A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

Reference Genome for the Highly Transformable Setaria viridis ME034V

(2020) Peter M. Thielen et al.   G3-Genes Genomes Genetics

The lignin toolbox of the model grass Setaria viridis

(2019) Sávio Siqueira Ferreira et al.   PLANT MOLECULAR BIOLOGY

Divergent gene expression networks underlie morphological diversity of abscission zones in grasses

(2019) Yunqing Yu et al.   NEW PHYTOLOGIST

Setaria viridis as a model for translational genetic studies of jasmonic acid-related insect defenses in Zea mays

(2019) Charles T Hunter et al.   PLANT SCIENCE

Anatomy and ultrastructure of embryonic leaves of the C4 species Setaria viridis

(2018) Nicia E G Junqueira et al.   ANNALS OF BOTANY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

(2018) Sandra Odonkor et al.   Frontiers in Plant Science

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

(2018) John T. Lovell et al.   Nature Communications

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology inSetaria viridis

(2017) Jiani Yang et al.   PLANT CELL

A multi-purpose toolkit to enable advanced genome engineering in plants

(2017) Tomas Cermak et al.   PLANT CELL

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

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

Abscission zone development in Setaria viridis and its domesticated relative, Setaria italica

(2016) John G. Hodge et al.   AMERICAN JOURNAL OF BOTANY

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Effects of abiotic stress on physiological plasticity and water use of Setaria viridis (L.)

(2016) Prasenjit Saha et al.   PLANT SCIENCE

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets: Fig. 1.

(2015) Colin A. Maclean et al.   MOLECULAR BIOLOGY AND EVOLUTION

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives

(2014) Daniel J. Layton et al.   AMERICAN JOURNAL OF BOTANY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

Population genetics ofSetaria viridis, a new model system

(2014) Pu Huang et al.   MOLECULAR ECOLOGY

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

(2014) Xiang Zhou et al.   NATURE METHODS

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

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

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

(2013) Hui Jiang et al.   Jove-Journal of Visualized Experiments

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

(2012) Pablo Cingolani et al.   FLY

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

(2012) James C. Schnable et al.   Genome Biology and Evolution

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1

(2012) Y. Zhou et al.   PLANT CELL

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Setaria viridis: A Model for C4 Photosynthesis

(2010) T. P. Brutnell et al.   PLANT CELL

Deletion in a gene associated with grain size increased yields during rice domestication

(2008) Ayahiko Shomura et al.   NATURE GENETICS

Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World

(2008) Harriet V. Hunt et al.   VEGETATION HISTORY AND ARCHAEOBOTANY