The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization

(2021) Zhaoyuan Wei et al.   Frontiers in Genetics

BlobToolKit - Interactive Quality Assessment of Genome Assemblies

(2020) Richard Challis et al.   G3-Genes Genomes Genetics

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

(2020) Nicholas Toda et al.   Genes

CAFE 5 models variation in evolutionary rates among gene families

(2020) Fábio K Mendes et al.   BIOINFORMATICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity

(2019) Prema S. Karunanithi et al.   Frontiers in Plant Science

ShinyGO: a graphical gene-set enrichment tool for animals and plants

(2019) Steven Xijin Ge et al.   BIOINFORMATICS

Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments

(2018) Guanglong Chen et al.   BMC GENOMICS

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

(2016) Eunyoung Seo et al.   Frontiers in Plant Science

GOplot: an R package for visually combining expression data with functional analysis: Fig. 1.

(2015) Wencke Walter et al.   BIOINFORMATICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Accumulation of terpenoid phytoalexins in maize roots is associated with drought tolerance

(2015) Martha M. Vaughan et al.   PLANT CELL AND ENVIRONMENT

Plant diterpene synthases: exploring modularity and metabolic diversity for bioengineering

(2015) Philipp Zerbe et al.   TRENDS IN BIOTECHNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Biosynthesis, elicitation and roles of monocot terpenoid phytoalexins

(2014) Eric A. Schmelz et al.   PLANT JOURNAL

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

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

Genome sequence of mungbean and insights into evolution within Vigna species

(2014) Yang Jae Kang et al.   Nature Communications

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Overexpression of stress-inducible OsBURP16, theβsubunit of polygalacturonase 1, decreases pectin content and cell adhesion and increases abiotic stress sensitivity in rice

(2013) HUANHUAN LIU et al.   PLANT CELL AND ENVIRONMENT

A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)

(2013) Mukesh Jain et al.   PLANT JOURNAL

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages

(2012) Domingos Cardoso et al.   AMERICAN JOURNAL OF BOTANY

Genome-Enabled Insights into Legume Biology

(2012) Nevin D. Young et al.   Annual Review of Plant Biology

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

(2012) Hai Fang et al.   NUCLEIC ACIDS RESEARCH

The cell wall-associated kinases, WAKs, as pectin receptors

(2012) Bruce D. Kohorn et al.   Frontiers in Plant Science

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Comparative analysis of peanut NBS-LRR gene clusters suggests evolutionary innovation among duplicated domains and erosion of gene microsynteny

(2011) Milind B. Ratnaparkhe et al.   NEW PHYTOLOGIST

The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom

(2011) Feng Chen et al.   PLANT JOURNAL

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

(2011) Y.-L. Guo et al.   PLANT PHYSIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.

(2009) David J Bertioli et al.   BMC GENOMICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The NCBI BioSystems database

(2009) Lewis Y. Geer et al.   NUCLEIC ACIDS RESEARCH

Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling

(2009) YONG-MEI BI et al.   PLANT CELL AND ENVIRONMENT

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster

(2008) E. D. Nagy et al.   GENOME RESEARCH

Recent duplications dominate NBS-encoding gene expansion in two woody species

(2008) Sihai Yang et al.   MOLECULAR GENETICS AND GENOMICS

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Refunctionalization of the ancient rice blast disease resistance genePitby the recruitment of a retrotransposon as a promoter

(2008) Keiko Hayashi et al.   PLANT JOURNAL

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

(2008) Brian J Haas et al.   GENOME BIOLOGY