, Javier Herrero, Álvaro Mateos, 2003, Artificial Intelligence Review.

Real world evidence of calcifediol or vitamin D prescription and mortality rate of COVID-19 in a retrospective cohort of hospitalized Andalusian patients

J. Dopazo, R. Bouillon, J. López-Miranda, 2021, Scientific Reports.

Using Papers Citations for Selecting the Best Genomic Databases

Oscar Pastor, Ana M. Levin, Joaquín Dopazo, 2011, 2011 30th International Conference of the Chilean Computer Science Society.

DBAli tools: mining the protein structure space

Marc A. Martí-Renom, Joaquín Dopazo, Narayanan Eswar, 2007, Nucleic Acids Res..

Real world evidence of calcifediol use and mortality rate of COVID-19 hospitalized in a large cohort of 16,401 Andalusian patients

J. Dopazo, R. Bouillon, J. López-Miranda, 2021, medRxiv.

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

Thomas Yu, Ka Yee Yeung, Maria K. Jaakkola, 2018, Nature Communications.

Comparison of vaccine strains and the virus causing the 1986 foot-and-mouth disease outbreak in Spain: epizootiological analysis.

A. Moya, J. Dopazo, J. Saiz, 1990, Virus research.

Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation

I. Gut, J. Dopazo, M. Talón, 2015, BMC Genomics.

Primary genetic characterization of HIV-1 isolates from WHO-sponsored vaccine evaluation sites by the RNase-A mismatch method.

J. Dopazo, S. Sánchez-Palomino, I. Olivares, 1995, Virus research.

Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas

J. Dopazo, I. Medina, M. Bleda, 2015, BMC Medical Genomics.

Pathways systematically associated to Hirschsprung’s disease

A. Chakravarti, J. Dopazo, M. Bleda, 2013, Orphanet Journal of Rare Diseases.

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing

Cristina Y. González, Marta Bleda, Francisco Salavert, 2012, Nucleic Acids Res..

Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis

J. Dopazo, A. Vidal-Puig, P. Bolan, 2015, Molecular metabolism.

Inferring the regulatory network behind a gene expression experiment

Marta Bleda, Francisco Salavert, Joaquín Dopazo, 2012, Nucleic Acids Res..

Ontology-driven approaches to analyzing data in functional genomics.

Fatima Al-Shahrour, Francisco Azuaje, Joaquin Dopazo, 2006, Methods in molecular biology.

SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types

Isabel A. Nepomuceno-Chamorro, J. Dopazo, C. Loucera, 2023, Biology.

Rapid degeneration of iPSC-derived motor neurons lacking Gdap1 engages a mitochondrial-sustained innate immune response

J. I. Izpisúa Belmonte, J. Dopazo, F. García-García, 2023, Cell death discovery.

Platform to study intracellular polystyrene nanoplastic pollution and clinical outcomes

J. Dopazo, M. Stojkovic, M. Lako, 2020, Stem cells.

Scalable RNA Sequencing on Clusters of Multicore Processors

Enrique S. Quintana-Ortí, Joaquín Dopazo, Ignacio Medina, 2015, 2015 IEEE Trustcom/BigDataSE/ISPA.

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

Joaquín Dopazo, Arcadi Navarro, Ignacio Medina, 2012, Int. J. Data Min. Bioinform..

Functional profiling methods in cancer.

Joaquín Dopazo, J. Dopazo, 2010, Methods in molecular biology.

Highly specific and accurate selection of siRNAs for high-throughput functional assays

Juan M. Vaquerizas, J. Dopazo, J. Santoyo, 2005, Bioinform..

The prognostic relevance of the nonstructural 5A gene interferon sensitivity determining region is different in infections with genotype 1b and 3a isolates of hepatitis C virus.

J. Dopazo, X. Forns, S. Ampurdanés, 1998, The Journal of infectious diseases.

The Iberian Roma genetic variant server; population structure, susceptibility to disease and adaptive traits.

Soriano, Negrillo, J. Dopazo, 2023, medRxiv.

Genome Maps, a new generation genome browser

Marta Bleda, Francisco Salavert, Rubén Sánchez, 2013, Nucleic Acids Res..

Serial Expression Analysis: a web tool for the analysis of serial gene expression data

Joaquín Dopazo, Ignacio Medina, Ana Conesa, 2010, Nucleic Acids Res..

Chemometrics and Intelligent Laboratory Systems

Joaquín Dopazo, Alberto Ferrer, Ana Conesa, 2011 .

Fast inexact mapping using advanced tree exploration on backward search methods

Andrés Tomás, Ignacio Blanquer, Joaquín Dopazo, 2015, BMC Bioinformatics.

Formulating and testing hypotheses in functional genomics

Joaquín Dopazo, J. Dopazo, 2009, Artif. Intell. Medicine.

Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung’s disease

Joaquín Dopazo, Ignacio Medina, David Montaner, 2012, Orphanet Journal of Rare Diseases.

Bmc Medical Genomics Biological Processes, Properties and Molecular Wiring Diagrams of Candidate Low-penetrance Breast Cancer Susceptibility Genes

J. Dopazo, A. Berenguer, M. Pujana, 2008 .

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

C. Auffray, H. Kitano, M. Gillespie, 2020, Scientific Data.

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

Matthew D. Schultz, M. Esteller, J. Dopazo, 2016, Translational psychiatry.

Functional profiling of microarray experiments using text-mining derived bioentities

Joaquín Dopazo, Fátima Al-Shahrour, David Montaner, 2007, Bioinform..

Drug repurposing for COVID-19 using machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection

Carlos Loucera, Marina Esteban-Medina, Kinza Rian, 2020, Signal Transduction and Targeted Therapy.

Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions

Joaquín Dopazo, Haiying Wang, Francisco Azuaje, 2005, Data Analysis and Visualization in Genomics and Proteomics.

Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences

J. Dopazo, F. Ortuño, N. Chueca, 2021, GigaScience.

Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

Joaquin Dopazo, J. Dopazo, Jose Carlos Adell, 1994, Journal of Molecular Evolution.

Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring–Opitz syndromes

J. Opitz, J. Dopazo, A. Alemán, 2016, American journal of medical genetics. Part A.

microRNAs‐mediated regulation of insulin signaling in white adipose tissue during aging: Role of caloric restriction

J. Dopazo, G. Medina-Gómez, M. Peña-Chilet, 2023, Aging cell.

A dynamic pipeline for RNA sequencing on multicore processors

Joaquín Dopazo, Enrique S. Quintana-Ortí, Sergio Barrachina, 2013, EuroMPI.

Concurrent and Accurate RNA Sequencing on Multicore Platforms pdf

Joaquín Dopazo, Enrique S. Quintana-Ortí, Ignacio Medina, 2013, ArXiv.

Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer

J. Dopazo, C. Çubuk, M. Peña-Chilet, 2023, International journal of molecular sciences.

Genomics and transcriptomics in drug discovery.

J. Dopazo, 2014, Drug discovery today.

Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes

J. Dopazo, A. Berenguer, M. Pujana, 2008, BMC Medical Genomics.

Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes

J. Dopazo, A. Berenguer, M. Pujana, 2008, BMC Medical Genomics.

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways

Rosa D. Hernansaiz-Ballesteros, Francisco Salavert, Joaquín Dopazo, 2015, Nucleic Acids Res..

Capturing the biological impact of CDKN2A and MC1R genes as an early predisposing event in melanoma and non melanoma skin cancer

S. Puig, J. Dopazo, M. del Río, 2013, OncoTarget.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Todd H. Stokes, Kevin C. Dorff, Aaron M. Smalter, 2010, Nature Biotechnology.

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape.

Marta R. Hidalgo, J. Dopazo, M. Pujana, 2018, Cancer research.

Parallel Implementation of DNAml Program on Message-Passing Architectures

Joaquín Dopazo, Emilio L. Zapata, José María Carazo, 1998, Parallel Comput..

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources

Joaquín Dopazo, Ignacio Medina, Pablo Marín-García, 2019, BMC Bioinformatics.

Sequence analysis of HIV-1vif gene in Spanish isolates

J. Dopazo, L. Menéndez-Arias, I. Olivares, 1995, Virus Genes.

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

R. Amann, H. Teeling, F. Glöckner, 2010, The ISME Journal.

ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing

Joaquín Dopazo, J. P. Florido, Antonio Rueda, 2014, Bioinform..

Two Novel Mutations in the BCKDK (Branched‐Chain Keto‐Acid Dehydrogenase Kinase) Gene Are Responsible for a Neurobehavioral Deficit in Two Pediatric Unrelated Patients

J. Dopazo, B. Merinero, M. Ugarte, 2014, Human mutation.

The role of the environment in Parkinson's disease.

Joaquín Dopazo, Ignacio Medina, Joaquín Tárraga, 1996, Nucleic Acids Res..

GEPAS, a web-based tool for microarray data analysis and interpretation

A. Conesa, J. Dopazo, J. Huerta-Cepas, 2008, Nucleic Acids Res..

Functional assessment of time course microarray data

Joaquín Dopazo, Ana Conesa, Alberto Ferrer, 2009, BMC Bioinformatics.

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

J. Dopazo, D. Montaner, Ignacio Medina, 2007, Bioinform..

Concurrent and Accurate RNA Sequencing on Multicore Platforms

María Isabel Castillo, J. Dopazo, S. Barrachina, 2013, ArXiv.

Inferring the functional effect of gene expression changes in signaling pathways

Francisco Salavert, Rubén Sánchez, Joaquín Dopazo, 2013, Nucleic Acids Res..

Clustering — Class Discovery in the Post-Genomic Era

J. Dopazo, 2007 .

Web-based network analysis and visualization using CellMaps

Joaquín Dopazo, Marta Bleda, Francisco Salavert, 2016, Bioinform..

Early Transcriptional Defense Responses in Arabidopsis Cell Suspension Culture under High-Light Conditions1[C][W][OA]

J. Revuelta, J. Dopazo, F. García-García, 2011, Plant Physiology.

Evolution and tropism of transmissible gastroenteritis coronavirus.

J. Dopazo, F. Gebauer, C. Sánchez, 1993, Advances in experimental medicine and biology.

Self-organizing tree growing network for classifying amino acids

Joaquín Dopazo, José María Carazo, Huaichun Wang, 1998 .

HPG pore: an efficient and scalable framework for nanopore sequencing data

Joaquín Dopazo, Ignacio Medina, Joaquín Tárraga, 2016, BMC Bioinformatics.

Visualization of automatically combined disease maps and pathway diagrams for rare diseases

V. Colonna, J. Dopazo, Reinhard Schneider, 2023, Frontiers Bioinform..

Bioinformatics Applications Note Systems Biology Paintomics: a Web Based Tool for the Joint Visualization of Transcriptomics and Metabolomics Data

A. Conesa, J. Dopazo, F. García-Alcalde, 2022 .

From genes to functional classes in the study of biological systems

J. Dopazo, J. Huerta-Cepas, D. Montaner, 2007, BMC Bioinformatics.

Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis

S. Puig, J. Dopazo, M. del Río, 2016, Oncotarget.

Supervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles

Joaquín Dopazo, Javier Herrero, Álvaro Mateos, 2002 .