List of works by Joaquín Dopazo

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

scientific article

A Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition

scientific article published on 08 August 2014

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

scientific article published on 30 June 2021

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

scientific article

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

scientific article published on 14 April 2015

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

scientific article published on 01 June 1998

A SILAC approach to MT1-MMP degradome in inflammatory angiogenesis

A comparison of mechanistic signaling pathway activity analysis methods

scientific article published on 01 September 2019

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

scientific article published on 24 June 2021

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

scientific article

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

scientific article published in January 2006

A hierarchical unsupervised growing neural network for clustering gene expression patterns

scientific article

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

scientific article

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

scientific article

A new overgrowth syndrome is due to mutations in RNF125.

scientific article published in December 2014

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

scientific article

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

article

A parallel and sensitive software tool for methylation analysis on multicore platforms

scientific article published on 10 June 2015

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

article

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.

scientific article published in October 1998

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

scientific article published in January 1996

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

scientific article published on 11 February 2021

A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.

scientific article

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

scientific article

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

scientific article

Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity

scientific article published on 16 August 2019

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

scientific article

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

scientific article published on 2 May 2016

An approach to inferring transcriptional regulation among genes from large-scale expression data.

scientific article

An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins

scientific article

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

scientific article published on January 2009

Analysis of genetic variability of populations of herpes simplex viruses

scientific article published on 01 June 1993

Analysis of normal-tumour tissue interaction in tumours: prediction of prostate cancer features from the molecular profile of adjacent normal cells

scientific article

Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate

scientific article

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

scientific article published on 20 August 2019

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

scientific article published on 15 September 2011

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

scientific article

Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties

scientific article

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

scientific article

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

scientific article published on 2 January 2016

Association Study of 69 Genes in the Ret Pathway Identifies Low-penetrance Loci in Sporadic Medullary Thyroid Carcinoma

article

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

scientific article published on 17 July 2020

B2G-FAR, a species-centered GO annotation repository

scientific article

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

scientific article

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

scientific article published on July 2006

BRCA1 Alternative splicing landscape in breast tissue samples.

scientific article

Babelomics 5.0: functional interpretation for new generations of genomic data.

scientific article

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

scientific article published on 31 May 2008

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

scientific article

Bioinformatics and cancer: an essential alliance

scientific article published on June 2006

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

scientific article

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

scientific article

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

scientific article

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

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

scientific article published on 05 May 2020

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

journal article from 'Molecular Systems Biology' published in 2021

CSVS, a crowdsourcing database of the Spanish population genetic variability

scientific article published on 29 September 2020

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

scientific article (publication date: 30 March 2014)

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

scientific article

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

scientific article

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

scientific article

Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies.

scientific article

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

scientific article published in September 2002

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

scientific article published on September 2015

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

scientific article published in February 1995

Comparing bacterial genomes through conservation profiles.

scientific article published on 14 April 2003

Concurrent and Accurate Short Read Mapping on Multicore Processors.

scientific article published on September 2015

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

scientific article

DBAli tools: mining the protein structure space

scientific article

DNA methylation epigenotypes in breast cancer molecular subtypes ⬇️

scientific article

DNMAD: web-based diagnosis and normalization for microarray data

scientific article

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

scientific article

Defining the genomic signature of totipotency and pluripotency during early human development

scientific article

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

scientific article published on 18 June 2015

Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray

scientific article

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

scientific article published on 23 September 2015

Differential expression in RNA-seq: a matter of depth

scientific article published on 8 September 2011

Differential lipid partitioning between adipocytes and tissue macrophages modulates macrophage lipotoxicity and M2/M1 polarization in obese mice ⬇️

scientific article

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

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

scientific article published on 01 March 2019

Differentiating Positive Selection from Acceleration and Relaxation in Human and Chimp

scholarly article by Leonardo Arbiza published in January 2005

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

scientific article published on 13 September 2008

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

scientific article

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

scientific article published on 27 July 2012

Discovery and hypothesis generation through bioinformatics

scientific article published on 27 February 2006

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

scientific article

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

scientific article published on 11 December 2020

Dysfunctional mitochondrial fission impairs cell reprogramming

scientific article

ERCC4Associated with Breast Cancer Risk: A Two-Stage Case-Control Study Using High-throughput Genotyping

ETE: a python Environment for Tree Exploration

scientific article published in 2010

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

scientific article

Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions.

scientific article published on 29 April 2011

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

article

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

scientific article published in March 1994

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

scientific article published on 22 April 2011

Evidence for systems-level molecular mechanisms of tumorigenesis

scientific article

Evolutionary analysis of the picornavirus family

scientific article published on April 1995

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

scientific article published on January 1994

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

scientific article

Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease

scientific article

Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies

scientific article

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

scientific article published in March 2009

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

scientific article published on 02 July 2019

Exploring the link between germline and somatic genetic alterations in breast carcinogenesis

scientific article

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

scientific article

Expression and microarrays.

scientific article published in January 2008

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

scientific article

Extensive translatome remodeling during ER stress response in mammalian cells

scientific article

FM19G11, a new hypoxia-inducible factor (HIF) modulator, affects stem cell differentiation status.

scientific article

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

scientific article published on September 2015

Fast inexact mapping using advanced tree exploration on backward search methods

scientific article

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

scientific article

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

scientific article

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

scientific article published in July 1991

Formulating and testing hypotheses in functional genomics

Fortunella margarita transcriptional reprogramming triggered by Xanthomonas citri subsp. citri

scientific article

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

scientific article published on 28 December 2012

From genes to functional classes in the study of biological systems

scientific article

Functional Interpretation of Microarray Experiments

scholarly article by Joaquín Dopazo published in September 2006

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

scientific article

Functional assessment of time course microarray data

scientific article (publication date: 16 June 2009)

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

scientific article published on February 2010

Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis

scientific article

Functional profiling and gene expression analysis of chromosomal copy number alterations

scientific article published on 10 April 2007

Functional profiling methods in cancer

scientific article published on 01 January 2010

Functional profiling of microarray experiments using text-mining derived bioentities

scientific article published on 13 September 2007

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

scientific article published on October 2009

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

scientific article

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

scientific article

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

scientific article

GGPS1 Mutation and Atypical Femoral Fractures with Bisphosphonates.

scientific article published in May 2017

Gene Expression Correlation and Gene Ontology-Based Similarity: An Assessment of Quantitative Relationships

scientific article published on 01 October 2004

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

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

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

scientific article

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

article

Gene expression analysis of the endometrium reveals that controlled ovarian stimulation induces a genomic delay with potential clinical implications

article

Gene expression data preprocessing.

scientific article

Gene set internal coherence in the context of functional profiling

scientific article

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

scientific article published on 05 June 2009

Gene-expression Profiling And Differential Pathways In The Sensitization And Tolerance To Allergens

article

Genetic characterization of populations of a de novo arisen sugar beet pest, Aubeonymus mariaefranciscae (Coleoptera, Curculionidae), by RAPD analysis

scientific article published on July 1997

Genetic evolution and tropism of transmissible gastroenteritis coronaviruses

scientific article

Genome Maps, a new generation genome browser

scientific article

Genome-scale evidence of the nematode-arthropod clade

scientific article

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

scientific article published on 15 May 2021

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

scientific article published on 09 March 2021

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

scientific article published on 24 December 2016

Genomics and transcriptomics in drug discovery

scientific article published on 15 June 2013

Genomics of the origin and evolution of Citrus.

scientific article published on 7 February 2018

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

scientific article published on 2 November 2015

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

scientific article

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

scientific article published on 22 November 2017

HCAD, closing the gap between breakpoints and genes

scientific article

HGVA: the Human Genome Variation Archive

scientific article

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

scientific article

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

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

scientific article published on 22 December 2016

High-throughput functional annotation and data mining with the Blast2GO suite

scientific article

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

scientific article published on 01 December 2021

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

scientific article published on 10 December 2004

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

scientific article published on 01 March 2010

IL1β induces mesenchymal stem cells migration and leucocyte chemotaxis through NF-κB.

scientific article

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

scientific article published on 27 April 2007

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

scientific article published on 21 December 2015

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

scientific article published on November 2002

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

scientific article published on February 2006

Immune Cell Associations with Cancer Risk

scientific article published on 20 June 2020

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

scientific article published in January 1994

Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron

article

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

scientific article

Inferring the functional effect of gene expression changes in signaling pathways.

scientific article published on 08 June 2013

Inferring the regulatory network behind a gene expression experiment.

scientific article

Initial genomics of the human nucleolus

scientific article published in March 2010

Integrated gene set analysis for microRNA studies.

scientific article

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

scientific article published on July 2015

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

scientific article

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

scientific article

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

article

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

scientific article published on 13 February 2015

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

scientific article published on 17 December 2007

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

scientific article

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

scientific article published on 21 September 2011

Mammosphere formation in breast carcinoma cell lines depends upon expression of E-cadherin

scientific article

Maslinic acid-enriched diet decreases intestinal tumorigenesis in Apc(Min/+) mice through transcriptomic and metabolomic reprogramming

scientific article

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

scientific article published on 29 June 2020

Mechanistic modeling of the SARS-CoV-2 disease map

scientific article published on 13 April 2020

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

scientific article published on 25 June 2020

Microarray Data Processing and Analysis

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

scientific article published on 22 August 2018

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

scientific article

Molecular epidemiology of HIV-1 in Madrid.

scientific article published in March 1994

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

scientific article

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

scientific article published on 01 March 1994

Multicore and Cloud-Based Solutions for Genomic Variant Analysis

Multidimensional gene set analysis of genomic data

scientific article

Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing

scientific article

Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa

scientific article

Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation

scientific journal article

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

scientific article published on 24 October 2015

Natural selection on functional modules, a genome-wide analysis

scientific article

New challenges in gene expression data analysis and the extended GEPAS

scientific article

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

scholarly article published 23 July 2021

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

scientific article published on 01 November 2020

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

scientific article

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

scientific article published on 25 March 2013

Ontology-driven approaches to analyzing data in functional genomics

scientific article

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

scientific article published on 05 October 2019

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

scientific article published on 31 October 2014

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

scientific article

Parallel implementation of DNAml program on message-passing architectures

article by C Ceron et al published June 1998 in Parallel Computing

Pathway network inference from gene expression data

scientific article

Pathways systematically associated to Hirschsprung's disease

scientific article published on 02 December 2013

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

scientific article published on 18 December 2018

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

scientific article published on 14 February 2020

Permanent cardiac sarcomere changes in a rabbit model of intrauterine growth restriction

scientific article

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

scientific article published on March 2005

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

scientific article

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

scientific article published on 22 April 2007

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

scientific article published on 01 February 1997

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

scientific article published on June 1996

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

scientific article published in August 2004

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

scientific article

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

scientific article

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

scientific article published on 01 July 2021

Platform to study intracellular polystyrene nanoplastic pollution and clinical outcomes

scientific article published on 02 July 2020

Point mutant frequencies in the pol gene of human immunodeficiency virus type 1 are two- to threefold lower than those of env.

scientific article published in August 1996

Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome

scientific article

Precision medicine needs pioneering clinical bioinformaticians.

scientific article published on 25 October 2017

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

scientific article

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

scientific article

Progress in pharmacogenetics: consortiums and new strategies

scientific article

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

scientific article

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

scientific article published on July 2004

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

scientific article

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

scientific article

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

scientific article published on 28 March 2019

Qualimap: evaluating next-generation sequencing alignment data.

scientific article

Quantitative characterization of antigens using monoclonal antibody reactivities

scientific article published in 1993

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

scientific article published on 30 March 2015

Reducing the effect of the data order in algorithms for constructing phylogenetic trees

scientific article

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

scientific article published on 29 July 2017

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

scientific article published on July 2013

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

scientific article published on 14 October 2020

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

scientific article published on 19 May 2009

SNP and haplotype mapping for genetic analysis in the rat.

scientific article

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

scientific article

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

scientific article published on 7 October 2015

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

scientific article published in January 2012

Selection upon genome architecture: conservation of functional neighborhoods with changing genes

scientific article

Selective Pressures at a Codon-level Predict Deleterious Mutations in Human Disease Genes

article

Self-organizing tree growing network for classifying amino acids.

scientific article published in January 1998

Sequence analysis of HIV-1 vif gene in Spanish isolates.

scientific article published in February 1995

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

article

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

scientific article published on 13 February 2014

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

scientific article

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

scientific article published on 12 February 2016

Signaling Pathway Activities Improve Prognosis for Breast Cancer

Split decomposition: a technique to analyze viral evolution

scientific article published on November 1993

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

scientific article

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

scientific article

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

scientific article published on 24 May 2021

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

scientific article

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

scientific article

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

scientific article

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

scientific article published on 13 October 2020

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

scientific article

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

scientific article published on 17 February 2016

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

scientific article published on 13 February 2018

The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid

scientific article published on 14 September 2018

The human phylome

scientific article published on January 2007

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

scientific article published in PLoS ONE

The pan-cancer pathological regulatory landscape

scientific article published on 21 December 2016

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

scientific article published on 02 August 2012

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

scientific article

The transcriptomics of an experimentally evolved plant-virus interaction.

scientific article published on 26 April 2016

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

scientific article published on 29 December 2014

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

scientific article published on 31 December 2020

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

scientific article published on 30 October 2012

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

scientific article

Understanding disease mechanisms with models of signaling pathway activities.

scientific article

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

scientific article published in January 2008

Using Papers Citations for Selecting the Best Genomic Databases

article published in 2011

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

scientific article

Using gene ontology on genome-scale studies to find significant associations of biologically relevant terms to groups of genes

article

Using mechanistic models for the clinical interpretation of complex genomic variation

scientific article published on 12 December 2019

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

scientific article

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.

scientific article published on 20 September 2017

Variable selection for multifactorial genomic data

Web-based network analysis and visualization using CellMaps

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient

scientific article

[Impact assessment on data protection in research projects]

scientific article published on 21 January 2020

myKaryoView: a light-weight client for visualization of genomic data

scientific article published in 2011

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

scientific article published on 26 February 2014

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