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

Network inference using steady-state data and Goldbeter–koshland kinetics

(2012) Chris J Oates et al.   BIOINFORMATICS

The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops

(2012) Alexandra Pokhilko et al.   Molecular Systems Biology

Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor

(2012) J. M. Gendron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

(2012) W. Huang et al.   SCIENCE

Reconstructing transcription factor activities in hierarchical transcription network motifs

(2011) Andrea Ocone et al.   BIOINFORMATICS

Large-scale learning of combinatorial transcriptional dynamics from gene expression

(2011) H. M. Shahzad Asif et al.   BIOINFORMATICS

Delay in Feedback Repression by Cryptochrome 1 Is Required for Circadian Clock Function

(2011) Maki Ukai-Tadenuma et al.   CELL

A robust two-gene oscillator at the core of Ostreococcus tauri circadian clock

(2011) Pierre-Emmanuel Morant et al.   CHAOS

Circadian rhythms persist without transcription in a eukaryote

(2011) John S. O’Neill et al.   NATURE

Multiple light inputs to a simple clock circuit allow complex biological rhythms

(2011) Carl Troein et al.   PLANT JOURNAL

Learning combinatorial transcriptional dynamics from gene expression data

(2010) Manfred Opper et al.   BIOINFORMATICS

ABC-SysBio--approximate Bayesian computation in Python with GPU support

(2010) J. Liepe et al.   BIOINFORMATICS

Robustness of Circadian Clocks to Daylight Fluctuations: Hints from the Picoeucaryote Ostreococcus tauri

(2010) Quentin Thommen et al.   PLoS Computational Biology

Switching regulatory models of cellular stress response

(2009) Guido Sanguinetti et al.   BIOINFORMATICS

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

(2009) Irene Cantone et al.   CELL