Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

Overexpression of the OsERF71 Transcription Factor Alters Rice Root Structure and Drought Resistance

(2016) Dong-Keun Lee et al.   PLANT PHYSIOLOGY

Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage

(2015) Boon Huat Cheah et al.   BMC GENOMICS

Pathway and network analysis of cancer genomes

(2015)   NATURE METHODS

Transcriptional regulation of drought response: a tortuous network of transcriptional factors

(2015) Dhriti Singh et al.   Frontiers in Plant Science

Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis

(2014) Sun-Goo Hwang et al.   GENE

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

(2014) Scott C. Stelpflug et al.   GENETICS

OsWRKY42 Represses OsMT1d and Induces Reactive Oxygen Species and Leaf Senescence in Rice

(2014) Muho Han et al.   MOLECULES AND CELLS

Machine Learning-Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis

(2014) C. Ma et al.   PLANT CELL

Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress

(2014) Madana M. R. Ambavaram et al.   Nature Communications

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

The integrative expression and co-expression analysis of the AGO gene family in rice

(2013) Yang Yang et al.   GENE

Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses

(2013) Søren Lindemose et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics

(2013) Hiroaki Sakai et al.   PLANT AND CELL PHYSIOLOGY

Impacts of acute ozone stress on superoxide dismutase (SOD) expression and reactive oxygen species (ROS) formation in rice leaves

(2013) Yoshiaki Ueda et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Genome-Wide Identification, Phylogenetic and Co-Expression Analysis of OsSET Gene Family in Rice

(2013) Zhanhua Lu et al.   PLoS One

Power calculation for overall hypothesis testing with high-dimensional commensurate outcomes

(2013) Yueh-Yun Chi et al.   STATISTICS IN MEDICINE

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference

(2012) Xiujun Zhang et al.   BIOINFORMATICS

High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice

(2012) Blanca E Barrera-Figueroa et al.   BMC PLANT BIOLOGY

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

(2012) A. Gitter et al.   GENOME RESEARCH

The C2H2-type Zinc Finger Protein ZFP182 is Involved in Abscisic Acid-Induced Antioxidant Defense in RiceF

(2012) Hong Zhang et al.   Journal of Integrative Plant Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

(2012) Lida Zhang et al.   PLoS One

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of WRKY transcription factors in plant abiotic stresses

(2011) Ligang Chen et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

AP2/ERF family transcription factors in plant abiotic stress responses

(2011) Junya Mizoi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

NAC transcription factors in plant abiotic stress responses

(2011) Kazuo Nakashima et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Strategies for aggregating gene expression data: The collapseRows R function

(2011) Jeremy A Miller et al.   BMC BIOINFORMATICS

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments

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

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

An Omics Approach to Understand the Plant Abiotic Stress

(2011) Mousumi Debnath et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

(2011) S. P. Ficklin et al.   PLANT PHYSIOLOGY

Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress

(2011) Shi-Yong Song et al.   PLANTA

Genetic dissection of the biotic stress response using a genome-scale gene network for rice

(2011) I. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

(2010) Liguo Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Progress studies of drought-responsive genes in rice

(2010) Toto Hadiarto et al.   PLANT CELL REPORTS

OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice

(2010) Ju-Seok Seo et al.   PLANT JOURNAL

Characterization of the  -Carotene Hydroxylase Gene DSM2 Conferring Drought and Oxidative Stress Resistance by Increasing Xanthophylls and Abscisic Acid Synthesis in Rice

(2010) H. Du et al.   PLANT PHYSIOLOGY

Root-Specific Expression of OsNAC10 Improves Drought Tolerance and Grain Yield in Rice under Field Drought Conditions

(2010) J. S. Jeong et al.   PLANT PHYSIOLOGY

Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants

(2010) Sarvajeet Singh Gill et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Functional analysis of six drought-inducible promoters in transgenic rice plants throughout all stages of plant growth

(2010) Nari Yi et al.   PLANTA

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One

Analysis and Computational Dissection of Molecular Signature Multiplicity

(2010) Alexander Statnikov et al.   PLoS Computational Biology

Overexpression of a NAC transcription factor enhances rice drought and salt tolerance

(2009) Xingnan Zheng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control

(2009) X.-Y. Huang et al.   GENES & DEVELOPMENT

Analysis of Gene Sets Based on the Underlying Regulatory Network

(2009) Ali Shojaie et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Characterization of Glossy1-homologous genes in rice involved in leaf wax accumulation and drought resistance

(2009) Mohammad Asadul Islam et al.   PLANT MOLECULAR BIOLOGY

A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

(2009) Sung Don Lim et al.   PLANT MOLECULAR BIOLOGY

Overexpression of the Transcription Factor AP37 in Rice Improves Grain Yield under Drought Conditions

(2009) S.-J. Oh et al.   PLANT PHYSIOLOGY

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Identification of drought-responsive genes in roots of upland rice (Oryza sativa L)

(2008) Aline R Rabello et al.   BMC GENOMICS

Over-expression of the stress-induced OsWRKY45 enhances disease resistance and drought tolerance in Arabidopsis

(2008) Y QIU et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Overexpression of a TFIIIA-type zinc finger protein geneZFP252enhances drought and salt tolerance in rice (Oryza sativaL.)

(2008) Dong-Qing Xu et al.   FEBS LETTERS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice

(2008) Yujie Fang et al.   MOLECULAR GENETICS AND GENOMICS

Expression profiling of rice cultivars differing in their tolerance to long-term drought stress

(2008) Thomas Degenkolbe et al.   PLANT MOLECULAR BIOLOGY

Overexpression of a rice OsDREB1F gene increases salt, drought, and low temperature tolerance in both Arabidopsis and rice

(2008) Qiuyun Wang et al.   PLANT MOLECULAR BIOLOGY

Overexpression of the trehalose-6-phosphate phosphatase gene OsTPP1 confers stress tolerance in rice and results in the activation of stress responsive genes

(2008) Liang-Fa Ge et al.   PLANTA