How to infer gene networks from expression profiles, revisited

High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation

(2011) E. Breeze et al.   PLANT CELL

Discovering transcriptional modules by Bayesian data integration

(2010) Richard S. Savage et al.   BIOINFORMATICS

On reverse engineering of gene interaction networks using time course data with repeated measurements

(2010) E. R. Morrissey et al.   BIOINFORMATICS

Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes

(2010) M. Grzegorczyk et al.   BIOINFORMATICS

A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

(2010) Oliver Stegle et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model

(2010) Alexandra Pokhilko et al.   Molecular Systems Biology

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

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

(2010) Alex Greenfield et al.   PLoS One

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

Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana

(2009) S. J. Kiddle et al.   BIOINFORMATICS

Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics

(2009) Tarmo Äijö et al.   BIOINFORMATICS

Granger causality vs. dynamic Bayesian network inference: a comparative study

(2009) Cunlu Zou et al.   BMC BIOINFORMATICS

R/BHC: fast Bayesian hierarchical clustering for microarray data

(2009) Richard S Savage et al.   BMC BIOINFORMATICS

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

(2009) Daniel Marbach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A MATLAB toolbox for Granger causal connectivity analysis

(2009) Anil K. Seth   JOURNAL OF NEUROSCIENCE METHODS

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Pulsatile Stimulation Determines Timing and Specificity of NF- B-Dependent Transcription

(2009) L. Ashall et al.   SCIENCE

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

(2008) Simon Rogers et al.   BIOINFORMATICS

Reconstruction of transcriptional dynamics from gene reporter data using differential equations

(2008) Bärbel Finkenstädt et al.   BIOINFORMATICS

A Review of Systems Biology Perspective on Genetic Regulatory Networks with Examples

(2008) Don Kulasiri et al.   Current Bioinformatics

Modularity defined

(2008) Herbert M Sauro   Molecular Systems Biology