In silico biotechnology. Era of reconstruction and interrogation.

Abstract

Bernhard Palsson is a Professor of Bioengineering and Adjunct Professor of Medicine at the University of California, San Diego. His current research focuses on: the reconstruction of genome-scale networks of cellular metabolism, transcriptional regulation and cellular signaling; the development of in silico modeling procedures, including the constraint-based modeling philosophy and approach that can be applied to genome-scale reconstructions; and experimental tests of predictions of microorganism phenotypes, including changes in DNA sequence, gene expression and growth rates. He is the founder and co-founder of several companies, including Genomatica, a company that is focused on in silico biology. Suddenly we hear about systems biology everywhere, but what is it? With the increased popularity of this subject there are many different definitions floating around. There seems to be a consensus building around a definition that is comprised of four principal factors: the enumeration of network components, the reconstruction of networks, the mathematical representation of networks and their mathematical interrogation to assess their properties, and experiments to verify or refute computational predictions. The process is seen as iterative [1,2]. Although systems analysis in biology is not new (e.g. pharmacokinetics has been in use since the early 1970s), the emergence of systems biology signifies a new level of detail and of scale of complexity in the analysis of living systems. Systems biology may be viewed as genome-scale science that is enabled by the development of highthroughput technologies.