selected publications
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article
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach. Plant Methods. 2025
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids. Plant Methods. 2025
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Evolutionary Trajectories of Methionine Metabolism in Mycobacterium and Its Application to Engineer a Vitamin
B12 Whole‐Cell Ribosensor. Microbial Biotechnology. 2025 - Mapping the genomic landscape of Prunus spp. with PrunusMap. Horticulture research. 2025
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Natural variation of response to glyphosate in
Sinapis alba (Brassicaceae): Physiological effects, shikimate accumulation and genetic mechanisms 2025 - Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach. Plant and Cell Physiology. 2025
- The PanOryza pangene catalog of Asian cultivated rice. Genome Research. 2025
- Diversity of gene expression responses to light quality in barley. Scientific Reports. 2023
- GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome Biology. 2023
- Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia. Frontiers in Microbiology. 2023
- Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis. Scientific Reports. 2023
- Updated guidelines for gene nomenclature in wheat.. Theoretical and Applied Genetics. 2023
- Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.. Nucleic Acids Research. 2022
- Pangenome Analysis of Plant Transcripts and Coding Sequences.. Methods in molecular biology (Clifton, N.J.). 2022
- Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon. Molecular Ecology. 2022
- RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Research. 2022
- Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR. F1000Research. 2022
- Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR [version 2; peer review: 2 approved] 2022
- The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data. Nucleic Acids Research. 2022
- Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids. The Plant journal : for cell and molecular biology. 2022
- Comparative genomics, evolution, and drought-induced expression of dehydrin genes in model brachypodium grasses. Plants (Basel, Switzerland). 2021
- K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes. The Plant Genome. 2021
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example. Plant Physiology. 2021
- A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat.. eLife. 9. 2020
- A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat.. eLife. 2020
- Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross. The Crop Journal. 2020
- Ensembl Genomes 2020-enabling non-vertebrate genomic research.. Nucleic Acids Research. 2020
- Genetic diversity, population structure and linkage disequilibrium assessment among international sunflower breeding collections. Genes. 2020
- Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.. Nature Communications. 2020
- Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. 2020
- TB1: from domestication gene to tool for many trades.. Journal of Experimental Botany. 2020
- A roadmap for gene functional characterisation in wheat 2019
- Fine-tuning of the flowering time control in winter barley: the importance of HvOS2 and HvVRN2 in non-inductive conditions.. BMC Plant Biology. 2019
- Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula.. Molecular Ecology. 2019
- Harnessing novel diversity from landraces to improve an elite barley variety. Frontiers in Plant Science. 2019
- RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.. Computational and structural biotechnology journal. 2019
- Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytologist. 2018
- Evolution of protein ductility in duplicated genes of plants. Frontiers in Plant Science. 2018
- GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Frontiers in Microbiology. 2018
- RSAT 2018: Regulatory sequence analysis tools 20th anniversary. Nucleic Acids Research. 2018
- Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike. Molecular Breeding. 2018
- Understanding the mechanisms behind the response to environmental perturbation in microbial mats: A metagenomic-network based approach. Frontiers in Microbiology. 2018
- Analysis of plant pan-genomes and transcriptomes with GET_HOMOLOGUES-EST, a clustering solution for sequences of the same species. Frontiers in Plant Science. 2017
- Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications. 2017
- Large differences in gene expression responses to drought and heat stress between elite barley cultivar scarlett and a Spanish landrace. Frontiers in Plant Science. 2017
- MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. GigaScience. 2017
- A cluster of nucleotide-binding site-leucine-rich repeat genes resides in a barley powdery mildew resistance quantitative trait loci on 7HL. The Plant Genome. 2016
- A shotgun proteomic approach reveals that fe deficiency causes marked changes in the protein profiles of plasma membrane and detergent-resistant microdomain preparations from beta vulgaris roots. Journal of Proteome Research. 2016
- FootprintDB: Analysis of plant Cis-regulatory elements, transcription factors, and binding interfaces. Methods in Molecular Biology. 2016
- In vivo chromatin targets of the transcription factor Yin Yang 2 in trophoblast stem cells. PLOS ONE. 2016
- Mycobacterium tuberculosis complex exhibits lineage-specific variations affecting protein ductility and epitope recognition. Genome Biology and Evolution. 2016
- RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.. Methods in Molecular Biology. 2016
- RSAT::Plants: Motif discovery in ChIP-seq peaks of plant genomes. Methods in Molecular Biology. 2016
- Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis.. Microbiology (United Kingdom). 2016
- Transcriptional responses in root and leaf of prunus persica under drought stress using RNA sequencing. Frontiers in Plant Science. 2016
- Analysis of the DNA-binding activities of the arabidopsis R2R3-MYB transcription factor family by one-hybrid experiments in yeast. PLOS ONE. 2015
- BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley 2015
- Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply.. Frontiers in Plant Science. 2015
- RSAT 2015: Regulatory sequence analysis tools. Nucleic Acids Research. 2015
- Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information 2015
- FootprintDB: A database of transcription factors with annotated cis elements and binding interfaces 2014
- HvFT1 polymorphism and effect-survey of barley germplasm and expression analysis. 2014
- Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes 2014
- Loss of neuronal 3d chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction 2014
- Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces 2013
- GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis 2013
- Genetic recombination is associated with intrinsic disorder in plant proteomes 2013
- OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors 2013
- The twilight zone of cis element alignments 2013
- Protein disorder in plants: A view from the chloroplast 2012
- HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys 2011
- Comparison of DNA binding across protein Superfamilies 2010
- Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach 2010
- Evolutionary divergence of chloroplast FAD synthetase proteins 2010
- 3D-footprint: A database for the structural analysis of protein DNA complexes 2009
- Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli 2009
- primers4clades: A web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies 2009
- An efficient conformational sampling method for homology modeling 2008
- Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent 2008
- Prediction of TF target sites based on atomistic models of protein-DNA complexes 2008
- RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation 2008
- The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks 2008
- TFmodeller: Comparative modelling of protein-DNA complexes 2007
- Comparative footprinting of DNA-binding proteins 2006
- Empirical limits for template-based protein structure prediction: The CASP5 example 2005
- A link between sequence conservation and domain motion within the AAA+ family 2004
- Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches 2003
- In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling 2003
- Novel Use of a Genetic Algorithm for Protein Structure Prediction: Searching Template and Sequence Alignment Space 2003
- OPCML at 11q25 is epigenetically inactivated and has tumor- suppressor function in epithelial ovarian cancer 2003
- Structural context of exons in protein domains: Implications for protein modelling and design 2003
- Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era. 2002
- Domain fishing: a first step in protein comparative modelling.. Bioinformatics. 2002
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book
- Pangenomic Analysis of theRhizobialesUsing the GET_HOMOLOGUES Software Package 2015
- Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: A case study of pIncA/C plasmids 2015
- Interface similarity improves comparison of DNA-binding proteins: The Homeobox example 2012
- Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics 2011
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chapter
- Scripting Analyses of Genomes in Ensembl Plants. Methods in Molecular Biology. 2022
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abstract
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document
- A pan-gene catalogue of Asian cultivated rice 2025
- Deconvolution of Single Homeologous Polymorphism (SHP) drives phylogenetic analysis of allopolyploids 2025
- Vernalization regulatory network identifies potential novel functions for ZCCT genes within HvVRN2 2025
- Mapping the genomic landscape of peach and almond with PrunusMap 2024
- Calling pangenes from plant genome alignments confirms presence-absence variation 2023
- ddRAD-seq-derived SNPs reveal novel association signatures for fruit-related traits in peach 2023
- Light spectra trigger divergent gene expression in barley cultivars 2022
- Efficient masking of plant genomes by combining kmer counting and curated repeats 2021
- Evolution and functional dynamics of dehydrins in model Brachypodium grasses. Horticulture research. 2021
- Light spectra trigger divergent gene expression in barley cultivars. Horticulture research. 2021
- Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon. Horticulture research. 2021
- Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids. Horticulture research. 2021
- Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model. Horticulture research. 2020
- The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data. Horticulture research. 2020
- A roadmap for gene functional characterisation in wheat 2019
- RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding. Horticulture research. 2019
- A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle. Horticulture research. 2017
- Algorithms for protein comparative modelling and some evolutionary implications.