Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

Linked read technology for assembling large complex and polyploid genomes

(2018) Alina Ott et al.   BMC GENOMICS

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

(2017) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The draft genome of tropical fruit durian (Durio zibethinus)

(2017) Bin Tean Teh et al.   NATURE GENETICS

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

(2016) Hong Yue et al.   BMC GENOMICS

Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.)

(2016) Santosh G. Rajput et al.   MOLECULAR BREEDING

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

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

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

(2016) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Reticulate evolution in Panicum (Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum

(2014) H. V. Hunt et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

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

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

New and continuing developments at PROSITE

(2012) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia

(2011) HARRIET V. HUNT et al.   MOLECULAR ECOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Chromosome Organization and Dynamics during Interphase, Mitosis, and Meiosis in Plants

(2011) C.-L. Tiang et al.   PLANT PHYSIOLOGY

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

A Phylogeny of Setaria (Poaceae, Panicoideae, Paniceae) and Related Genera Based on the Chloroplast Gene ndhF

(2009) Elizabeth A. Kellogg et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

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

Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago

(2009) H. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The polychromatic Helitron landscape of the maize genome

(2009) C. Du et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS