The coordinated expression of the different genes in an organism is essential to sustain
functionality under the random external perturbations to which the organism might be …

We discuss different mathematical models of gene regulatory networks as relevant to the
onset and development of cancer. After discussion of alternative modelling approaches, we …

The use of modeling to observe and analyze the mechanisms of complex biochemical
network function is becoming an important methodological tool in the systems biology era …

Biological networks, such as gene regulatory networks, possess desirable properties. They
are more robust and controllable than random networks. This motivates the search for …

Living systems comprise interacting biochemical components in very large networks. Given
their high connectivity, biochemical dynamics are surprisingly not chaotic but quite robust to …

Boolean functions can be represented in many ways including logical forms, truth tables,
and polynomials. Additionally, Boolean functions have different canonical representations …

Time-and state-discrete dynamical systems are frequently used to model molecular
networks. This paper provides a collection of mathematical and computational tools for the …

Boolean network models have gained popularity in computational systems biology over the
last dozen years. Many of these networks use canalizing Boolean functions, which has led to …

We introduce the nested canalyzing depth of a function, which measures the extent to which
it retains a nested canalyzing structure. We characterize the structure of functions with a …

Introduction Pseudomonas aeruginosa infections are one of the leading causes of death in
immunocompromised patients with cystic fibrosis, diabetes, and lung diseases such as …