Biological Networks: The Tinkerer as an Engineer
Can a biologist fix a radio? - Or, what I learned while studying apoptosis
How to read a scientific paper
Modelling biological processes using workflow and Petri Net models
Hybrid Petri Net representation of gene regulatory networks
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post-genomic Era
Prediction of mutant expression patterns using gene circuits
Structure and function of the feed-forward loop network motif
Using Bayesian Networks to Analyze Expression Data
Inferring Subnetworks from Perturbed Expression Profiles
Developing a Logical Model of Yeast Metabolism
Functional genomic hypothesis generation and experimentation by a robot scientist
Abductive Inference of Genetic Networks
A knowledge based approach for representing and reasoning about signaling networks
The Computational Versatility of Proteomic Signaling Networks
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
Modeling transcriptional regulatory networks
Design of gene circuits: lessons from bacteria
Robustness in simple biochemical networks
The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks
Negative Autoregulation Speeds the Response Times of Transcription Networks
Genomic analysis of regulatory network dynamics reveals large topological changes