Gene regulatory network and its constituent transcription factors that control nitrogen‐deficiency responses in rice

Dynamics of gene expression in single root cells of A. thaliana

(2019) Ken Jean-Baptiste et al.   PLANT CELL

Managing nitrogen to restore water quality in China

(2019) ChaoQing Yu et al.   NATURE

Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants

(2019) Yoshiaki Ueda et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling

(2019) Philippa Borrill et al.   PLANT PHYSIOLOGY

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

(2019) Matthew D. Brooks et al.   Nature Communications

Nitrate‐inducible NIGT1 proteins modulate phosphate uptake and starvation signalling via transcriptional regulation of SPX genes

(2019) Yoshiaki Ueda et al.   PLANT JOURNAL

The Defense Phytohormone Signaling Network Enables Rapid, High-Amplitude Transcriptional Reprogramming during Effector-Triggered Immunity

(2018) Akira Mine et al.   PLANT CELL

An SPX-RLI1 Module Regulates Leaf Inclination in Response to Phosphate Availability in Rice

(2018) Wenyuan Ruan et al.   PLANT CELL

Repression of Nitrogen Starvation Responses by Members of the Arabidopsis GARP-Type Transcription Factor NIGT1/HRS1 Subfamily

(2018) Takatoshi Kiba et al.   PLANT CELL

Lack of ACTPK1, an STY kinase, enhances ammonium uptake and use, and promotes growth of rice seedlings under sufficient external ammonium

(2018) Marcel P. Beier et al.   PLANT JOURNAL

Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice

(2018) Asis Shrestha et al.   PLoS One

Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

(2018) Kranthi Varala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis

(2018) Yoshie Maeda et al.   Nature Communications

Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

(2018) Parul Goel et al.   Scientific Reports

A Nitrogen Molecular Sensing System, Comprised of the ALLANTOINASE and UREIDE PERMEASE 1 Genes, Can Be Used to Monitor N Status in Rice

(2018) Dong-Keun Lee et al.   Frontiers in Plant Science

Transcriptional regulation of nitrogen-associated metabolism and growth

(2018) Allison Gaudinier et al.   NATURE

Laser microdissection-based tissue specific transcriptome analyses reveals novel regulatory network of genes involved in heat-induced grain chalk in rice endosperm

(2018) Tsutomu Ishimaru et al.   PLANT AND CELL PHYSIOLOGY

Computational prediction of gene regulatory networks in plant growth and development

(2018) Samiul Haque et al.   CURRENT OPINION IN PLANT BIOLOGY

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

Discovery of nitrate–CPK–NLP signalling in central nutrient–growth networks

(2017) Kun-hsiang Liu et al.   NATURE

Can natural variation in grain P concentrations be exploited in rice breeding to lower fertilizer requirements?

(2017) Fanmiao Wang et al.   PLoS One

Variation in cooking and eating quality traits in Japanese rice germplasm accessions

(2016) Kiyosumi Hori et al.   BREEDING SCIENCE

Performance and Limitations of Phosphate Quantification: Guidelines for Plant Biologists

(2016) Satomi Kanno et al.   PLANT AND CELL PHYSIOLOGY

Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativaL.)

(2016) Lin-Bo Wu et al.   PLANT CELL AND ENVIRONMENT

DSDecode: A Web-Based Tool for Decoding of Sequencing Chromatograms for Genotyping of Targeted Mutations

(2015) Weizhi Liu et al.   Molecular Plant

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies

(2015) Bin Hu et al.   NATURE GENETICS

A systems biology approach identifies new regulators of poplar root development under low nitrogen

(2015) Madhumita Dash et al.   PLANT JOURNAL

Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice

(2015) Masafumi Mikami et al.   PLANT MOLECULAR BIOLOGY

Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice

(2015) Mariana Obertello et al.   PLANT PHYSIOLOGY

Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.)

(2015) Elsa Matthus et al.   THEORETICAL AND APPLIED GENETICS

Gene Networks in Plant Biology: Approaches in Reconstruction and Analysis

(2015) Yupeng Li et al.   TRENDS IN PLANT SCIENCE

AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip

(2015) Anna Medici et al.   Nature Communications

Overexpression of the CC-type glutaredoxin, OsGRX6 affects hormone and nitrogen status in rice plants

(2015) Ashraf El-Kereamy et al.   Frontiers in Plant Science

Metabolic and co-expression network-based analyses associated with nitrate response in rice

(2014) Viktoriya Coneva et al.   BMC GENOMICS

Emergence of a new step towards understanding the molecular mechanisms underlying nitrate-regulated gene expression

(2014) Mineko Konishi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response ofArabidopsis thalianaroots

(2014) José M. Alvarez et al.   PLANT JOURNAL

Nitrogen deprivation promotesPopulusroot growth through global transcriptome reprogramming and activation of hierarchical genetic networks

(2013) Hairong Wei et al.   NEW PHYTOLOGIST

A Nitrate-Inducible GARP Family Gene Encodes an Auto-Repressible Transcriptional Repressor in Rice

(2013) Naoya Sawaki et al.   PLANT AND CELL PHYSIOLOGY

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles

(2013) Youko Oono et al.   PLANT MOLECULAR BIOLOGY

Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots

(2013) E. A. Vidal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis NIN-like transcription factors have a central role in nitrate signalling

(2013) Mineko Konishi et al.   Nature Communications

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

(2013) Chloé Marchive et al.   Nature Communications

Plant Nitrogen Assimilation and Use Efficiency

(2012) Guohua Xu et al.   Annual Review of Plant Biology

Plant stoichiometry at different scales: element concentration patterns reflect environment more than genotype

(2012) Göran I. Ågren et al.   NEW PHYTOLOGIST

RiceFREND: a platform for retrieving coexpressed gene networks in rice

(2012) Yutaka Sato et al.   NUCLEIC ACIDS RESEARCH

Approaches towards nitrogen- and phosphorus-efficient rice

(2012) K. K. Vinod et al.   AoB Plants

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Spatial expression and regulation of rice high-affinity nitrate transporters by nitrogen and carbon status

(2011) Huimin Feng et al.   JOURNAL OF EXPERIMENTAL BOTANY

Rice DUR3 mediates high-affinity urea transport and plays an effective role in improvement of urea acquisition and utilization when expressed in Arabidopsis

(2011) Wei-Hong Wang et al.   NEW PHYTOLOGIST

Rice OsNAR2.1 interacts with OsNRT2.1, OsNRT2.2 and OsNRT2.3a nitrate transporters to provide uptake over high and low concentration ranges

(2011) MING YAN et al.   PLANT CELL AND ENVIRONMENT

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

(2011) Hinako Takehisa et al.   PLANT JOURNAL

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

(2011) Adam N. Famoso et al.   PLoS Genetics

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

(2011) Gabriel Krouk et al.   GENOME BIOLOGY

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions

(2010) Y. Sato et al.   NUCLEIC ACIDS RESEARCH

Photosynthesis, Grain Yield, and Nitrogen Utilization in Rice and Wheat

(2010) A. Makino   PLANT PHYSIOLOGY

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana

(2010) E. A. Vidal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Development of mini core collection of Japanese rice landrace

(2008) Kaworu Ebana et al.   BREEDING SCIENCE

Mutual interaction in network motifs robustly sharpens gene expression in developmental processes

(2008) Shuji Ishihara et al.   JOURNAL OF THEORETICAL BIOLOGY

An expression analysis profile for the entire sucrose synthase gene family in rice

(2008) Tatsuro Hirose et al.   PLANT SCIENCE

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

(2008) R. A. Gutierrez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA