De Novo Transcriptome Assembly of a Fern, Lygodium japonicum, and a Web Resource Database, Ljtrans DB

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

(2014) H. Sakai et al.   DNA RESEARCH

High-Throughput Transcriptome Analysis of the Leafy Flower Transition of Catharanthus roseus Induced by Peanut Witches’-Broom Phytoplasma Infection

(2014) Li-Yu Daisy Liu et al.   PLANT AND CELL PHYSIOLOGY

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

(2014) Kenlee Nakasugi et al.   PLoS One

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

(2014) F.-W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

(2013) Joshua P Der et al.   BMC GENOMICS

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome

(2013) Yvan Wenger et al.   BMC GENOMICS

Assessing De Novo transcriptome assembly metrics for consistency and utility

(2013) Shawn T O’Neil et al.   BMC GENOMICS

De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

(2013) A. Munoz-Merida et al.   DNA RESEARCH

RAB5 Activation is Required for Multiple Steps in Arabidopsis thaliana Root Development

(2013) Takeshi Inoue et al.   PLANT AND CELL PHYSIOLOGY

CathaCyc, a Metabolic Pathway Database Built from Catharanthus roseus RNA-Seq Data

(2013) Alex Van Moerkercke et al.   PLANT AND CELL PHYSIOLOGY

Glycyrrhiza uralensis Transcriptome Landscape and Study of Phytochemicals

(2013) Jordan A. Ramilowski et al.   PLANT AND CELL PHYSIOLOGY

Analysis of the Alfalfa Root Transcriptome in Response to Salinity Stress

(2013) Olga A. Postnikova et al.   PLANT AND CELL PHYSIOLOGY

RNA-seq analysis identifies potential modulators of gravity response in spores of Ceratopteris (Parkeriaceae): Evidence for modulation by calcium pumps and apyrase activity

(2012) Thomas J. Bushart et al.   AMERICAN JOURNAL OF BOTANY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Whole Genomic Sequencing of RT98 Mitochondria Derived from Oryza rufipogon and Northern Blot Analysis to Uncover a Cytoplasmic Male Sterility-Associated Gene

(2012) Keisuke Igarashi et al.   PLANT AND CELL PHYSIOLOGY

Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research

(2012) Eli Meyer et al.   PLANT JOURNAL

Gene expression associated with apogamy commitment in Ceratopteris richardii

(2012) Angela R. Cordle et al.   SEXUAL PLANT REPRODUCTION

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

(2011) Qiong-Yi Zhao et al.   BMC BIOINFORMATICS

Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds

(2011) Cheng-Ying Shi et al.   BMC GENOMICS

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

Unfurling Fern Biology in the Genomics Age

(2010) Michael S. Barker et al.   BIOSCIENCE

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

(2010) Kazuki Hamada et al.   PLANT AND CELL PHYSIOLOGY

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

(2010) A. S. Chanderbali et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FrameDP: sensitive peptide detection on noisy matured sequences

(2009) J. Gouzy et al.   BIOINFORMATICS

Selaginella and 400 Million Years of Separation

(2008) Jo Ann Banks   Annual Review of Plant Biology

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH