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Gene regulatory networks

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

Vân Anh Huynh-Thu, Alexandre Irrthum, Louis Wehenkel, Pierre Geurts

Adaptive Response of a Gene Network to Environmental Changes by Fitness-Induced Attractor Selection

Akiko Kashiwagi, Itaru Urabe, Kunihiko Kaneko, Tetsuya Yomo

Passing Messages between Biological Networks to Refine Predicted Interactions

Kimberly Glass, Curtis Huttenhower, John Quackenbush, Guo-Cheng Yuan

Comparing Statistical Methods for Constructing Large Scale Gene Networks

Jeffrey D. Allen, Yang Xie, [ ... ], Guanghua Xiao

Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis

Matthieu Vignes, Jimmy Vandel, [ ... ], Simon de Givry

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

Jacob Beal, Ting Lu, Ron Weiss

The PLOS ONE Synthetic Biology Collection: Six Years and Counting

Jean Peccoud, Mark Isalan

MIDER: Network Inference with Mutual Information Distance and Entropy Reduction

Alejandro F. Villaverde, John Ross, Federico Morán, Julio R. Banga

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

Kevin Y. Yip, Roger P. Alexander, Koon-Kiu Yan, Mark Gerstein

ChIP-seq Defined Genome-Wide Map of TGFβ/SMAD4 Targets: Implications with Clinical Outcome of Ovarian Cancer

Brian A. Kennedy, Daniel E. Deatherage, [ ... ], Victor X. Jin

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

Ling-Hong Hung, Daniel Kristiyanto, Sung Bong Lee, Ka Yee Yeung

A Gene Regulatory Network Model for Floral Transition of the Shoot Apex in Maize and Its Dynamic Modeling

Zhanshan Dong, Olga Danilevskaya, [ ... ], Mark Cooper

Network Evolution of Body Plans

Koichi Fujimoto, Shuji Ishihara, Kunihiko Kaneko

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