Memory functions reveal structural properties of gene regulatory networks

Approximation and inference methods for stochastic biochemical kinetics—a tutorial review

(2017) David Schnoerr et al.   Journal of Physics A-Mathematical and Theoretical

Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs

(2016) Eva Kutejova et al.   DEVELOPMENTAL CELL

Michaelis-Menten dynamics in protein subnetworks

(2016) Katy J. Rubin et al.   JOURNAL OF CHEMICAL PHYSICS

Morphisms of reaction networks that couple structure to function

(2014) Luca Cardelli   BMC Systems Biology

A theoretical framework for the regulation of Shh morphogen-controlled gene expression

(2014) M. Cohen et al.   DEVELOPMENT

Memory effects in biochemical networks as the natural counterpart of extrinsic noise

(2014) Katy J. Rubin et al.   JOURNAL OF THEORETICAL BIOLOGY

Morphogen interpretation: the transcriptional logic of neural tube patterning

(2013) Michael Cohen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Simplifying biochemical models with intermediate species

(2013) E. Feliu et al.   Journal of the Royal Society Interface

The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions

(2012) Philipp Thomas et al.   BMC Systems Biology

Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

(2012) Nikolaos Balaskas et al.   CELL

Complexity reduction preserving dynamical behavior of biochemical networks

(2012) Mochamad Apri et al.   JOURNAL OF THEORETICAL BIOLOGY

Thermodynamic State Ensemble Models of cis-Regulation

(2012) Marc S. Sherman et al.   PLoS Computational Biology

A method for zooming of nonlinear models of biochemical systems

(2011) Mikael Sunnåker et al.   BMC Systems Biology

Organism-Scale Modeling of Early Drosophila Patterning via Bone Morphogenetic Proteins

(2010) David M. Umulis et al.   DEVELOPMENTAL CELL

Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation

(2010) S. Kondo et al.   SCIENCE

Dynamically consistent reduction of logical regulatory graphs

(2010) Aurélien Naldi et al.   THEORETICAL COMPUTER SCIENCE

Transcription by the numbers redux: experiments and calculations that surprise

(2010) Hernan G. Garcia et al.   TRENDS IN CELL BIOLOGY

Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network

(2008) E. Dessaud et al.   DEVELOPMENT

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY