M. Gonzalo Claros

Publications

• S-nitroso- and nitro- proteomes in the olive (Olea europaea L.) pollen. Predictive versus experimental data by nano-LC-MS
• Automated identification of reference genes based on RNA-seq data
• DEVELOPMENT OF GENOMIC TOOLS IN SENEGALESE SOLE: TRANSCRIPTOME ASSEMBLY, ANNOTATED DATABASE, MICROARRAY AND GENOME DRAFT
• Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing
• Transcriptional analysis of porcine intestinal mucosa infected with Salmonella Typhimurium revealed a massive inflammatory response and disruption of bile acid absorption in ileum
• Whole-exome sequencing analysis in twin sibling males with an anterior cruciate ligament rupture
• Bioinformatic Prediction of S-Nitrosylation Sites in Large Protein Datasets.
• Obtaining the Most Accurate de novo Transcriptomes for Non-model Organisms: The Case of Castanea sativa
• Biomarker potential of repetitive-element transcriptome in lung cancer
• Identification of reference genes in lung cancer from RNA-seq data
• TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms
• Characterization of Iodine-Related Molecular Processes in the Marine Microalga Tisochrysis lutea (Haptophyta)
• BLASSO: integration of biological knowledge into a regularized linear model
• Regulatory role of microRNA in mesenteric lymph nodes after Salmonella Typhimurium infection
• Identification of the mobile elements differentially expressed in lung cancer
• Identification and functional annotation of genes differentially expressed in the reproductive tissues of the olive tree (Olea europaea L.) through the generation of subtractive libraries
• Micro-Variations from RNA-seq Experiments for Non-model Organisms
• Genetic parameter estimates and identification of SNPs associated with growth traits in Senegalese sole
• Expression profiling of redox-metabolism-related genes and proteins during sweet pepper (Capsicum annuum L.) fruit ripening
• Expression Change Correlations Between Transposons and Their Adjacent Genes in Lung Cancers Reveal a Genomic Location Dependence and Highlights Cancer-Significant Genes
• QuasiFlow: a bioinformatic tool for genetic variability analysis from next generation sequencing data
• OliveAtlas: A Gene Expression Atlas Tool for Olea europaea
• Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss
• Generation of nitric oxide by olive (Olea europaea L.) pollen during in vitro germination and assessment of the S-nitroso- and nitro-proteomes by computational predictive methods
• Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole.
• TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
• Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish
• Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus
• Structural and Functional Features of Glutathione Reductase Transcripts from Olive (Olea europaea L.) Seeds
• Identification and in silico analysis of glutathione reductase transcripts expressed in olive (Olea europaea L.) pollen and pistil
• Demography, genetic diversity and expansion load in the colonizing species Leontodon longirostris (Asteraceae) throughout its native range
• An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae.
• The Genomic Landscape Resource of Pseudomonas syringae pv. syringae Strains Isolated from Mango Trees
• Decoding Neuromuscular Disorders Using Phenotypic Clusters Obtained From Co-Occurrence Networks
• Insights into ROS-dependent signalling underlying transcriptomic plant responses to the herbicide 2,4-D
• Genomic characterization and expression analysis of four apolipoprotein A-IV paralogs in Senegalese sole (Solea senegalensis Kaup)
• Automatic workflow for the identification of constitutively-expressed genes based on mapped NGS reads
• Current status in other finfish species: Description of current genomic resources for the gilthead seabream (Sparus aurata) and soles (Solea senegalensis and Solea solea)
• Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
• AutoFlow, a Versatile Workflow Engine Illustrated by Assembling an Optimised de novo Transcriptome for a Non-Model Species, such as Faba Bean (Vicia faba)
• Transcriptome-Based Identification of a Seed Olive Legumin (11S Globulin). Characterization of Subunits, 3D Modelling and Molecular Assessment of Allergenicity
• Nitric oxide-dependent regulation of sweet pepper fruit ripening
• The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi
• De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow
• Genomic analysis of the marine fish pathogen Photobacterium damselae subsp. piscicida: Insertion sequences proliferation is associated with chromosomal reorganisations and rampant gene decay
• NearTrans Can Identify Correlated Expression Changes Between Retrotransposons and Surrounding Genes in Human Cancer
• First draft genome assembly of the Argane tree (Argania spinosa) [version 1; referees: awaiting peer review]
• De novo assembly and functional annotation of Citrus aurantifolia transcriptome from Candidatus Liberibacter asiaticus infected and non-infected trees
• Expression-based, consistent biomarkers for prognosis and diagnosis in lung cancer
• Genetic Estimates for Growth and Shape-Related Traits in the Flatfish Senegalese Sole
• Identification of distinctive variants of the olive pollen allergen Ole e 5 (Cu,Zn superoxide dismutase) throughout the analysis of the olive pollen transcriptome
• Identification and in silico analysis of NADPH oxidase homologues involved in allergy from an olive pollen transcriptome
• De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology
• A web tool to discover full-length sequences - Full-lengther
• On selecting the best pre-processing method for affymetrix genechips
• GENote v.β: A web tool prototype for annotation of unfinished sequences in non-model eukaryotes
• The impassive assistant
• Evaluation of Transit XV for translators of medical and related science texts
• Patents - more than biology, medicine, pharmacy and chemistry together
• InterTerm: Internet dictionaries at a single click
• English-Spanish vocabulary of biochemistry and molecular biology (6th presentation)
• SeqTrim - A validation and trimming tool for all purpose sequence reads
• Basic advice on how to improve scientific texts translated from English to Spanish (I)
• AUTOMATED CONSTRUCTION OF TRANSCRIPTOME DATABASES FOR UNCHARACTERISED-GENOME PLANTS, SUCH AS OLIVE TREE
• De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: Integration in a database and design of a microarray
• Genetic and physical mapping of the QTL(AR3) controlling blight resistance in chickpea (Cicer arietinum L)
• A microRNA Signature Associated with Early Recurrence in Breast Cancer
• Robust gene signatures from microarray data using genetic algorithms enriched with biological pathway keywords
• Sma3s: a three-step modular annotator for large sequence datasets
• Interoperability with Moby 1.0 - Its better than sharing your toothbrush
• Detecting and correcting mis-assembled reads in contigs
• Pyroptosis and adaptive immunity mechanisms are promptly engendered in mesenteric lymph-nodes during pig infections with Salmonella enterica serovar Typhimurium
• Functional genomics of nitrogen metabolism in conifer trees
• Gene expression profiling in the stem of young maritime pine trees: detection of ammonium stress-responsive genes in the apex
• Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
• Why assembling plant genome sequences is so challenging
• EuroPineDB: a high-coverage web database for maritime pine transcriptome
• Gene expression pattern in swine neutrophils after lipopolysaccharide exposure: a time course comparison
• AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences
• Evidence for an operative glutamine translocator in chloroplasts from maritime pine (Pinus pinaster Ait.) cotyledons
• SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
• PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data
• Amine System Project
• SeqTrim - A validation and trimming tool for all purpose sequence reads
• Toward a Pinus pinaster bacterial artificial chromosome library
• Effect of pre-processing methods on microarray-based SVM classifiers in affymetrix genechips
• IN THE SEARCH FOR NON DESCRIBED OLIVE TREE ALLERGENS BY TRANSCRIPTOME-MINING
• AutoFlow: an easy way to build workflows
• Large-scale transcriptome analysis in faba bean (vicia faba L.) under ascochyta fabae infection
• Genome-wide gene expression analysis during Solea sp. embryo-larval development.
• Intuitive bioinformatics for genomics applications: Omega-brigid workflow framework
• Bioinformatics analyses to separate species specific mRNAs from unknown sequences in de novo assembled transcriptomes
• DEgenes hunter - A self-customised gene expression analysis workflow for non-model organisms
• New strategy for Pinus pinaster genomic library construction in bacterial artificial chromosomes,Nueva estrategia para la construcción de una genoteca genómica de Pinus pinaster en cromosomas artificiales de bacterias
• A bit of style in medical translation: what you would like to know but do not know where to find
• How to write a scientific article in English
• "Blacklists" of words: a little known IT resource that facilitates terminology consistency
• FQbin: a compatible and optimized format for storing and managing sequence data
• ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome.
• MOWServ: a web client for integration of bioinformatic resources.
• MITOPROT, A MACINTOSH APPLICATION FOR STUDYING MITOCHONDRIAL PROTEINS
• CYCLOHEXIMIDE RESISTANCE - A DOMINANT SELECTION MARKER FOR TRANSFORMATION OF LABORATORY AND INDUSTRIAL YEASTS
• CYCLOHEXIMIDE RESISTANCE AS A YEAST CLONING MARKER
• MedTrad: a medical translation forum on the Internet
• Prediction of N-terminal protein sorting signals
• RNA isolation from plant tissues: a practical experience for biological undergraduates
• Genomic evidence for a repetitive nature of the RAPD polymorphisms in Olea europaea (olive-tree)
• Genetic correction of mitochondrial diseases - Using the natural migration of mitochondrial genes to the nucleus in chlorophyte algae as a model system
• Isolation of bacterial artificial chromosome DNA by means of improved alkaline lysis and double potassium acetate precipitation
• Isolation of DNA from olive oil and oil sediments: Application in oil fingerprinting
• Cytochrome f and subunit IV, two essential components of the photosynthetic bf complex typically encoded in the chloroplast genome, are nucleus-encoded in Euglena gracilis
• Identification of olive-tree cultivars with SCAR markers
• Molecular and enzymatic analysis of ammonium assimilation in woody plants
• The typically mitochondrial DNA-encoded ATP6 subunit of the F1F0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii
• Subunit II of cytochrome c oxidase in chlamydomonad algae is a heterodimer encoded by two independent nuclear genes
• DNA fingerprinting and classification of geographically related genotypes of olive-tree (Olea europaea L.)
• Unusual location of a mitochondrial gene - Subunit III of cytochrome c oxidase is encoded in the nucleus of chlamydomonad algae
• Overexpression of yeast karyopherin Pse1p/Kap121p stimulates the mitochondrial import of hydrophobic proteins in vivo
• Rapid high quality RNA preparation from pine seedlings
• Allotopic expression of yeast mitochondrial maturase to study mitochondrial import of hydrophobic proteins
• Computational method to predict mitochondrially imported proteins and their targeting sequences
• ISOLATION AND EXPRESSION IN SACCHAROMYCES-CEREVISIAE OF A GENE ENCODING AN ALPHA-AMYLASE FROM SCHWANNIOMYCES-CASTELLII
• SIMILAR SHORT ELEMENTS IN THE 5' REGIONS OF THE ST-A2 AND SGA GENES FROM SACCHAROMYCES-CEREVISIAE
• TOPPRED-II - AN IMPROVED SOFTWARE FOR MEMBRANE-PROTEIN STRUCTURE PREDICTIONS
• PCR as a specific, sensitive and simple method suitable for diagnostics
• The promoter element GTACAAG of the SGA and STA2 genes is a possible target site for repression by the STA10 gene product from Saccharomyces cerevisiae
• Limitations to in vivo Import of Hydrophobic Proteins into Yeast Mitochondria: The Case of a Cytoplasmically Synthesized Apocytochrome b
• Molecular structure of the SWA2 gene encoding an AMY1-related α-amylase from Schwanniomyces occidentalis
• Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish
• Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors
• Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus