De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

Genomic dissection and expression analysis of stress-responsive genes in C4 panicoid models, Setaria italica and Setaria viridis

(2020) Mehanathan Muthamilarasan et al.   JOURNAL OF BIOTECHNOLOGY

SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus

(2019) Jun Ma et al.   PeerJ

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

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

(2016) Kevin J. Tsai et al.   Scientific Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Molecular basis of ALS- and/or ACCase-inhibitor resistance in shortawn foxtail (Alopecurus aequalis Sobol.)

(2015) Wenwen Xia et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Distribution and analysis of the mechanisms of resistance of barnyardgrass (Echinochloa crus-galli) to imidazolinone and quinclorac herbicides

(2014) F. O. MATZENBACHER et al.   JOURNAL OF AGRICULTURAL SCIENCE

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Resistance to AHAS inhibitor herbicides: current understanding

(2013) Qin Yu et al.   PEST MANAGEMENT SCIENCE

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses

(2012) Charu Lata et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

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

Single nucleotide mutation in the barley acetohydroxy acid synthase (AHAS) gene confers resistance to imidazolinone herbicides

(2011) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Setaria viridis: A Model for C4 Photosynthesis

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Foxtail Millet: A Sequence-Driven Grass Model System

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

Agricultural origins and the isotopic identity of domestication in northern China

(2009) L. Barton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY