Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

Draft Sequences of the Radish (Raphanus sativus L.) Genome

(2014) Hiroyasu Kitashiba et al.   DNA RESEARCH

Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula

(2014) D.-H. Oh et al.   PLANT PHYSIOLOGY

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

Development of anArabis alpinagenomic contig sequence data set and application to single nucleotide polymorphisms discovery

(2013) Stéphane Lobréaux et al.   Molecular Ecology Resources

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

(2013) S. Cheng et al.   PLANT CELL

The Reference Genome of the Halophytic Plant Eutrema salsugineum

(2013) Ruolin Yang et al.   Frontiers in Plant Science

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

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

Insights into salt tolerance from the genome ofThellungiella salsuginea

(2012) Hua-Jun Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

(2011) Zhen Li et al.   BMC GENOMICS

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

MicroRNA Gene Evolution inArabidopsis lyrataandArabidopsis thaliana

(2010) Noah Fahlgren et al.   PLANT CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae

(2008) M. A. Lysak et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS