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Human genomics projects and precision medicine

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Resequencing of the Leishmania infantum (strain JPCM5) genome and de novo assembly into 36 contigs

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Complete and de novo assembly of the Leishmania braziliensis (M2904) genome

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Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp.

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Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation

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ARAMIS: From systematic errors of NGS long reads to accurate assemblies

project

The soil biodiversity and functionality of Mediterranean olive groves: a holistic analysis of the influence of land management on olive oil quality and safety HE/MISS -SOIL/0199 101091255

project

Genética y pangenómica de cebadas mediterráneas para su adaptación a estreses abióticos, pre-mejora y mejora PID2022-142116OB-I00

project

Variables agroclimáticas de alta resolución para ensayos agronómicos y adaptación de cereales MMT24-EEAD-01

service unit

Agrigenomics and Climate Data Science (EEAD)

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MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: Unraveling the sulfur cycle

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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

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Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross

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Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research

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The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

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Tracking the Ancestry of Known and ‘Ghost’ Homeologous Subgenomes in Model Grass Brachypodium Polyploids

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Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

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Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

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Mapping the genomic landscape of peach and almond with PrunusMap

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Domain fishing: A first step in protein comparative modelling

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Structural context of exons in protein domains: Implications for protein modelling and design

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OPCML at 11q25 is epigenetically inactivated and has tumor- suppressor function in epithelial ovarian cancer

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Novel Use of a Genetic Algorithm for Protein Structure Prediction: Searching Template and Sequence Alignment Space

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In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling

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Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

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A link between sequence conservation and domain motion within the AAA+ family

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Empirical limits for template-based protein structure prediction: The CASP5 example

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Comparative footprinting of DNA-binding proteins

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TFmodeller: Comparative modelling of protein-DNA complexes

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The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

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RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

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Prediction of TF target sites based on atomistic models of protein-DNA complexes

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Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent

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primers4clades: A web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies

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Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli

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3D-footprint: A database for the structural analysis of protein DNA complexes

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Evolutionary divergence of chloroplast FAD synthetase proteins

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Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach

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Comparison of DNA binding across protein Superfamilies

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Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics

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HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys

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Protein disorder in plants: A view from the chloroplast

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Interface similarity improves comparison of DNA-binding proteins: The Homeobox example

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The twilight zone of cis element alignments

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OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors

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Genetic recombination is associated with intrinsic disorder in plant proteomes

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GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis

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Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces

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Loss of neuronal 3d chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction

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Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes

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FootprintDB: A database of transcription factors with annotated cis elements and binding interfaces

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Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information

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Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: A case study of pIncA/C plasmids

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BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley

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Analysis of the DNA-binding activities of the arabidopsis R2R3-MYB transcription factor family by one-hybrid experiments in yeast

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RSAT 2015: Regulatory sequence analysis tools

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Pangenomic Analysis of theRhizobialesUsing the GET_HOMOLOGUES Software Package

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Transcriptional responses in root and leaf of prunus persica under drought stress using RNA sequencing

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RSAT::Plants: Motif discovery in ChIP-seq peaks of plant genomes

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RSAT:: Plants: Motif discovery within clusters of upstream sequences in plant genomes

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In vivo chromatin targets of the transcription factor Yin Yang 2 in trophoblast stem cells

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FootprintDB: Analysis of plant Cis-regulatory elements, transcription factors, and binding interfaces

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A cluster of nucleotide-binding site-leucine-rich repeat genes resides in a barley powdery mildew resistance quantitative trait loci on 7HL

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Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis

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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

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Mycobacterium tuberculosis complex exhibits lineage-specific variations affecting protein ductility and epitope recognition

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Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition

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Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species

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Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace

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A new multi-genomic approach for the study of biogeochemical cycles at global scale: The molecular reconstruction of the sulfur cycle

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Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

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Understanding the mechanisms behind the response to environmental perturbation in microbial mats: A metagenomic-network based approach

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Resequencing theVrs1 gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike

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RSAT 2018: Regulatory sequence analysis tools 20th anniversary

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Evolution of protein ductility in duplicated genes of plants

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Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes

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Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula

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Fine-tuning of the flowering time control in winter barley: The importance of HvOS2 and HvVRN2 in non-inductive conditions

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Harnessing novel diversity from landraces to improve an elite barley variety

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RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

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Ensembl Genomes 2020-enabling non-vertebrate genomic research

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RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

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Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model

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Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections

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A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat

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Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

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TB1: From domestication gene to tool for many trades

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Evolutionary and structural analysis of ductile proteins (IDPs) and flavoenzymes

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Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon

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Light spectra trigger divergent gene expression in barley cultivars

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High-resolution agroclimatic indices for field trials and adaptation studies

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Efficient masking of plant genomes by combining kmer counting and curated repeats

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Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example

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Pangenomics and transcriptional regulation of grasses

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Evolution and functional dynamics of dehydrins in model Brachypodium grasses

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K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes

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Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

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Scripting Analyses of Genomes in Ensembl Plants

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RSAT 2022: regulatory sequence analysis tools

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Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon

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Computational Biology and Bioinformatics (BCB)

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