RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions

Growth Platform-Dependent and -Independent Phenotypic and Metabolic Responses of Arabidopsis and Its Halophytic Relative, Eutrema salsugineum, to Salt Stress

(2013) Y. Kazachkova et al.   PLANT PHYSIOLOGY

Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity

(2012) David R Guevara et al.   BMC PLANT BIOLOGY

Comparison of freezing tolerance, compatible solutes and polyamines in geographically diverse collections of Thellungiella sp. and Arabidopsis thaliana accessions

(2012) Yang Lee et al.   BMC PLANT BIOLOGY

Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components

(2012) Yogesh Mishra et al.   BMC PLANT BIOLOGY

Improving yield by exploiting mechanisms underlying natural variation of photosynthesis

(2012) Tracy Lawson et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

Water deficit and growth. Co-ordinating processes without an orchestrator?

(2011) François Tardieu et al.   CURRENT OPINION IN PLANT BIOLOGY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

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

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

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

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Natural Variation in Arabidopsis: From Molecular Genetics to Ecological Genomics

(2011) D. Weigel   PLANT PHYSIOLOGY

Pleiotropy, plasticity, and the evolution of plant abiotic stress tolerance

(2010) David L. Des Marais et al.   Annals of the New York Academy of Sciences

Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex

(2010) Lianwei Peng et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

The Importance of Energy Balance in Improving Photosynthetic Productivity

(2010) D. M. Kramer et al.   PLANT PHYSIOLOGY

The Scale of Population Structure in Arabidopsis thaliana

(2010) Alexander Platt et al.   PLoS Genetics

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Learning from Evolution: Thellungiella Generates New Knowledge on Essential and Critical Components of Abiotic Stress Tolerance in Plants

(2009) Anna Amtmann   Molecular Plant

PRGdb: a bioinformatics platform for plant resistance gene analysis

(2009) Walter Sanseverino et al.   NUCLEIC ACIDS RESEARCH

Loss of Halophytism by Interference with SOS1 Expression

(2009) D.-H. Oh et al.   PLANT PHYSIOLOGY

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

(2008) G. Zeller et al.   GENOME RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH