Bruno Contreras‐Moreira

Genomics and adaptive divergence of the allopolyploid grass Brachypodium hybridum in a pangenotypic framework

This study analyzes the origins and evolutionary dynamics of the allopolyploid grass Brachypodium hybridum using whole-genome sequencing and phylogenomic approaches, revealing three independent allopolyploidization events and subgenome-specific evolutionary patterns.

A pangenome-graph approach for mapping and imputing barley sequences

Pan20, a Practical Haplotype Graph of 20 barley genomes, assigns sequences MorexV3 coordinates and imputes genotyping-by-sequencing (GBS) reads at 0.06% base-call error versus 0.32% for variant calling.

From tiny to massive: exploring genome evolution in the model 1 grass genus Brachypodium

This study presents chromosome-level assemblies of two perennial Brachypodium species, revealing genomic features like polyploidy and transposable element dynamics that shaped genome evolution.

Vernalization regulatory network identifies potential novel functions for ZCCT genes within HvVRN2

This study identifies novel functions of HvVRN2 genes in barley vernalization by analyzing transcriptomic responses and regulatory networks.

Deconvolution of Single Homeologous Polymorphism (SHP) drives phylogenetic analysis of allopolyploids

AlloSHP detects single homeologous polymorphisms in allopolyploids without genome assembly, enabling phylogenetic analysis of diploid-polyploid complexes.

A pan-gene catalogue of Asian cultivated rice

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

Mapping the genomic landscape of peach and almond with PrunusMap

PrunusMap is a web tool that maps genetic markers to peach and almond genomes, aiding breeders in locating SNPs and genes.

Calling pangenes from plant genome alignments confirms presence-absence variation

The paper introduces get_pangenes to identify pangenes from genome alignments, showing it outperforms existing methods and confirms presence-absence variation in barley.

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

The paper introduces a hybrid repeat masking method for plant genomes using k-mer counting and curated repeat libraries, achieving efficient and accurate results.

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

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

Evolution and functional dynamics of dehydrins in model Brachypodium grasses

The paper studies dehydrin genes in Brachypodium species, identifying their genomic organization, expression patterns, and functional roles in drought tolerance across different ecotypes.

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

The paper identifies regulatory motifs in peach using co-expression networks and RSAT::Plants, finding that small promoter regions are optimal for motif discovery.

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

The paper introduces Var-tools, a framework for predicting the impact of regulatory variants on transcription factor binding, with four case studies demonstrating its functionality.

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

The paper introduces GET_PHYLOMARKERS, a software package for selecting optimal orthologous clusters for phylogenomics, and applies it to revise the taxonomy of the genus Stenotrophomonas.

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

MEBS evaluates (meta)genomic datasets to infer metabolic capabilities, particularly for the sulfur cycle, using entropy-based scoring and Pfam domains.

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

The paper introduces a method to analyze the sulfur cycle using genomic data, producing a sulfur score that classifies microorganisms and identifies key environments.