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

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

(2010) Kevin Y. Yip et al.   PLoS One

DREAM3: Network Inference Using Dynamic Context Likelihood of Relatedness and the Inferelator

(2010) Aviv Madar et al.   PLoS One

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

(2010) Robert J. Prill 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

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

Benchmarking regulatory network reconstruction with GRENDEL

(2009) B. C. Haynes et al.   BIOINFORMATICS

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data

(2009) Paul D. W. Kirk et al.   BIOINFORMATICS

Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling

(2009) Johanna Mazur et al.   BMC BIOINFORMATICS

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives

(2009) Feng He et al.   JOURNAL OF BIOTECHNOLOGY

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

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

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

Learning biological networks: from modules to dynamics

(2008) Richard Bonneau   Nature Chemical Biology