In cell and molecular biology, metabolism is the only system that can be fully simulated at
genome scale. Metabolic systems biology offers powerful abstraction tools to simulate all …

Shifting from chemical to biotechnological processes is one of the cornerstones of 21st
century industry. The production of a great range of chemicals via biotechnological means is …

Highlights•Computational tools identify new biological routes to chemicals.•Genome-scale
models suggest genetic engineering strategies to improve production.•Methods that …

Molecular communication is a new paradigm for nanomachines to exchange information, by
utilizing biological mechanism and/or components to transfer information (eg, molecular …

More than a decade ago, the first genome-scale metabolic models for two of the most
relevant microbes for biotechnology applications, Escherichia coli and Saccaromyces …

Production of chemicals in microorganisms is no longer restricted to products arising from
native metabolic potential. In this review, we highlight the evolution of metabolic engineering …

The concept of minimal cut sets (MCS) provides a flexible framework for analyzing
properties of metabolic networks and for computing metabolic intervention strategies. In …

Bacterial phenotypic traits and lifestyles in response to diverse environmental conditions
depend on changes in the internal molecular environment. However, predicting bacterial …

Metabolic modelling has entered a mature phase with dozens of methods and software
implementations available to the practitioner and the theoretician. It is not easy for a …

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 …