Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice

(2012) Yidan Ouyang et al.   BMC GENOMICS

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

(2012) Papapit Ingkasuwan et al.   BMC Systems Biology

Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches

(2012) A. Fukushima et al.   PLANT PHYSIOLOGY

Comparing Statistical Methods for Constructing Large Scale Gene Networks

(2012) Jeffrey D. Allen et al.   PLoS One

Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana

(2011) Cheng-Wei Yao et al.   BMC BIOINFORMATICS

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana

(2011) Ana Pop et al.   BMC Systems Biology

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

(2011) Sohyun Hwang et al.   Nature Protocols

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

(2011) Keiichi Mochida et al.   PLANT AND CELL PHYSIOLOGY

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species

(2011) M. Mutwil et al.   PLANT CELL

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

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

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

(2011) Kevin L. Childs et al.   PLoS One

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

Towards Establishment of a Rice Stress Response Interactome

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

TobEA: an atlas of tobacco gene expression from seed to senescence

(2010) Kieron D Edwards et al.   BMC GENOMICS

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

A Biologically Inspired Measure for Coexpression Analysis

(2010) S Bandyopadhyay et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

CORNET: A User-Friendly Tool for Data Mining and Integration

(2010) S. De Bodt et al.   PLANT PHYSIOLOGY

IsoRankN: spectral methods for global alignment of multiple protein networks

(2009) C.-S. Liao et al.   BIOINFORMATICS

Arabidopsis gene co-expression network and its functional modules

(2009) Linyong Mao et al.   BMC BIOINFORMATICS

Regularized estimation of large-scale gene association networks using graphical Gaussian models

(2009) Nicole Krämer et al.   BMC BIOINFORMATICS

From gene expression to gene regulatory networks in Arabidopsis thaliana

(2009) Chris J Needham et al.   BMC Systems Biology

Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

(2009) Osnat Atias et al.   BMC Systems Biology

A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism

(2009) Jen-hwa Chu et al.   BMC Systems Biology

Coordinations between gene modules control the operation of plant amino acid metabolic networks

(2009) Hadar Less et al.   BMC Systems Biology

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

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

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

ArabidopsisMAPKs: a complex signalling network involved in multiple biological processes

(2008) Jean Colcombet et al.   BIOCHEMICAL JOURNAL

Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler

(2008) Marco Grzegorczyk et al.   BIOINFORMATICS

Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism

(2008) Wieslawa I Mentzen et al.   BMC PLANT BIOLOGY

Gene networks in Arabidopsis thaliana for metabolic and environmental functions

(2008) Shisong Ma et al.   Molecular BioSystems

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

GeneCAT—novel webtools that combine BLAST and co-expression analyses

(2008) Marek Mutwil et al.   NUCLEIC ACIDS RESEARCH

ATTED-II provides coexpressed gene networks for Arabidopsis

(2008) T. Obayashi et al.   NUCLEIC ACIDS RESEARCH

GENE REGULATORY NETWORK RECONSTRUCTION BY BAYESIAN INTEGRATION OF PRIOR KNOWLEDGE AND/OR DIFFERENT EXPERIMENTAL CONDITIONS

(2008) ADRIANO V. WERHLI et al.   Journal of Bioinformatics and Computational Biology

Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’

(2007) Kazuki Saito et al.   TRENDS IN PLANT SCIENCE