Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

Distinctive phytohormonal and metabolic profiles of Arabidopsis thaliana and Eutrema salsugineum under similar soil drying

(2019) Carla Pinheiro et al.   PLANTA

Twentieth-century hydroclimate changes consistent with human influence

(2019) Kate Marvel et al.   NATURE

Drought resistance is mediated by divergent strategies in closely related Brassicaceae

(2019) Nora Marín‐de la Rosa et al.   NEW PHYTOLOGIST

Prediction of plant lncRNA by ensemble machine learning classifiers

(2018) Caitlin M. A. Simopoulos et al.   BMC GENOMICS

Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum

(2018) Xiao-Juan Wang et al.   MOLECULAR ECOLOGY

Where are the drought tolerant crops? An assessment of more than two decades of plant biotechnology effort in crop improvement

(2018) Michael L. Nuccio et al.   PLANT SCIENCE

Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

(2018) Xinyue Zhao et al.   Nature Communications

Natural antisense transcripts are significantly involved in regulation of drought stress in maize

(2017) Jie Xu et al.   NUCLEIC ACIDS RESEARCH

The E3 Ligase DROUGHT HYPERSENSITIVE Negatively Regulates Cuticular Wax Biosynthesis by Promoting the Degradation of Transcription Factor ROC4 in Rice

(2017) Zhenyu Wang et al.   PLANT CELL

A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance

(2017) Tao Qin et al.   PLANT PHYSIOLOGY

Priming: A promising strategy for crop production in response to future climate

(2017) Xiao WANG et al.   Journal of Integrative Agriculture

Molecular and Evolutionary Mechanisms of Cuticular Wax for Plant Drought Tolerance

(2017) Dawei Xue et al.   Frontiers in Plant Science

Salt stress responses in a geographically diverse collection of Eutrema/Thellungiella spp. accessions

(2016) Yang Ping Lee et al.   FUNCTIONAL PLANT BIOLOGY

Acclimation of the cruciferEutrema salsugineumto phosphate limitation is associated with constitutively high expression of phosphate-starvation genes

(2016) Vera Marjorie Elauria Velasco et al.   PLANT CELL AND ENVIRONMENT

Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress

(2016) Sultana Rasheed et al.   Frontiers in Plant Science

Environmental Stress and Pre-mRNA Splicing

(2015) Peng Cui et al.   Molecular Plant

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Exposure of twoEutrema salsugineum(Thellungiella salsuginea) accessions to water deficits reveals different coping strategies in response to drought

(2015) Mitchell J.R. MacLeod et al.   PHYSIOLOGIA PLANTARUM

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs inArabidopsis thaliana

(2015) John T. Lovell et al.   PLANT CELL

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

(2014) Eli Meyer et al.   BMC GENOMICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Improved tolerance to drought stress after anthesis due to priming before anthesis in wheat (Triticum aestivum L.) var. Vinjett

(2014) Xiao Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novelArabidopsis thalianaabiotic stress genes

(2014) Vanessa Ransbotyn et al.   PLANT BIOTECHNOLOGY JOURNAL

Arabidopsis Cuticular Wax Biosynthesis Is Negatively Regulated by the DEWAX Gene Encoding an AP2/ERF-Type Transcription Factor

(2014) Y. S. Go et al.   PLANT CELL

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

(2013) Marc J Champigny et al.   BMC GENOMICS

Four distinct types of dehydration stress memory genes in Arabidopsis thaliana

(2013) Yong Ding et al.   BMC PLANT BIOLOGY

Leaf cuticular lipids on the Shandong and Yukon ecotypes of saltwater cress,Eutrema salsugineum, and their response to water deficiency and impact on cuticle permeability

(2013) Xiaojing Xu et al.   PHYSIOLOGIA PLANTARUM

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

(2012) Yong Ding et al.   Nature Communications

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

System responses to long-term drought and re-watering of two contrasting alfalfa varieties

(2011) Yun Kang et al.   PLANT JOURNAL

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana

(2010) Reena Narsai et al.   BMC PLANT BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth

(2010) A. Harb et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Galactinol and Raffinose Constitute a Novel Function to Protect Plants from Oxidative Damage

(2008) A. Nishizawa et al.   PLANT PHYSIOLOGY