Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

diploS/HIC: An Updated Approach to Classifying Selective Sweeps

(2018) Andrew D. Kern et al.   G3-Genes Genomes Genetics

Parasitism drives host genome evolution: Insights from thePasteuria ramosa-Daphnia magnasystem

(2017) Yann Bourgeois et al.   EVOLUTION

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

(2017) Christoph Stritt et al.   Genome Biology and Evolution

The Plant Cell Reviews Plant Immunity: Receptor-Like Kinases, ROS-RLK Crosstalk, Quantitative Resistance, and the Growth/Defense Trade-Off

(2017) Nancy A. Eckardt   PLANT CELL

Vegetation of Eurasia from the last glacial maximum to present: Key biogeographic patterns

(2017) Heather Binney et al.   QUATERNARY SCIENCE REVIEWS

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

(2017) Sean P. Gordon et al.   Nature Communications

Discoal: flexible coalescent simulations with selection

(2016) Andrew D. Kern et al.   BIOINFORMATICS

A Photoreceptor Contributes to the Natural Variation of Diapause Induction inDaphnia magna

(2016) Anne C. Roulin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Molecular genetics and evolution of disease resistance in cereals

(2016) Simon G. Krattinger et al.   NEW PHYTOLOGIST

Population Structure in the Model Grass Is Highly Correlated with Flowering Differences across Broad Geographic Areas

(2016) Ludmila Tyler et al.   Plant Genome

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning

(2016) Daniel R. Schrider et al.   PLoS Genetics

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

(2015) D. Lopez-Alvarez et al.   AMERICAN JOURNAL OF BOTANY

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools

(2015) Zachary L. Fuller et al.   BMC GENOMICS

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Detecting balancing selection in genomes: limits and prospects

(2015) Anna Fijarczyk et al.   MOLECULAR ECOLOGY

Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

(2015) Florencia Schlamp et al.   MOLECULAR ECOLOGY

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

(2015) Sangeeta Singh et al.   PLoS One

Diversity and evolution of Rp1 rust resistance genes in four maize lines

(2015) Suchitra Chavan et al.   THEORETICAL AND APPLIED GENETICS

Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima)

(2015) Yan Zhong et al.   Scientific Reports

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

(2014) Matteo Dell’Acqua et al.   BMC GENOMICS

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

(2014) Emma Mace et al.   BMC PLANT BIOLOGY

The impact of linked selection on plant genomic variation

(2014) T. Slotte   Briefings in Functional Genomics

Advantageous diversity maintained by balancing selection in humans

(2014) Felix M Key et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Genomic variability as a driver of plant–pathogen coevolution?

(2014) Talia L Karasov et al.   CURRENT OPINION IN PLANT BIOLOGY

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Stripe Rust Resistance Gene Yr10 Encodes an Evolutionary-Conserved and Unique CC–NBS–LRR Sequence in Wheat

(2014) Wei Liu et al.   Molecular Plant

The Brachypodium distachyon BdWRKY36 gene confers tolerance to drought stress in transgenic tobacco plants

(2014) Jiutong Sun et al.   PLANT CELL REPORTS

Genome diversity inBrachypodium distachyon:deep sequencing of highly diverse inbred lines

(2014) Sean P. Gordon et al.   PLANT JOURNAL

Genome-Wide Inference of Ancestral Recombination Graphs

(2014) Matthew D. Rasmussen et al.   PLoS Genetics

Nonhost resistance to rust pathogens – a continuation of continua

(2014) Jan Bettgenhaeuser et al.   Frontiers in Plant Science

Comparative analysis of the cold acclimation and freezing tolerance capacities of seven diploid Brachypodium distachyon accessions

(2013) Katia Colton-Gagnon et al.   ANNALS OF BOTANY

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grassMiscanthus sinensis

(2013) Gancho T. Slavov et al.   NEW PHYTOLOGIST

On the importance of balancing selection in plants

(2013) Lynda F. Delph et al.   NEW PHYTOLOGIST

Evolution and Conservation of Plant NLR Functions

(2013) Florence Jacob et al.   Frontiers in Immunology

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

(2012) Mathieu Gautier et al.   BIOINFORMATICS

Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella

(2012) Gesseca Gos et al.   BMC EVOLUTIONARY BIOLOGY

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

(2012) Mirko Barbieri et al.   GENOME

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling

(2012) Chang-Jin Park et al.   Frontiers in Plant Science

Evolution of Grasses and Grassland Ecosystems

(2011) Caroline A.E. Strömberg   Annual Review of Earth and Planetary Sciences

Plant-Parasite Coevolution: Bridging the Gap between Genetics and Ecology

(2011) James K. M. Brown et al.   Annual Review of Phytopathology

Diversity ofPuccinia striiformison Cereals and Grasses

(2011) Mogens S. Hovmøller et al.   Annual Review of Phytopathology

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Environmental aridity is associated with cytotype segregation and polyploidy occurrence in Brachypodium distachyon (Poaceae)

(2011) Antonio J. Manzaneda et al.   NEW PHYTOLOGIST

Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon

(2011) Naxin Huo et al.   THEORETICAL AND APPLIED GENETICS

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Natural variation of drought response in Brachypodium distachyon

(2010) Na Luo et al.   PHYSIOLOGIA PLANTARUM

Rapid Decline of a Grassland System and Its Ecological and Conservation Implications

(2010) Gerardo Ceballos et al.   PLoS One

Selection upon Genome Architecture: Conservation of Functional Neighborhoods with Changing Genes

(2010) Fátima Al-Shahrour et al.   PLoS Computational Biology

The Scale of Population Structure in Arabidopsis thaliana

(2010) Alexander Platt et al.   PLoS Genetics

Goldacre paper: Recognition events and host–pathogen co-evolution in gene-for-gene resistance to flax rust

(2009) Peter Dodds et al.   FUNCTIONAL PLANT BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Who believes in whole-genome scans for selection?

(2009) J Hermisson   HEREDITY

Human influence lowers plant genetic diversity in communities with extinction debt

(2009) Aveliina Helm et al.   JOURNAL OF ECOLOGY

Testing for local adaptation inAvena barbata: a classic example of ecotypic divergence

(2009) ROBERT G. LATTA   MOLECULAR ECOLOGY

Cadmium and lead contamination in vegetables collected from industrial, traffic and rural areas in Bursa Province, Turkey

(2008) F. Mor et al.   Food Additives and Contaminants Part A-Chemistry Analysis Control Exposure & Risk Assessment

Glacial refugia of temperate trees in Europe: insights from species distribution modelling

(2008) Jens-Christian Svenning et al.   JOURNAL OF ECOLOGY

Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

(2008) Gerben van Ooijen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Brachypodium distachyon: making hay with a wild grass

(2008) Magdalena Opanowicz et al.   TRENDS IN PLANT SCIENCE