cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

The DNA-binding network of Mycobacterium tuberculosis

(2015) Kyle J. Minch et al.   Nature Communications

A system-level model for the microbial regulatory genome

(2014) A. N. Brooks et al.   Molecular Systems Biology

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis

(2014) Eliza J.R. Peterson et al.   NUCLEIC ACIDS RESEARCH

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

(2013) Sung Ho Yoon et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Molecular mechanisms of system responses to novel stimuli are predictable from public data

(2013) Samuel A. Danziger et al.   NUCLEIC ACIDS RESEARCH

Network portal: a database for storage, analysis and visualization of biological networks

(2013) Serdar Turkarslan et al.   NUCLEIC ACIDS RESEARCH

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

(2012) C. L. Plaisier et al.   GENOME RESEARCH

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior

(2012) S. A. Ament et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Seq analysis in MeV

(2011) E. A. Howe et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling

(2011) C. L. Plaisier et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

(2011) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

A new framework for identifying cis-regulatory motifs in prokaryotes

(2010) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

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

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

(2010) P. S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Detailing regulatory networks through large scale data integration

(2009) C. Huttenhower et al.   BIOINFORMATICS

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

(2009) Tom Michoel et al.   BMC Systems Biology

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

(2009) Yonit Halperin et al.   NUCLEIC ACIDS RESEARCH

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

(2009) Pavel S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey 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

MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders

(2008) Edward Wijaya et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences

(2008) Matthieu Defrance et al.   Nature Protocols

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY