High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome

Gene set by de novo assembly of Perilla species and expression profiling between P. frutescens (L.) var. frutescens and var. crispa

(2015) Wei Tong et al.   GENE

Essential oils of green and red Perilla frutescens as potential sources of compounds for mosquito management

(2015) Nurhayat Tabanca et al.   INDUSTRIAL CROPS AND PRODUCTS

A network perspective on nitrogen metabolism from model to crop plants using integrated ‘omics’ approaches

(2014) Atsushi Fukushima et al.   JOURNAL OF EXPERIMENTAL BOTANY

Analysis of expressed sequence tags from a normalized cDNA library of perilla (Perilla frutescens)

(2014) Sang-Choon Lee et al.   JOURNAL OF PLANT BIOLOGY

A flavonoid 3-O-glucoside:2″-O-glucosyltransferase responsible for terminal modification of pollen-specific flavonols inArabidopsis thaliana

(2014) Keiko Yonekura-Sakakibara et al.   PLANT JOURNAL

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence

(2013) Elsa Góngora-Castillo et al.   NATURAL PRODUCT REPORTS

DDBJ progress report: a new submission system for leading to a correct annotation

(2013) Takehide Kosuge et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity

(2013) Kazuki Saito et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Genetic analysis of the metabolome exemplified using a rice population

(2013) L. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis

(2012) Fumio Matsuda et al.   PLANT JOURNAL

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

(2012) Elsa Góngora-Castillo et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway

(2011) Imène Hichri et al.   JOURNAL OF EXPERIMENTAL BOTANY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana

(2011) Keiko Yonekura-Sakakibara et al.   PLANT JOURNAL

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

Abiotic and Biotic Stresses and Changes in the Lignin Content and Composition in Plants

(2010) Jullyana Cristina Magalhães Silva Moura et al.   Journal of Integrative Plant Biology

A candidate cDNA clone for (−)-limonene-7-hydroxylase from Perilla frutescens

(2010) Christopher J.D. Mau et al.   PHYTOCHEMISTRY

Evolutionary and comparative analysis of MYB and bHLH plant transcription factors

(2010) Antje Feller et al.   PLANT JOURNAL

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Monoterpene and sesquiterpene synthases and the origin of terpene skeletal diversity in plants

(2009) Jörg Degenhardt et al.   PHYTOCHEMISTRY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes

(2008) Mami Yamazaki et al.   FEBS Journal

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene-Metabolite Correlations in Arabidopsis

(2008) K. Yonekura-Sakakibara et al.   PLANT CELL