Network Modeling to Understand Plant Immunity

MAPK Cascades in Plant Disease Resistance Signaling

(2013) Xiangzong Meng et al.   Annual Review of Phytopathology

Calcium/calmodulin-mediated regulation of plant immunity

(2013) Cécilia Cheval et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

A coherent feedforward loop design principle to sustain robustness of biological networks

(2013) Duc-Hau Le et al.   BIOINFORMATICS

Wigwams: identifying gene modules co-regulated across multiple biological conditions

(2013) Krzysztof Polanski et al.   BIOINFORMATICS

Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to ‘Candidatus Liberibacter asiaticus’ infection

(2013) Zhi-Liang Zheng et al.   BMC GENOMICS

The Mycobacterium tuberculosis regulatory network and hypoxia

(2013) James E. Galagan et al.   NATURE

Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants

(2013) R. Bhosale et al.   PLANT CELL

A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves

(2013) Richard Hickman et al.   PLANT JOURNAL

Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways

(2013) Shisong Ma et al.   PLoS Genetics

Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks

(2012) C. A. Penfold et al.   BIOINFORMATICS

Ubiquitination in NB-LRR-mediated immunity

(2012) Yu Ti Cheng et al.   CURRENT OPINION IN PLANT BIOLOGY

Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane DuringArabidopsisImmune Signaling

(2012) James Mitch Elmore et al.   MOLECULAR & CELLULAR PROTEOMICS

The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops

(2012) Alexandra Pokhilko et al.   Molecular Systems Biology

Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

(2012) Michaël Bekaert et al.   NEW PHYTOLOGIST

Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin

(2012) M. Naseem et al.   PLANT CELL

Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants

(2012) Laura Baxter et al.   PLANT CELL

Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis

(2012) O. Windram et al.   PLANT CELL

Two-Component Elements Mediate Interactions between Cytokinin and Salicylic Acid in Plant Immunity

(2012) Cristiana T. Argueso et al.   PLoS Genetics

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

(2012) Lanay Tierney et al.   Frontiers in Microbiology

Prediction of protein–protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

(2011) Zhi-Gang Li et al.   AMINO ACIDS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions

(2011) G. W. Bassel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network

(2011) M. S. Mukhtar et al.   SCIENCE

How to infer gene networks from expression profiles, revisited

(2011) C. A. Penfold et al.   Interface Focus

Towards Establishment of a Rice Stress Response Interactome

(2011) Young-Su Seo et al.   PLoS Genetics

Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network

(2011) Pengcheng Zhu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

A Genome-Scale Metabolic Model Accurately Predicts Fluxes in Central Carbon Metabolism under Stress Conditions

(2010) Thomas C.R. Williams et al.   PLANT PHYSIOLOGY

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling

(2010) Masanao Sato et al.   PLoS Pathogens

A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

(2010) Sylvie Lalonde   Frontiers in Physiology

Networking by small-molecule hormones in plant immunity

(2009) Corné M J Pieterse et al.   Nature Chemical Biology

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions

(2009) Javier Carrera et al.   GENOME BIOLOGY

Extracting expression modules from perturbational gene expression compendia

(2008) Steven Maere et al.   BMC Systems Biology

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

(2008) S. C. Popescu et al.   GENES & DEVELOPMENT

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans

(2008) Insuk Lee et al.   NATURE GENETICS

Getting to grips with the plant metabolic network

(2007) Lee J. Sweetlove et al.   BIOCHEMICAL JOURNAL