The organization, regulation and dynamical responses of biological systems are in many
cases too complex to allow intuitive predictions and require the support of mathematical …

This paper reviews the application of multiobjective optimization in the fields of
bioinformatics and computational biology. A survey of existing work, organized by …

We introduce a computational framework termed OptReg that determines the optimal
reaction activations/inhibitions and eliminations for targeted biochemical production. A …

Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools
that facilitate the analysis of dynamic biological systems. This paper depicts major …

Many optimal control problems are characterized by their multiple performance measures
that are often noncommensurable and competing with each other. The presence of multiple …

We developed a dynamic flux balance model for fed‐batch Saccharomyces cerevisiae
fermentation that couples a detailed steady‐state description of primary carbon metabolism …

Proteins are composed by amino acids, which are created by genes. To understand how
different genes interact to create different proteins, we need to model the gene regulatory …

Motivation: Most previous approaches to model biochemical networks have focused either
on the characterization of a network structure with a number of components or on the …

Background Optimality principles have been used to explain the structure and behavior of
living matter at different levels of organization, from basic phenomena at the molecular level …

In this work we consider Pareto optimality for automated design in synthetic biology. We
present a generalized framework based on a mixed-integer dynamic optimization …