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

The New phytologist, 2018-06, Vol.218 (4), p.1631-1644

2018

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GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

Applied and Environmental Microbiology, 2013-12, Vol.79 (24), p.7696-7701

2013

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Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

The Plant journal : for cell and molecular biology, 2022-03, Vol.109 (6), p.1535-1558

2022

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

Molecular ecology, 2019-04, Vol.28 (8), p.1994-2012

2019

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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

Applied and Environmental Microbiology, 2008-11, Vol.74 (22), p.6987-6996

2008

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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

Frontiers in microbiology, 2018-05, Vol.9, p.771-771

2018

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

The plant genome, 2021-11, Vol.14 (3), p.e20143-n/a

2021

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

Genes, 2020-03, Vol.11 (3), p.283

2020

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

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D91-D97

Contreras-Moreira, Bruno

2010

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

Nature communications, 2017-12, Vol.8 (1), p.2184-13, Article 2184

2017

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

Methods in molecular biology (Clifton, N.J.), 2016-01, Vol.1482, p.259

2016

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Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

Scientific reports, 2023-12, Vol.13 (1), p.22168-22168, Article 22168

2023

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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

The plant genome, 2016-07, Vol.9 (2), p.1-14

2016

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GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

Genome Biology, 2023-10, Vol.24 (1), p.223-223, Article 223

2023

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

Molecular breeding, 2015, Vol.35 (1), Article 13

2015

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

Nature communications, 2020-07, Vol.11 (1), p.3670-3670, Article 3670

2020

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

PloS one, 2015-10, Vol.10 (10), p.e0141044-e0141044

2015

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Protein disorder in plants: a view from the chloroplast

BMC plant biology, 2012-09, Vol.12 (1), p.165-165

2012

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

Plant physiology (Bethesda), 2021-04, Vol.185 (3), p.1242-1258

2021

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

PloS one, 2009-10, Vol.4 (10), p.e7526-e7526

2009

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Diversity of gene expression responses to light quality in barley

Scientific reports, 2023-10, Vol.13 (1), p.17143-17143, Article 17143

2023

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

Frontiers in plant science, 2016-11, Vol.7, p.1715-1715

2016

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Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety

Frontiers in plant science, 2019-04, Vol.10, p.434-434

2019

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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, 2023-01, Vol.13, p.1076797-1076797

2023

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

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

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

Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent

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

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

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

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

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

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

Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis

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

GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

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

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

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

Protein disorder in plants: a view from the chloroplast

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

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

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

Diversity of gene expression responses to light quality in barley

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

Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety

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

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