Bernhard Palsson, Ph.D.
The sequencing of the first genomes in the 1990s fundamentally changed life sciences. The functional annotation of the ORFs led to the first genome-scale metabolic network reconstructions. Flux-balance analysis of these reconstructions could lead to computed phenotypic states. Thus, the first full genome-scale mechanistic genotype-phenotype relations were established. Genome-scale models (GEMs) became more comprehensive over the next 20 years. GEMs have led to whole cell models to study growth under a given condition in great mechanistic detail. One might characterize this undertaking as a Descartian approach. Its applications should reveal the nature of the growth process and play a role in designing de novo genomes. A massive drop in the cost of DNA sequencing enabled a second line of inquiry. We now have a series of databases with data analytics for the major data types that constitute the basic ‘dogma of molecular biology’ in addition to metabolic features. These half a dozen or so databases are now being made interoperable with each other, as well as with GEMs. Looking at these developments in the context of other technology drivers leads one to the hypothesis that before this decade is up, leading universities will establish Departments of Genome Engineering.