Large scale gene regulatory network inference with a multi-level strategy

Assessment of Network Inference Methods: How to Cope with an Underdetermined Problem

(2014) Caroline Siegenthaler et al.   PLoS One

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms

(2014) Joeri Ruyssinck et al.   PLoS One

ENNET: inferring large gene regulatory networks from expression data using gradient boosting

(2013) Janusz Sławek et al.   BMC Systems Biology

Gene selection with guided regularized random forest

(2013) Houtao Deng et al.   PATTERN RECOGNITION

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

(2012) Anne-Claire Haury et al.   BMC Systems Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Gene Regulatory Network Inference from Multifactorial Perturbation Data Using both Regression and Correlation Analyses

(2012) Jie Xiong et al.   PLoS One

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

(2011) Thomas Schaffter et al.   BIOINFORMATICS

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge

(2010) Patricia Menéndez 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

Lessons from the DREAM2 Challenges

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

Regularized estimation of large-scale gene association networks using graphical Gaussian models

(2009) Nicole Krämer et al.   BMC BIOINFORMATICS

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

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

Comparing different ODE modelling approaches for gene regulatory networks

(2009) A. Polynikis et al.   JOURNAL OF THEORETICAL BIOLOGY

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria

(2008) Wentao Zhao et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics