Bruno Contreras Moreira
Biography
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Computational biologist specialized on plant genomics, phylogenomics and structural bioinformatics. Tenured Scientist (Científico Titular) and group leader of the Computational and Structural Biology lab at the EEAD-CSIC (Zaragoza) since October 2021; previously funded by ARAID (2007-2018) and at EMBL-EBI (2018-2021). Lecturer in the International Master in Plant Genetics, Genomics and Breeding at CIHEAM Zaragoza since December 2020, and invited lecturer at the Universidad Nacional Autónoma de México since February 2026. Research board member (Vocal de investigación) of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC) since December 2025, and member of the CSIC BCB Connection since September 2023. (Description curated from publicly available data.) |
Profile
| Institution | EEAD |
| Position | Tenured Scientist, Group Leader |
| Home page | https://www.linkedin.com/in/brunocontrerasm/ |
| Contact email | bcontreras@eead.csic.es |
| ORCID | 0000-0002-5462-907X |
BCB Hub
| BCB Committee | Expertise mapping, Future Plan |
| BCB Tools | RSAT Plants, GET_HOMOLOGUES, footprintDB, 3D-footprint, BARLEYMAP |
| BCB Services | Agrigenomics and Climate Data Science (EEAD) |
Research
Research topics
OmicsComputational MethodsResourcesTranscriptomicsBioinformatics Software and ToolsApplications of Computational BiologyBioinformatics enabling techniquesGenomicsStructural bioinformaticsBioinformatics InfrastructureBiological DatabasesComputational models and simulations
View all (15 more)
Gene regulatory networksComputational TechniquesHigh-performance ComputingParallel ComputingMolecular evolutionFAIRficationBioinformatics educationEvolutionary modellingSequence analysisPhylogenetic AnalysisPlant genomicsStructure predictionNon-model organismsPopulation dynamicsPhylogenomics
Research lines
Projects, networks, transfer & teaching
Research networks
National
International
Teaching
Master programs
- Erasmus Mundus Master Degree in Plant Breeding (emPLANT+) - Universitat Politècnica de València (interuniversity) - https://www.upv.es/estudios/master/muememplant/en/home/
- International Master in Plant Genetics, Genomics and Breeding - CIHEAM Zaragoza (IAMZ)
Doctoral programs
- Doctoral Programme in Agricultural and Natural Environment Sciences (Programa de Doctorado en Ciencias Agrarias y del Medio Natural) - Universidad de Zaragoza - https://estudios.unizar.es/estudio/ver-doct?id=7096
Funded projects 3
- Variables agroclimáticas de alta resolución para ensayos agronómicos y adaptación de cereales MMT24-EEAD-01
- Genética y pangenómica de cebadas mediterráneas para su adaptación a estreses abióticos, pre-mejora y mejora PID2022-142116OB-I00
- The soil biodiversity and functionality of Mediterranean olive groves: a holistic analysis of the influence of land management on olive oil quality and safety
Publications 104 entries
- Genomics and adaptive divergence of the allopolyploid grass Brachypodium hybridum in a pangenotypic framework Preprint · 24 Aug 2026
- A pangenome-graph approach for mapping and imputing barley sequences Preprint · 10 Aug 2026
- From tiny to massive: exploring genome evolution in the model grass genus Brachypodium Preprint · 21 Jul 2026
- Vernalization regulatory network identifies potential novel functions for genes in the HvVRN2 locus Article · 12 Apr 2026
- The PanOryza pangene catalog of Asian cultivated rice Article · 12 Dec 2025
View all (99 more)
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids Article · 24 Oct 2025
- Natural variation of response to glyphosate in Sinapis alba (Brassicaceae): Physiological effects, shikimate accumulation and genetic mechanisms Article · Sep 2025
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach Article · 22 Jul 2025
- Temporal regulation of gene expression during auxin-triggered crown root formation in barley: an integrated approach Article · 13 Jul 2025
- Evolutionary Trajectories of Methionine Metabolism in Mycobacterium and Its Application to Engineer a Vitamin B12 Whole‐Cell Ribosensor Article · Jun 2025
- Mapping the genomic landscape of Prunus spp. with PrunusMap Article · 24 Oct 2024
- Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis Article · 13 Dec 2023
- Diversity of gene expression responses to light quality in barley Article · 10 Oct 2023
- GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation Article · 5 Oct 2023
- ddRAD-seq-derived SNPs reveal novel association signatures for fruit-related traits in peach Preprint · 2 Aug 2023
- Updated guidelines for gene nomenclature in wheat Article · 23 Mar 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 Article · 4 Jan 2023
- Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon Article · 26 Aug 2022
- Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR Article · 19 May 2022
- RSAT 2022: regulatory sequence analysis tools Software · 11 May 2022
- Light spectra trigger divergent gene expression in barley cultivars Preprint · 30 Mar 2022
- Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids Article · 8 Feb 2022
- Pangenome Analysis of Plant Transcripts and Coding Sequences Software · 2022
- Scripting Analyses of Genomes in Ensembl Plants Book / chapter · 2022
- Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses Article · 3 Dec 2021
- Ensembl Genomes 2022: an expanding genome resource for non-vertebrates Article · 13 Nov 2021
- The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data Article · 11 Oct 2021
- K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes Article · 25 Sep 2021
- Evolution and functional dynamics of dehydrins in model Brachypodium grasses Preprint · 4 Sep 2021
- Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross Article · Aug 2021
- Efficient masking of plant genomes by combining kmer counting and curated repeats Preprint · 24 Mar 2021
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example Article · 13 Jan 2021
- Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research Article · 10 Nov 2020
- TB1: From domestication gene to tool for many trades Article · 6 Aug 2020
- Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors Article · 29 Jul 2020
- A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat Article · 24 Mar 2020
- Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections Article · 6 Mar 2020
- Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model Preprint · 4 Mar 2020
- A roadmap for gene functional characterisation in wheat Preprint · 18 Dec 2019
- Ensembl Genomes 2020-enabling non-vertebrate genomic research Article · 10 Oct 2019
- Harnessing novel diversity from landraces to improve an elite barley variety Article · 11 Apr 2019
- Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula Article · Apr 2019
- Fine-tuning of the flowering time control in winter barley: The importance of HvOS2 and HvVRN2 in non-inductive conditions Article · 25 Mar 2019
- RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding Article · Jan 2019
- Understanding the mechanisms behind the response to environmental perturbation in microbial mats: A metagenomic-network based approach Article · 28 Nov 2018
- Evolution of protein ductility in duplicated genes of plants Article · 20 Aug 2018
- RSAT 2018: Regulatory sequence analysis tools 20th anniversary Article · 2 May 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 Article · 1 May 2018
- Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike Article · 12 Apr 2018
- Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure Article · 19 Dec 2017
- Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes Article · 5 Dec 2017
- MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle Article · 23 Oct 2017
- A new multi-genomic approach for the study of biogeochemical cycles at global scale: The molecular reconstruction of the sulfur cycle Preprint · 11 Jun 2017
- Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace Article · 1 May 2017
- Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species Software · 14 Feb 2017
- Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition Article · 6 Jan 2017
- Transcriptional responses in root and leaf of prunus persica under drought stress using RNA sequencing Article · 23 Nov 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 Article · 12 Jul 2016
- A cluster of nucleotide-binding site-leucine-rich repeat genes resides in a barley powdery mildew resistance quantitative trait loci on 7HL Article · Jul 2016
- In vivo chromatin targets of the transcription factor Yin Yang 2 in trophoblast stem cells Article · 18 May 2016
- Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis Article · 1 Mar 2016
- RSAT::Plants: Motif discovery in ChIP-seq peaks of plant genomes Book / chapter · 2016
- RSAT:: Plants: Motif discovery within clusters of upstream sequences in plant genomes Book / chapter · 2016
- FootprintDB: Analysis of plant Cis-regulatory elements, transcription factors, and binding interfaces Software · 2016
- Analysis of the DNA-binding activities of the arabidopsis R2R3-MYB transcription factor family by one-hybrid experiments in yeast Article · 20 Oct 2015
- Pangenomic Analysis of theRhizobialesUsing the GET_HOMOLOGUES Software Package Other · 14 Jul 2015
- RSAT 2015: Regulatory sequence analysis tools Article · 22 Apr 2015
- Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply Article · 18 Mar 2015
- Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information Article · Jan 2015
- BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley Software · Jan 2015
- Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: A case study of pIncA/C plasmids Software · 2015
- Loss of neuronal 3d chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction Article · 18 Jul 2014
- HvFT1 polymorphism and effect—survey of barley germplasm and expression analysis Article · 6 Jun 2014
- Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes Article · 28 Apr 2014
- GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis Software · 15 Dec 2013
- FootprintDB: A database of transcription factors with annotated cis elements and binding interfaces Software · 14 Nov 2013
- Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces Article · 26 Sep 2013
- OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors Article · 24 May 2013
- Genetic recombination is associated with intrinsic disorder in plant proteomes Article · 2013
- The twilight zone of cis element alignments Article · 24 Dec 2012
- Protein disorder in plants: A view from the chloroplast Article · 2012
- Interface similarity improves comparison of DNA-binding proteins: The Homeobox example Book / chapter · 2012
- Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics Other · 3 May 2011
- HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys Article · 30 Jan 2011
- Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach Article · 14 Jul 2010
- Evolutionary divergence of chloroplast FAD synthetase proteins Article · 2010
- Comparison of DNA binding across protein Superfamilies Article · 27 Nov 2009
- Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli Article · 19 Oct 2009
- 3D-footprint: A database for the structural analysis of protein DNA complexes Software · 18 Sep 2009
- primers4clades: A web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies Article · 21 May 2009
- Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent Article · 15 Nov 2008
- Prediction of TF target sites based on atomistic models of protein-DNA complexes Article · 16 Oct 2008
- The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks Article · Jun 2008
- RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation Article · 23 Dec 2007
- TFmodeller: Comparative modelling of protein-DNA complexes Article · 25 Apr 2007
- Comparative footprinting of DNA-binding proteins Article · 15 Jul 2006
- Empirical limits for template-based protein structure prediction: The CASP5 example Article · 19 Jan 2005
- A link between sequence conservation and domain motion within the AAA+ family Article · Apr 2004
- Structural context of exons in protein domains: Implications for protein modelling and design Article · Nov 2003
- Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches Article · Oct 2003
- OPCML at 11q25 is epigenetically inactivated and has tumor- suppressor function in epithelial ovarian cancer Article · 22 Jun 2003
- In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling Article · May 2003
- Novel Use of a Genetic Algorithm for Protein Structure Prediction: Searching Template and Sequence Alignment Space Article · 2003
- Domain fishing: A first step in protein comparative modelling Article · 1 Aug 2002