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

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat

(2013) Yoichi Motomura et al.   BREEDING SCIENCE

Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing

(2013) T. M. Beissinger et al.   GENETICS

Complex Patterns of Local Adaptation in Teosinte

(2013) Tanja Pyhäjärvi et al.   Genome Biology and Evolution

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

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

(2013) Asher D. Cutter 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

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

MYB transcription factor genes as regulators for plant responses: an overview

(2013) Supriya Ambawat et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Evolution and taxonomic split of the model grass Brachypodium distachyon

(2012) Pilar Catalán et al.   ANNALS OF BOTANY

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

Genic and nongenic contributions to natural variation of quantitative traits in maize

(2012) X. Li et al.   GENOME RESEARCH

Local Adaptation in the Flowering-Time Gene Network of Balsam Poplar, Populus balsamifera L.

(2012) S. R. Keller et al.   MOLECULAR BIOLOGY AND EVOLUTION

The trouble with isolation by distance

(2012) PATRICK G. MEIRMANS   MOLECULAR ECOLOGY

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies

(2012) Bogdan Pasaniuc et al.   NATURE GENETICS

Evidence of widespread selection on standing variation in Europe at height-associated SNPs

(2012) Michael C Turchin et al.   NATURE GENETICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Accounting for multiple comparisons in a genome-wide association study (GWAS)

(2011) Randall C Johnson et al.   BMC GENOMICS

Integrating statistical genetic and geospatial methods brings new power to phylogeography

(2011) Lauren M. Chan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

(2011) J. L. Strasburg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Natural Variation in Arabidopsis: From Molecular Genetics to Ecological Genomics

(2011) D. Weigel   PLANT PHYSIOLOGY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Mapping Salinity Tolerance during Arabidopsis thaliana Germination and Seedling Growth

(2011) Leah DeRose-Wilson et al.   PLoS One

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

Adaptations to Climate-Mediated Selective Pressures in Humans

(2011) Angela M. Hancock et al.   PLoS Genetics

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

(2010) BÉNÉDICTE N. PONCET et al.   MOLECULAR ECOLOGY

Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks

(2010) RODNEY J. DYER et al.   MOLECULAR ECOLOGY

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)

(2010) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Mixed linear model approach adapted for genome-wide association studies

(2010) Zhiwu Zhang et al.   NATURE GENETICS

Association genetics of complex traits in plants

(2010) Pär K. Ingvarsson et al.   NEW PHYTOLOGIST

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genome scan to assess the respective role of host-plant and environmental constraints on the adaptation of a widespread insect

(2009) Stéphanie Manel et al.   BMC EVOLUTIONARY BIOLOGY

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

(2009) Einar E Nielsen et al.   BMC EVOLUTIONARY BIOLOGY

Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon

(2009) John P Vogel et al.   BMC PLANT BIOLOGY

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Revealing cryptic spatial patterns in genetic variability by a new multivariate method

(2008) T Jombart et al.   HEREDITY

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Integrating GIS-based environmental data into evolutionary biology

(2008) Kenneth H. Kozak et al.   TRENDS IN ECOLOGY & EVOLUTION

Brachypodium distachyon: making hay with a wild grass

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

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

(2007) B. C.Y Collard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES