Comparative transcriptomics of rice plants under cold, iron, and salt stresses

Differential expression of photosynthesis-related genes and quantification of gas exchange in rice plants under abiotic stress

(2016) Marcelo Nogueira do Amaral et al.   ACTA PHYSIOLOGIAE PLANTARUM

Drought stress tolerance strategies revealed by RNA-Seq in two sorghum genotypes with contrasting WUE

(2016) Alessandra Fracasso et al.   BMC PLANT BIOLOGY

Angiotensin-converting enzyme gene I/D polymorphism in Pakistani systemic lupus erythematosus patients

(2016) N Hussain et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress

(2015) Ratan Chopra et al.   BMC GENOMICS

Transcriptome-based discovery of AP2/ERF transcription factors related to temperature stress in tea plant (Camellia sinensis)

(2015) Zhi-Jun Wu et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions

(2014) Yuhya Wakasa et al.   BMC PLANT BIOLOGY

C2H2 type of zinc finger transcription factors in foxtail millet define response to abiotic stresses

(2014) Mehanathan Muthamilarasan et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

(2014) Chunxiu Shen et al.   JOURNAL OF PLANT BIOLOGY

Transcriptome analysis of salinity responsiveness in contrasting genotypes of finger millet (Eleusine coracana L.) through RNA-sequencing

(2014) Hifzur Rahman et al.   PLANT MOLECULAR BIOLOGY

Genome-Wide Transcriptome Analysis Reveals that Cadmium Stress Signaling Controls the Expression of Genes in Drought Stress Signal Pathways in Rice

(2014) Youko Oono et al.   PLoS One

A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes

(2013) Neelam Soda et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Maintaining elevated Fe2+ concentration in solution culture for the development of a rapid and repeatable screening technique for iron toxicity tolerance in rice (Oryza sativa L.)

(2013) Venus Elec et al.   PLANT AND SOIL

Progress and challenges for abiotic stress proteomics of crop plants

(2013) Bronwyn J. Barkla et al.   PROTEOMICS

Effects of abiotic stress on plants: a systems biology perspective

(2012) Grant R Cramer et al.   BMC PLANT BIOLOGY

Iron homeostasis and fortification in rice

(2012) Sichul Lee et al.   JOURNAL OF PLANT BIOLOGY

Cloning and characterization of the stress-induced bZIP gene ZmbZIP60 from maize

(2012) Bo Wang et al.   MOLECULAR BIOLOGY REPORTS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Combined transcriptomic and physiological approaches reveal strong differences between short- and long-term response of rice (Oryza sativa) to iron toxicity

(2012) MURIEL QUINET et al.   PLANT CELL AND ENVIRONMENT

Vacuolar membrane transporters OsVIT1 and OsVIT2 modulate iron translocation between flag leaves and seeds in rice

(2012) Yu Zhang et al.   PLANT JOURNAL

Exploring plant transcriptomes using ultra high-throughput sequencing

(2011) L. Wang et al.   Briefings in Functional Genomics

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

mRNA-Seq Reveals a Comprehensive Transcriptome Profile of Rice under Phosphate Stress

(2011) Youko Oono et al.   Rice

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)

(2010) Hiroshi Mizuno et al.   BMC GENOMICS

Effects of root anatomy and Fe plaque on arsenic uptake by rice seedlings grown in solution culture

(2010) Dan Deng et al.   ENVIRONMENTAL POLLUTION

Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice

(2010) S.-J. Sun et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cold stress tolerance mechanisms in plants. A review

(2009) Sudesh Kumar Yadav   Agronomy for Sustainable Development

New insights into ferritin synthesis and function highlight a link between iron homeostasis and oxidative stress in plants

(2009) Jean-Francois Briat et al.   ANNALS OF BOTANY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

Distinct physiological responses of two rice cultivars subjected to iron toxicity under field conditions

(2008) R.J. Stein et al.   ANNALS OF APPLIED BIOLOGY

Mechanisms of Salinity Tolerance

(2008) Rana Munns et al.   Annual Review of Plant Biology

Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L.

(2008) Sumita Kumari et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Potassium transport and plant salt tolerance

(2008) Sergey Shabala et al.   PHYSIOLOGIA PLANTARUM

Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range

(2008) BJÖRN USADEL et al.   PLANT CELL AND ENVIRONMENT