Preface
Ranking Genes by Their Co-expression to Subsets of Pathway Members
Creating Reference Datasets for Systems Biology Applications Using Text Mining
The Condition-Dependent Transcriptional Network in Escherichia coli
Reverse-Engineering Transcriptional Modules from Gene Expression Data
Specification of Spatial Relationships in Directed Graphs of Cell Signaling Networks
Uncovering Metabolic Objectives Pursued by Changes of Enzyme Levels
Modeling of Gene Regulatory Network Dynamics Using Threshold Logic
Global Robustness and Identifiability of Random, Scale-Free, and Small-World Networks
The Five-Gene-Network Data Analysis with Local Causal Discovery Algorithm Using Causal Bayesian Networks
Combining Multiple Results of a Reverse-Engineering Algorithm
Network Inference by Combining Biologically Motivated Regulatory Constraints with Penalized Regression
A Gene Network Simulator to Assess Reverse Engineering Algorithms
A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium
Lessons from the DREAM2 Challenges
DREAM2 Challenge
A Data Integration Framework for Prediction of Transcription Factor Targets
Inferring Direct Regulatory Targets of a Transcription Factor in the DREAM2 Challenge
A Probabilistic Graph-Theoretic Approach to Integrate Multiple Predictions for the Protein–Protein Subnetwork Prediction Challenge
Replaying the Evolutionary Tape
Inferring Gene Networks
NIRest
Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions
Prediction of Pairwise Gene Interaction Using Threshold Logic
Inferring Gene Networks
Inference of Regulatory Gene Interactions from Expression Data Using Three-Way Mutual Information