Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

Structure, organization and evolution of ADP-ribosylation factors in rice and foxtail millet and their expression in rice

(2016) Mehanathan Muthamilarasan et al.   Scientific Reports

Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria

(2016) Margarita Mauro-Herrera et al.   PLoS One

Amyo-inositol-1-phosphate synthase gene,IbMIPS1, enhances salt and drought tolerance and stem nematode resistance in transgenic sweet potato

(2015) Hong Zhai et al.   PLANT BIOTECHNOLOGY JOURNAL

Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection

(2015) Hari D. Upadhyaya et al.   Plant Genome

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

(2014) Jinn-Jy Lin et al.   BMC GENOMICS

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]

(2014) Shuo Zhang et al.   BMC GENOMICS

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

(2014) Jie Xu et al.   BMC PLANT BIOLOGY

Further evidence that a terminal drought tolerance QTL of pearl millet is associated with reduced salt uptake

(2014) Parbodh C. Sharma et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica×Setaria viridis

(2014) Lufeng Qie et al.   PLoS One

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

(2014) A. N. Doust et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses

(2014) Mehanathan Muthamilarasan et al.   THEORETICAL AND APPLIED GENETICS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

(2013) Kajal Kumari et al.   PLoS One

Uterine Endoplasmic Reticulum Stress and Its Unfolded Protein Response May Regulate Caspase 3 Activation in the Pregnant Mouse Uterus

(2013) Arvind Suresh et al.   PLoS One

Assembler for de novo assembly of large genomes

(2013) Te-Chin Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae)

(2013) Margarita Mauro-Herrera et al.   G3-Genes Genomes Genetics

Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

(2012) Deepmala Sehgal et al.   BMC PLANT BIOLOGY

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Molecular mapping of quantitative trait loci for drought tolerance in maize plants

(2011) H. Rahman et al.   GENETICS AND MOLECULAR RESEARCH

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses

(2011) P. Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Using genetic mapping and genomics approaches in understanding and improving drought tolerance in pearl millet

(2010) R. S. Yadav et al.   JOURNAL OF EXPERIMENTAL BOTANY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Integrating Phylogeny into Studies of C4 Variation in the Grasses

(2009) P.-A. Christin et al.   PLANT PHYSIOLOGY

Foxtail Millet: A Sequence-Driven Grass Model System

(2009) A. N. Doust et al.   PLANT PHYSIOLOGY

Chemoenzymatic syntheses of prenylated aromatic small molecules using Streptomyces prenyltransferases with relaxed substrate specificities

(2008) Takuto Kumano et al.   BIOORGANIC & MEDICINAL CHEMISTRY

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH