Generalizing complexity: a fruitful partnership of functional genomics and systems biology

Despite of the astounding complexity of biological systems, the history of biology is marked by attempts to discern generalizable principles. Functional genomics and its ultimate integration with systems biology remain pivotal to enabling advances in experimental technology that provide detailed and comprehensive information about networks of biological interactions. The Functional Genomics and Systems Biology 2011 conference focused on recent, largely unpublished developments in sequencing-based approaches and computational methods, including their application to chromatin and proteome systems biology. Experts at the meeting also discussed advances in translating these findings to the clinic, with the ultimate goal of promoting personalized medicine. Here, we summarize some of the highlights presented at this exciting conference.A relatively simple genome and the availability of powerful methods for their genetic manipulation make yeast models the central paradigm in systems biology. Brenda Andrews (University of Toronto, Canada) presented the latest applications of synthetic genetic array (SGA) technology to proteome localization, allowing quantitative determination of subcellular localizations for the majority of yeast proteins. Published work from the laboratories of Andrews and Charles Boone (University of Toronto, Canada) exploited the SGA method to produce a genome-scale landscape of genetic interactions in Saccharomyces cerevisiae. Integration of this technology with high-content microscopy screening of a green fluorescent protein fusion library allowed construction of abundance localization networks across the yeast proteome, including flux networks of dynamic protein localization changes. Frank Holstege (University Medical Center Utrecht, The Netherlands) emphasized the importance of specificity and redundancy in understanding regulatory processes. Work in his laboratory employed gene expression changes in S. cerevisiae upon single or double deletion of 16