Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

Novel cross-talk within the IKK family controls innate immunity

(2011) Kristopher Clark et al.   BIOCHEMICAL JOURNAL

How to infer gene networks from expression profiles, revisited

(2011) C. A. Penfold et al.   Interface Focus

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction

(2010) Matthew Hansen et al.   Algorithms for Molecular Biology

geWorkbench: an open source platform for integrative genomics

(2010) Aris Floratos et al.   BIOINFORMATICS

Tissue-specific disallowance of housekeeping genes: The other face of cell differentiation

(2010) L. Thorrez et al.   GENOME RESEARCH

Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers

(2010) Y Tamada et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

(2010) K.-K. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Inferring Gene Networks: Dream or Nightmare?

(2009) Alan Scheinine et al.   Annals of the New York Academy of Sciences

NIRest: A Tool for Gene Network and Mode of Action Inference

(2009) Mario Lauria et al.   Annals of the New York Academy of Sciences

Lessons from the DREAM2 Challenges

(2009) Gustavo Stolovitzky et al.   Annals of the New York Academy of Sciences

A roadmap of clustering algorithms: finding a match for a biomedical application

(2009) B. Andreopoulos et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium

(2009) Hyunjin Yoon et al.   PLoS Pathogens

Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia

(2008) Elissa J. Cosgrove et al.   BIOINFORMATICS

Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

(2008) Wei Jiang et al.   BMC Systems Biology

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

Mistranslation of Membrane Proteins and Two-Component System Activation Trigger Antibiotic-Mediated Cell Death

(2008) Michael A. Kohanski et al.   CELL

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

(2008) G. Della Gatta et al.   GENOME RESEARCH

PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes

(2008) Logan Everett et al.   NUCLEIC ACIDS RESEARCH

FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

(2008) A. Pisarev et al.   NUCLEIC ACIDS RESEARCH