Wisdom of crowds for robust gene network inference

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor–DNA Interactions with Expression Data: An Entropy-Based Approach

(2012) Guy Karlebach et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Inference of the Transcriptional Regulatory Network in Staphylococcus aureus by Integration of Experimental and Genomics-Based Evidence

(2011) D. A. Ravcheev et al.   JOURNAL OF BACTERIOLOGY

Multiple models to capture the variability in biological neurons and networks

(2011) Eve Marder et al.   NATURE NEUROSCIENCE

Statistical inference of the time-varying structure of gene-regulation networks

(2010) Sophie Lèbre et al.   BMC Systems Biology

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

(2010) Kevin Y. Yip et al.   PLoS One

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

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

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

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

(2010) Alex Greenfield et al.   PLoS One

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

Analysis and Computational Dissection of Molecular Signature Multiplicity

(2010) Alexander Statnikov et al.   PLoS Computational Biology

Lessons from the DREAM2 Challenges

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

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

Combining Multiple Results of a Reverse-Engineering Algorithm: Application to the DREAM Five-Gene Network Challenge

(2009) Daniel Marbach et al.   Annals of the New York Academy of Sciences

Systems analysis of cellular networks under uncertainty

(2009) Hans-Michael Kaltenbach et al.   FEBS LETTERS

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

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

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

(2009) Karen Lemmens et al.   GENOME BIOLOGY

SIRENE: supervised inference of regulatory networks

(2008) F. Mordelet et al.   BIOINFORMATICS