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List of works by Bruno Contreras-Moreira

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

scientific article

A Cluster of Nucleotide-Binding Site-Leucine-Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL.

scientific article published in July 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.

scientific article published on 20 June 2016

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

scientific article published in April 2004

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

scientific article published on 24 March 2020

An efficient conformational sampling method for homology modeling.

scientific article

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

scientific article published on 14 February 2017

Analysis of the DNA-Binding Activities of the Arabidopsis R2R3-MYB Transcription Factor Family by One-Hybrid Experiments in Yeast.

scientific article published on 20 October 2015

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

Comparative footprinting of DNA-binding proteins

scientific article published in July 2006

Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era.

scientific article

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

scientific article published on 5 December 2017

Comparison of DNA binding across protein superfamilies.

scientific article published in January 2010

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

scientific article

Domain fishing: a first step in protein comparative modelling

scientific article published in August 2002

Ensembl Genomes 2020-enabling non-vertebrate genomic research

scientific article published on 01 January 2020

Evolution of Protein Ductility in Duplicated Genes of Plants

scientific article published in 2018

Evolutionary divergence of chloroplast FAD synthetase proteins ⬇️

scientific article published on October 18, 2010

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

scientific article published on 19 December 2017

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

article

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

article

FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces.

scientific article

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

scientific article

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

scientific article published on 04 October 2013

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.

scientific article

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

scientific article published on 06 March 2020

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

scientific article published on 02 April 2019

Genetic recombination is associated with intrinsic disorder in plant proteomes

scientific article

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

scientific article

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

scientific article published on 29 July 2020

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

scientific article published on 10 November 2020

Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety

scientific article published on 11 April 2019

HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys

scientific article published on 30 January 2011

HvFT1 polymorphism and effect-survey of barley germplasm and expression analysis

scientific article published on 6 June 2014

In Vivo Chromatin Targets of the Transcription Factor Yin Yang 2 in Trophoblast Stem Cells.

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 18 July 2014

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

scientific article published on 23 October 2017

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

scientific article published on 6 January 2017

Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.

scientific article

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

scientific article

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

scientific article

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

scientific article

Protein disorder in plants: a view from the chloroplast.

scientific article

Protein profile of Beta vulgaris leaf apoplastic fluid and changes induced by Fe deficiency and Fe resupply

scientific article published on 18 March 2015

RSAT 2015: Regulatory Sequence Analysis Tools.

scientific article published on 22 April 2015

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

scientific article published in July 2018

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

scientific article published on 07 November 2019

RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes

scientific article published in January 2016

RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes

scientific article published on January 2016

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

scientific article published in 2022

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

scientific article

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

article

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

scientific article published on January 2015

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

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

scientific article

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

scientific article

TFmodeller: comparative modelling of protein-DNA complexes

scientific article

The role of DNA-binding specificity in the evolution of bacterial regulatory networks

scientific article

The twilight zone of cis element alignments

scientific article published on 24 December 2012

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing.

scientific article

Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach

scientific article published on 28 November 2018

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

scientific article

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

scientific article published on 21 May 2009

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