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Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria

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PanRNA: An RNAseq pipeline for semi-reference guided analysis

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Sterol‐Targeted Laboratory Evolution Allows the Isolation of Thermotolerant and Respiratory‐Competent Clones of the Industrial Yeast Saccharomyces cerevisiae

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Exploring the Diversity of the Human Blood Virome

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An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus

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Exploring the universal healthy human gut microbiota around the World

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The Effects of Sourdough Fermentation on the Biochemical Properties, Aroma Profile and Leavening Capacity of Carob Flour

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DVGfinder: A Metasearch Engine for Identifying Defective Viral Genomes in RNA-Seq Data

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Exploring nutritional quality and bioactive compounds in Mediterranean bean landraces

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DVGfinder: A Metasearch Tool for Identifying Defective Viral Genomes in RNA-Seq Data

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Genomic Signature in Evolutionary Biology: A Review

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Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts

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Alternative Splicing Across the Tree of Life: A Comparative Study

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Evolutionary trends of alternative splicing

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Metrics of Genomic Complexity in the Evolution of Bacterial Endosymbiosis

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Evidence-driven biases in alternative splicing inferred from NCBI Eukaryotic Genome Annotation Pipeline metadata

research group

Systems biomedicine

Our group is interested in computational data analysis in systems biomedicine, focusing primarily on the...

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Cloning and characterization of the Arabidopsis thaliana SQS1 gene encoding squalene synthase - Involvement of the C-terminal region of the enzyme in the channeling of squalene through the sterol pathway

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Distinct light-mediated pathways regulate the biosynthesis and exchange of isoprenoid precursors during Arabidopsis seedling development

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The metabolic imbalance underlying lesion formation in Arabidopsis thaliana overexpressing farnesyl diphosphate synthase (isoform 1S) leads to oxidative stress and is triggered by the developmental decline of endogenous HMGR activity

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Subcellular localization of Arabidopsis 3-hydroxy-3-methylglutaryl-coenzyme A reductase

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EU-OSTID: A collection of transposon insertional mutants for functional genomics in rice

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Structure of two melon regions reveals high microsynteny with sequenced plant species

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Characterisation of the gene family encoding acetoacetyl-CoA thiolase in Arabidopsis

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Generation of a BAC-based physical map of the melon genome

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Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

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Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries

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Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

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The genome of melon (Cucumis melo L.)

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High presence/absence gene variability in defense-related gene clusters of Cucumis melo

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Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome

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Evolution of NBS-LRR Gene Copies among Dicot Plants and its Regulation by Members of the miR482/2118 Superfamily of miRNAs

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Robust transcriptional indicators of immune cell death revealed by spatiotemporal transcriptome analyses

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Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety

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Association of Microbiome Diversity with Disease Symptoms in Brassica oleracea Leaves

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Cultivar-Dependent Variations in the Microbiome of Grapevine Leaves

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Wavelet-based denoising methods: A comparative study with applications in microscopy

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A variant to the 'random approximation' of the reference-free alignment algorithm

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Organising multi-dimensional biological image information: The BioImage database

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Design and realization of an on-line database for multidimensional microscopic images of biological specimens

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New electron microscopy database and deposition system

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FEMME database: Topologic and geometric information of macromolecules

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EMDep: A web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information

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Designing and executing scientific workflows with a programmable integrator

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Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology

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Integrated analysis of gene expression by association rules discovery

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Discovering semantic features in the literature: A foundation for building functional associations

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BioNMF: A versatile tool for non-negative matrix factorization in biology

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A literature-based similarity metric for biological processes

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GENECODIS: A web-based tool for finding significant concurrent annotations in gene lists

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Functional Classification of Genes Using Non-Negative Independent Component Analysis

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CBR-Tagger

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Assessment of protein set coherence using functional annotations

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SENT: Semantic features in text

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Named entity recognition and normalization: A domain-specific language approach

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Nuclear but not cytosolic phosphoinositide 3-kinase beta has an essential function in cell survival

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MBRole: Enrichment analysis of metabolomic data

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Genetic polymorphisms among C57BL/6 mouse inbred strains

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Structural characterization of the bacteriophage T7 tail machinery

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Structural characterization of T7 tail machinery reveals a conserved tubular structure among otherPodoviridaefamily members and suggests a common mechanism for DNA delivery

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Strigolactone promotes degradation of DWARF14, an α/β hydrolase essential for strigolactone signaling in Arabidopsis

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Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex

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Functional signature for the recognition of specific target mRNAs by human Staufen1 protein

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Practical protein bioinformatics

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Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases

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Functional Analysis of Metabolomics Data

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Clinical, genetics and bioinformatics characterization of a campomelic dysplasia case report

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Characterization of clinical signs in the human interactome

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Rare disease relations through common genes and protein interactions

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Practical analysis of specificity-determining residues in protein families

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MBROLE 2.0—functional enrichment of chemical compounds

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Factors affecting interactome-based prediction of human genes associated with clinical signs

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Applications of molecular networks in biomedicine

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Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program

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Phosphorylation-Related Crosstalk Between Distant Regions of the Core Region of the Coat Protein Contributes to Virion Assembly of Plum Pox Virus

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Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations

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Predicting biological pathways of chemical compounds with a profile-inspired approach

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CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature

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Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View

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Urinary Metabolomics Study on the Protective Role of Cocoa in Zucker Diabetic Rats via ¹H-NMR-Based Approach

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PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information

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Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation

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Cell atlases and the Developmental Foundations of the Phenotype

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MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis

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Roadmap for the integration of gastro‐intestinal (GI) tract microbiomes (human and domestic animal) in risk assessments under EFSA's remit

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CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature

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Disentangling protein metabolic costs in human cells and tissues

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Relevance of gut microbiome research in food safety assessment

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Testing similarity measures with continuous and discrete protein models

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Local interactions in protein folding determined through an inverse folding model

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Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations

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Protein disorder in the centrosome correlates with complexity in cell types number

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Learning protein folding and evolution with a snake puzzle

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Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis originome

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Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

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Site-specific structure and stability constrained substitution models improve phylogenetic inference

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PC_sim: An integrated measure of protein sequence and structure similarity for improved alignments and evolutionary inference

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The topography of DNA replication origins in Eukarya: GGN clusters, landmark nucleosomes, CDC6 and G4 structures

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orcid publication

Multivariate resolution of NMR labile signals by means of hard- and soft-modelling methods