Detailing regulatory networks through large scale data integration

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

(2009) Yonit Halperin et al.   NUCLEIC ACIDS RESEARCH

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

(2009) Karen Lemmens et al.   GENOME BIOLOGY

Systems Approaches to Identifying Gene Regulatory Networks in Plants

(2008) Terri A. Long et al.   Annual Review of Cell and Developmental Biology

Eukaryotic transcription factor binding sites--modeling and integrative search methods

(2008) S. Hannenhalli   BIOINFORMATICS

Assessing the functional structure of genomic data

(2008) C. Huttenhower et al.   BIOINFORMATICS

The Sleipnir library for computational functional genomics

(2008) C. Huttenhower et al.   BIOINFORMATICS

Let Me Count the Ways: Mechanisms of Gene Regulation by miRNAs and siRNAs

(2008) Ligang Wu et al.   MOLECULAR CELL

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

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

A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast

(2008) Anshul Kundaje et al.   PLoS Computational Biology

Analyzing ChIP-chip Data Using Bioconductor

(2008) Joern Toedling et al.   PLoS Computational Biology

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL