Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization

Gel-free/label-free proteomic analysis of root tip of soybean over time under flooding and drought stresses

(2016) Xin Wang et al.   Journal of Proteomics

Reactive Nitrogen Species in Mitochondria and Their Implications in Plant Energy Status and Hypoxic Stress Tolerance

(2016) Kapuganti Jagadis Gupta et al.   Frontiers in Plant Science

Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq

(2016) Wei Chen et al.   Frontiers in Plant Science

Comprehensive analysis of the endoplasmic reticulum stress response in the soybean genome: conserved and plant-specific features

(2015) Priscila Alves Silva et al.   BMC GENOMICS

Daytime soybean transcriptome fluctuations during water deficit stress

(2015) Fabiana Aparecida Rodrigues et al.   BMC GENOMICS

Endoplasmic Reticulum Stress Signaling in Plant Immunity—At the Crossroad of Life and Death

(2015) Camilla Kørner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Plant Mediator complex and its critical functions in transcription regulation

(2015) Yan Yang et al.   Journal of Integrative Plant Biology

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

(2015) Michael V. Mickelbart et al.   NATURE REVIEWS GENETICS

Mediator independently orchestrates multiple steps of preinitiation complex assemblyin vivo

(2015) Fanny Eyboulet et al.   NUCLEIC ACIDS RESEARCH

Soybean DREB1/CBF-type transcription factors function in heat and drought as well as cold stress-responsive gene expression

(2015) Satoshi Kidokoro et al.   PLANT JOURNAL

The Arabidopsis Mediator Complex Subunit16 Is a Key Component of Basal Resistance against the Necrotrophic Fungal PathogenSclerotinia sclerotiorum

(2015) Chenggang Wang et al.   PLANT PHYSIOLOGY

Understanding abiotic stress tolerance mechanisms in soybean: A comparative evaluation of soybean response to drought and flooding stress

(2015) Raymond N. Mutava et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

The bioenergetic costs of a gene

(2015) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression of chickpea CIPK25 enhances root growth and tolerance to dehydration and salt stress in transgenic tobacco

(2015) Mukesh K. Meena et al.   Frontiers in Plant Science

Plant, Animal, and Fungal Micronutrient Queuosine Is Salvaged by Members of the DUF2419 Protein Family

(2014) Rémi Zallot et al.   ACS Chemical Biology

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa

(2014) Eran Elhaik et al.   BMC BIOINFORMATICS

Reference genes for quantitative real-time polymerase chain reaction studies in soybean plants under hypoxic conditions

(2014) T.J. Nakayama et al.   GENETICS AND MOLECULAR RESEARCH

Genome-Wide Association of Mediator and RNA Polymerase II in Wild-Type and Mediator Mutant Yeast

(2014) Emily Paul et al.   MOLECULAR AND CELLULAR BIOLOGY

Plant perception of β-aminobutyric acid is mediated by an aspartyl-tRNA synthetase

(2014) Estrella Luna et al.   Nature Chemical Biology

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

The Molecular Chaperone Binding Protein BiP Prevents Leaf Dehydration-Induced Cellular Homeostasis Disruption

(2014) Humberto H. Carvalho et al.   PLoS One

Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia inArabidopsis

(2014) Reed Sorenson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis

(2014) Sylvain Glémin et al.   TRENDS IN GENETICS

A Nutrient-Driven tRNA Modification Alters Translational Fidelity and Genome-wide Protein Coding across an Animal Genus

(2014) John M. Zaborske et al.   PLOS BIOLOGY

The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat

(2014) Kazuo Nakashima et al.   Frontiers in Plant Science

Methylated nucleosides in tRNA and tRNA methyltransferases

(2014) Hiroyuki Hori   Frontiers in Genetics

Molecular cloning and functional characterization of a novel cotton CBL-interacting protein kinase gene (GhCIPK6) reveals its involvement in multiple abiotic stress tolerance in transgenic plants

(2013) Liangrong He et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Cross-Species Analysis of Genic GC3 Content and DNA Methylation Patterns

(2013) Tatiana Tatarinova et al.   Genome Biology and Evolution

Metabolic and Regulatory Responses in Citrus Rootstocks in Response to Adverse Environmental Conditions

(2013) Rosa Argamasilla et al.   JOURNAL OF PLANT GROWTH REGULATION

Label-Free Quantitative Proteomic Analysis of Abscisic Acid Effect in Early-Stage Soybean under Flooding

(2013) Setsuko Komatsu et al.   JOURNAL OF PROTEOME RESEARCH

Interactions between soybean ABA receptors and type 2C protein phosphatases

(2013) Ge Bai et al.   PLANT MOLECULAR BIOLOGY

Queuosine Biosynthesis Is Required for Sinorhizobium meliloti-Induced Cytoskeletal Modifications on HeLa Cells and Symbiosis with Medicago truncatula

(2013) Marta Marchetti et al.   PLoS One

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of oxygen deficiency on nitrogen assimilation and amino acid metabolism of soybean root segments

(2012) Halley Caixeta Oliveira et al.   AMINO ACIDS

Identification and expression analysis of the Glycine max CYP707A gene family in response to drought and salt stresses

(2012) Yan Zheng et al.   ANNALS OF BOTANY

Co-transcriptional regulation of alternative pre-mRNA splicing

(2012) Sanjeev Shukla et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A Role for tRNA Modifications in Genome Structure and Codon Usage

(2012) Eva Maria Novoa et al.   CELL

Mapping of Quantitative Trait Loci Associated with Resistance to and Flooding Tolerance in Soybean

(2012) V. T. Nguyen et al.   CROP SCIENCE

Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries

(2012) Alessandro Vannini et al.   MOLECULAR CELL

The Mediator subunit SFR6/MED16 controls defence gene expression mediated by salicylic acid and jasmonate responsive pathways

(2012) Deepthi L. Wathugala et al.   NEW PHYTOLOGIST

Pivotal role of the AREB/ABF-SnRK2 pathway in ABRE-mediated transcription in response to osmotic stress in plants

(2012) Yasunari Fujita et al.   PHYSIOLOGIA PLANTARUM

TheArabidopsisMediator Complex Subunit16 Positively Regulates Salicylate-Mediated Systemic Acquired Resistance and Jasmonate/Ethylene-Induced Defense Pathways

(2012) Xudong Zhang et al.   PLANT CELL

Waterproofing Crops: Effective Flooding Survival Strategies

(2012) J. Bailey-Serres et al.   PLANT PHYSIOLOGY

GmDREB2A;2, a Canonical DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN2-Type Transcription Factor in Soybean, Is Posttranslationally Regulated and Mediates Dehydration-Responsive Element-Dependent Gene Expression

(2012) J. Mizoi et al.   PLANT PHYSIOLOGY

Making sense of low oxygen sensing

(2012) Julia Bailey-Serres et al.   TRENDS IN PLANT SCIENCE

Transfer RNA modifications: nature's combinatorial chemistry playground

(2012) Jane E. Jackman et al.   Wiley Interdisciplinary Reviews-RNA

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Identification of Cis-Acting Promoter Elements in Cold- and Dehydration-Induced Transcriptional Pathways in Arabidopsis, Rice, and Soybean

(2011) K. Maruyama et al.   DNA RESEARCH

The role of Mediator in small and long noncoding RNA production inArabidopsis thaliana

(2011) Yun Ju Kim et al.   EMBO JOURNAL

Knockdown of SAMS genes encoding S-adenosyl-l-methionine synthetases causes methylation alterations of DNAs and histones and leads to late flowering in rice

(2011) Wenxuan Li et al.   JOURNAL OF PLANT PHYSIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings

(2011) Yohei Nanjo et al.   PLANT MOLECULAR BIOLOGY

The Binding Protein BiP Attenuates Stress-Induced Cell Death in Soybean via Modulation of the N-Rich Protein-Mediated Signaling Pathway

(2011) P. A. A. Reis et al.   PLANT PHYSIOLOGY

Insights into Hypoxic Systemic Responses Based on Analyses of Transcriptional Regulation in Arabidopsis

(2011) Fu-Chiun Hsu et al.   PLoS One

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

FIBRILLIN4 Is Required for Plastoglobule Development and Stress Resistance in Apple and Arabidopsis

(2010) D. K. Singh et al.   PLANT PHYSIOLOGY

Glycolysis and the Tricarboxylic Acid Cycle Are Linked by Alanine Aminotransferase during Hypoxia Induced by Waterlogging of Lotus japonicus

(2010) M. Rocha et al.   PLANT PHYSIOLOGY

The TATA box regulates TATA-binding protein (TBP) dynamics in vivo

(2010) Laszlo Tora et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

A Comprehensive Analysis of the Soybean Genes and Proteins Expressed under Flooding Stress using Transcriptome and Proteome Techniques

(2009) Setsuko Komatsu et al.   JOURNAL OF PROTEOME RESEARCH

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

(2009) Yoko Hattori et al.   NATURE

Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome

(2009) Folkert J van Werven et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays

(2009) Andrew J. Bonham et al.   NUCLEIC ACIDS RESEARCH

Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants

(2008) Joost T. van Dongen et al.   ANNALS OF BOTANY

Flooding Stress: Acclimations and Genetic Diversity

(2008) J. Bailey-Serres et al.   Annual Review of Plant Biology

The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

(2008) Felipe F Aceituno et al.   BMC GENOMICS

Hormonal Modulation of Citrus Responses to Flooding

(2008) Vicent Arbona et al.   JOURNAL OF PLANT GROWTH REGULATION

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation inArabidopsis thaliana

(2008) Cristina Branco-Price et al.   PLANT JOURNAL

Identification of SFR6, a key component in cold acclimation acting post-translationally on CBF function

(2008) Heather Knight et al.   PLANT JOURNAL

Differential Response of Gray Poplar Leaves and Roots Underpins Stress Adaptation during Hypoxia

(2008) J. Kreuzwieser et al.   PLANT PHYSIOLOGY

Rapidly regulated genes are intron poor

(2008) Daniel C. Jeffares et al.   TRENDS IN GENETICS