Contreras-Moreira, Bruno Person

Publications in VIVO

Co-author Network

Publications
Contact
Identity
View All

selected publications

article
- 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.. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2023
- Updated guidelines for gene nomenclature in wheat.. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2023
- 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. 2022
- Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross 2021
- Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses. Plants. 2021
- Ensembl Genomes 2022: An expanding genome resource for non-vertebrates. Nucleic Acids Research. 2021
- Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. 2021
- K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes. Plant Genome. 2021
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: The peach example. Plant Physiology. 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
- A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat.. eLife. 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
- TB1: From domestication gene to tool for many trades. Journal of Experimental Botany. 2020
- A roadmap for gene functional characterisation in wheat 2019
- A roadmap for gene functional characterisation in wheat. PeerJ. 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 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 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 2017
- MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: Unraveling the sulfur cycle. GigaScience. 2017
- Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition. Genome Biology and Evolution. 2017
- 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
- A cluster of nucleotide-binding site-leucine-rich repeat genes resides in a barley powdery mildew resistance quantitative trait loci on 7HL. Plant Genome. 2016
- FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces. 2016
- In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells.. PLOS ONE. 2016
- RSAT:: Plants: Motif discovery within clusters of upstream sequences in plant genomes 2016
- RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes. 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 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 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
- 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
book
chapter
- Scripting Analyses of Genomes in Ensembl Plants 2022
document
manuscript
- Calling pangenes from plant genome alignments confirms presence-absence variation 2023
THEME 5: WHEAT IMPROVEMENT:BREEDING, PHYSIOLOGY, ENABLING TECHNOLOGIES
- COMPUTATIONAL TOOLS AND RESOURCES TO ACCELERATE WHEAT RESEARCH AND BREEDING 2019