Combining tree-based and dynamical systems for the inference of gene regulatory networks

Large-scale modeling of condition-specific gene regulatory networks by information integration and inference

(2014) Daniel Christian Ellwanger et al.   NUCLEIC ACIDS RESEARCH

Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics

(2013) Andrea Ocone et al.   BIOINFORMATICS

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

How to infer gene networks from expression profiles, revisited

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

Host Defense against Viral Infection Involves Interferon Mediated Down-Regulation of Sterol Biosynthesis

(2011) Mathieu Blanc et al.   PLOS BIOLOGY

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

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

(2009) Irene Cantone et al.   CELL

Supervised learning with decision tree-based methods in computational and systems biology

(2009) Pierre Geurts et al.   Molecular BioSystems