Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships

(2010) Junhee Seok et al.   BMC BIOINFORMATICS

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis

(2010) Christoph Kaleta et al.   BMC Systems Biology

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

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

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

From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis

(2010) Andrea Pinna et al.   PLoS One

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

(2010) Alex Greenfield et al.   PLoS One

Inference of Regulatory Gene Interactions from Expression Data Using Three-Way Mutual Information

(2009) John Watkinson et al.   Annals of the New York Academy of Sciences

Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data

(2008) C. Chang et al.   BIOINFORMATICS

Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities

(2008) P. Gao et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

EcoCyc: A comprehensive view of Escherichia coli biology

(2008) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH