We aim to gain an integrated view of how a simple eukaryotic cell, the baker’s yeast, Saccharomyces cerevisiae, works. Yeast was the first eukaryote to have its genome completely sequenced and we are determining how its 6,000 genes interact to allow it to grow, divide, develop, and respond to environmental changes . This integrative view of yeast should provide an important 'navigational aid' to guide our studies of the more complex genomes of humans, crop plants, and farm animals.
Our work involves both experiments with living cells and the construction of mathematical models of pathways and networks for use in computer simulations that generate predictions that we can test in vivo. These predictions include how genes interact in metabolism, which is essential to engineering novel pathways in yeast using synthetic biology. They also enable us to automate the process of generating hypotheses, designing and executing experiments, and evaluating data. This “Robot Scientist” approach enabled the discovery of novel scientific knowledge by a machine, without human intervention.
The models and experimental systems we use with yeast sometimes lead us in unexpected directions, such as predicting the impact of gene copy number variation in cancer, constructing network models to identify genes important in Alzheimer’s Disease, or using yeast ‘surrogates’ to screen for drugs against parasitic diseases .
Lab members: Prachi Balyan, Dan Bean, Elizabeth Bilsland, Ayca Cankorur Cetinkaya, Lu Cao, Joao Dias, Duygu Dikicioglu, Giorgio Favrin, Petra Ghassemi Ahari, Midori Harris, Andy Hesketh, Kim Rutherford, Trevor Sawyer, Marta Vergnano, Yuchong Wang, Valerie Wood, Nianshu Zhang
1. Szappanos B, KovácsK….OliverSG, PálC, Papp B (2011) An integrated approach to elucidate the organization principles of genetic interaction networks in yeast metabolism. Nature Genetics 43, 656-662.
2. de Clare M, Pir P, Oliver SG (2011) Haploinsufficiency and the sex chromosomes from yeasts to humans. BMC Biology 9: 15 (11 pages).
3. Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG (2010) Nutrient control of eukaryote cell growth: a systems biology study in yeast. BMC Biology 8: 68 (20 pages).
4. KingRD, Rowland J, Oliver SG, YoungM,AubreyW, ByrneE, LiakataM, MarkhamM, PirP, Soldatova LN, SparkesA, WhelanKE, Clare A (2009) The automation of science. Science 324, 85-89.