Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

pophelper: an R package and web app to analyse and visualize population structure

(2016) R. M. Francis   Molecular Ecology Resources

UsingPopulusas a lignocellulosic feedstock for bioethanol

(2015) Ilga Porth et al.   Biotechnology Journal

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

(2015) Wellington Muchero et al.   BMC GENOMICS

From association to prediction: statistical methods for the dissection and selection of complex traits in plants

(2015) Alexander E Lipka et al.   CURRENT OPINION IN PLANT BIOLOGY

Comparative interrogation of the developing xylem transcriptomes of two wood-forming species:Populus trichocarpaandEucalyptus grandis

(2015) Charles A. Hefer et al.   NEW PHYTOLOGIST

UsingPopulusas a lignocellulosic feedstock for bioethanol

(2015) Ilga Porth et al.   Biotechnology Journal

Rare-Variant Association Analysis: Study Designs and Statistical Tests

(2014) Seunggeung Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes

(2014) Vassily Trubetskoy et al.   BIOINFORMATICS

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

(2014) Christine F Baes et al.   BMC GENOMICS

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

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

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

(2014) L. Zhou et al.   MOLECULAR ECOLOGY

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

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

(2014) Luke M Evans et al.   NATURE GENETICS

Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations ofPopulus trichocarpa

(2014) Athena D. McKown et al.   NEW PHYTOLOGIST

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

Interactions between chromosomal and nonchromosomal elements reveal missing heritability

(2014) M. D. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Explaining additional genetic variation in complex traits

(2014) Matthew R. Robinson et al.   TRENDS IN GENETICS

Genomic selection in crops, trees and forages: a review

(2014) Z. Lin et al.   Crop & Pasture Science

Sequence Kernel Association Tests for the Combined Effect of Rare and Common Variants

(2013) Iuliana Ionita-Laza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Quantifying single nucleotide variant detection sensitivity in exome sequencing

(2013) Alison M Meynert et al.   BMC BIOINFORMATICS

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

(2013) Bartel Vanholme et al.   NEW PHYTOLOGIST

Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of naturalPopulus trichocarpaaccessions

(2013) Ilga Porth 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

Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies

(2012) Seunggeun Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrating genomic selection into dairy cattle breeding programmes: a review

(2012) A. Bouquet et al.   Animal

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

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

(2012) Pablo Cingolani et al.   FLY

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Association genetics of chemical wood properties in black poplar (Populus nigra)

(2012) Fernando P. Guerra et al.   NEW PHYTOLOGIST

Population Structure of Hispanics in the United States: The Multi-Ethnic Study of Atherosclerosis

(2012) Ani Manichaikul et al.   PLoS Genetics

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

(2011) Michael C. Wu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) H. Li   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

(2011) Fabio Marroni et al.   Tree Genetics & Genomes

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Genome-wide association studies in plants: the missing heritability is in the field

(2011) Benjamin Brachi et al.   GENOME BIOLOGY

Poplar as a feedstock for biofuels: A review of compositional characteristics

(2010) Poulomi Sannigrahi et al.   Biofuels Bioproducts & Biorefining-Biofpr

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE 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

The origin and evolution of lignin biosynthesis

(2010) Jing-Ke Weng et al.   NEW PHYTOLOGIST

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

ThePopulusGenome Integrative Explorer (PopGenIE): a new resource for exploring thePopulusgenome

(2009) Andreas Sjödin et al.   NEW PHYTOLOGIST

Quantitative genetic analysis of biomass and wood chemistry ofPopulusunder different nitrogen levels

(2009) Evandro Novaes et al.   NEW PHYTOLOGIST

Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data

(2008) Bingshan Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Comparative analysis of the transcriptomes ofPopulus trichocarpaandArabidopsis thalianasuggests extensive evolution of gene expression regulation in angiosperms

(2008) Tania Quesada et al.   NEW PHYTOLOGIST