Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures

Noise and Information Transmission in Promoters with Multiple Internal States

(2014) Georg Rieckh et al.   BIOPHYSICAL JOURNAL

The future of whole-cell modeling

(2014) Derek N Macklin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Cause and cure of sloppiness in ordinary differential equation models

(2014) Christian Tönsing et al.   PHYSICAL REVIEW E

Regulation of Noise in Gene Expression

(2013) Alvaro Sanchez et al.   Annual Review of Biophysics

Inferring gene networks from discrete expression data

(2013) Lin Zhang et al.   BIOSTATISTICS

Systematic Identification of Signal-Activated Stochastic Gene Regulation

(2013) G. Neuert et al.   SCIENCE

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

(2012) Colm J. Ryan et al.   MOLECULAR CELL

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Interplay between gene expression noise and regulatory network architecture

(2012) Guilhem Chalancon et al.   TRENDS IN GENETICS

Fundamental limits on the suppression of molecular fluctuations

(2010) Ioannis Lestas et al.   NATURE

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators

(2010) N. Bhardwaj et al.   Science Signaling

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

(2009) Raja Jothi et al.   Molecular Systems Biology

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

The evolution of hierarchical gene regulatory networks

(2009) Douglas H. Erwin et al.   NATURE REVIEWS GENETICS

Spectral solutions to stochastic models of gene expression with bursts and regulation

(2009) Andrew Mugler et al.   PHYSICAL REVIEW E

A stochastic spectral analysis of transcriptional regulatory cascades

(2009) A. M. Walczak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS