Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS

(2013) Eli Rodgers-Melnick et al.   BMC GENOMICS

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress

(2013) Jian Sun et al.   Genes & Genomics

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Complex Patterns of Local Adaptation in Teosinte

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

A 34K SNP genotyping array forPopulus trichocarpa: Design, application to the study of natural populations and transferability to otherPopulusspecies

(2013) A. Geraldes et al.   Molecular Ecology Resources

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

(2013) Guanqing Jia et al.   NATURE GENETICS

Breeding with rare defective alleles (BRDA): a naturalPopulus nigraHCT mutant with modified lignin as a case study

(2013) Bartel Vanholme et al.   NEW PHYTOLOGIST

Geographical and environmental gradients shape phenotypic trait variation and genetic structure inPopulus trichocarpa

(2013) Athena D. McKown et al.   NEW PHYTOLOGIST

Genome-wide association mapping for wood characteristics inPopulusidentifies an array of candidate single nucleotide polymorphisms

(2013) Ilga Porth et al.   NEW PHYTOLOGIST

Interlocking Feedback Loops Govern the Dynamic Behavior of the Floral Transition in Arabidopsis

(2013) K. E. Jaeger et al.   PLANT CELL

The Ureide-Degrading Reactions of Purine Ring Catabolism Employ Three Amidohydrolases and One Aminohydrolase in Arabidopsis, Soybean, and Rice

(2013) A. K. Werner et al.   PLANT PHYSIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

A model-based approach for analysis of spatial structure in genetic data

(2012) Wen-Yun Yang et al.   NATURE GENETICS

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

(2012) Shancen Zhao et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Improved whole-chromosome phasing for disease and population genetic studies

(2012) Olivier Delaneau et al.   NATURE METHODS

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest treePopulus trichocarpa

(2012) Gancho T. Slavov et al.   NEW PHYTOLOGIST

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Callose Biosynthesis Regulates Symplastic Trafficking during Root Development

(2011) Anne Vatén et al.   DEVELOPMENTAL CELL

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus

(2011) E. Rodgers-Melnick et al.   GENOME RESEARCH

ClimateWNA—High-Resolution Spatial Climate Data for Western North America

(2011) Tongli Wang et al.   Journal of Applied Meteorology and Climatology

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Chilling of Dormant Buds HyperinducesFLOWERING LOCUS Tand Recruits GA-Inducible 1,3-β-Glucanases to Reopen Signal Conduits and Release Dormancy inPopulus

(2011) Päivi L.H. Rinne et al.   PLANT CELL

PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis

(2011) Sabrina Iñigo et al.   PLANT JOURNAL

FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar

(2011) C.-Y. Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Map of Local Adaptation in Arabidopsis thaliana

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

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrating environmental and genetic effects to predict responses of tree populations to climate

(2010) Tongli Wang et al.   ECOLOGICAL APPLICATIONS

Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading

(2010) A. Platt et al.   GENETICS

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Adaptation – not by sweeps alone

(2010) Jonathan K. Pritchard et al.   NATURE REVIEWS GENETICS

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem

(2010) Jill L. Wegrzyn et al.   NEW PHYTOLOGIST

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

CalS7 encodes a callose synthase responsible for callose deposition in the phloem

(2010) Bo Xie et al.   PLANT JOURNAL

Populus CEN/TFL1 regulates first onset of flowering, axillary meristem identity and dormancy release in Populus

(2010) Rozi Mohamed et al.   PLANT JOURNAL

Genomic selection in forest tree breeding

(2010) Dario Grattapaglia et al.   Tree Genetics & Genomes

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution

(2009) James A. Birchler et al.   NEW PHYTOLOGIST

Estimation of significance thresholds for genomewide association scans

(2008) Frank Dudbridge et al.   GENETIC EPIDEMIOLOGY

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Extending Genomics to Natural Communities and Ecosystems

(2008) T. G. Whitham et al.   SCIENCE

Forests and Climate Change: Forcings, Feedbacks, and the Climate Benefits of Forests

(2008) G. B. Bonan   SCIENCE