I started to work on yeast as a graduate student and have studied it ever since, with occasional excursions into the filamentous fungi and even Streptomyces bacteria. The yeast genome-sequencing project was initiated in my lab in the mid-1980’s when we started to sequence chromosome III. This turned into a major European Project, which eventually led to the sequencing of the entire yeast genome. I then took up the challenge presented by all the genes of unknown function revealed by the genome sequence, leading the EUROFAN Consortium that pioneered many of the ‘omic and other high-throughput technologies in current use.
My lab is dedicated to unravelling the workings of the yeast cell, using both top-down and bottom-up systems biology strategies. We are alos concerned with developing yeasts as systems to both understand and combat human diseases, including through the use of automated (‘Robot Scientist’ methods in collaboration with Ross King’s group in Aberystwyth).
Finally, we take an interest, at both the bioinformatic and experimental levels, in the evolution of genomes and networks, and are starting to apply this to mammalian systems
Members of the Oliver Laboratory include, top row from left: Jorge Julvez, Yuchong Wang, Giorgio Favrin, Andy Hesketh, Leonardo Mancini, Middle row: Nianshu Zhang, Elizabeth Bilsland, Lu Cao, Midori Harris, Marta Vergnano, Ayca Cankorur Cetinkaya, Duygu Dikicioglu. Front row: Steve Oliver, Yingzhi Tang, Petra Ahari, Ceyda Kasavi.
Identification and analysis of high-flux control (HFC) genes in yeast.
Analysis of the transition to stationary phase in nutrient-starved yeast cells (with Nianshu Zhang).
Bioinformatic analysis of the impact of the whole-genome duplication in the evolutionary history of Saccharomyces yeasts on their regulatory circuitry and the chromosomal distribution of HFC genes.
Development and exploitation of logical and stoichiometric models of yeast metabolism.
Regulatory circuitry and the control of flux in yeast.
Development of statistical techniques for the analysis of high-throughput metabolomic data (with Wolfgang Huber).
Systems analysis of the barriers to the efficient secretion of heterologous proteins by the yeast, Pichia pastoris.
Humanisation of yeast for use as a living test-bed for drug discovery and design using the Robot Scientist.
Development of yeast as a test-bed for the study of the metabolism of parasitic protozoa.
A Systems Biology strategy for understanding the genome-wide control of growth rate and metabolic flux in yeast: BBSRC Research Grant.
A robot scientist for yeast systems biology: BBSRC Research Grant. (With Ross King, Aberystwyth; Douglas Kell, Manchester; Stephen Muggleton, Imperial College.)
Identifying and overcoming protein secretion bottlenecks in yeast and filamentous fungal cell factories: BBSRC BRIC Award.
A Robot Scientist for drug design and chemical genomics: BBSRC Research Grant. (With Ross King, Jem Rowland, and Mike Young, Aberystwyth).
Yeast Systems Biology Network (YSBN)
Eukaryotic unicellular organism biology - systems biology of cell growth and proliferation (UNICELLSYS)
Ciryam P, Lambert-Smith I, Bean D, Freer R, Tartaglia G, Cid F, Saunders D, Wilson M, Oliver SG, Morimoto R, Dobson C, Vendruscolo M, Favrin G, Yerbury JJ (2017) Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. Proc Natl Acad Sci USA (In Press.)
Cankorur-Cetinkaya A, Dias JML, Kludas J, Rousu J, Slater NKH, Oliver SG, Dikicioglu D (2017) CamOptimus: a tool for exploiting complex adaptive evolution to optimise experiments and processes in biotechnology. Microbiology (In Press.)
Vlastaridis P, Papakyriakou A, Chaliotis A, Stratikos E, Oliver SG*, AmoutziasGD* (2017) The pivotal role of protein phosphorylation in the control of yeast central metabolism. G3: Genes, Genomes, Genetics doi:10.1534/g3.116.037218
Vlastaridis P, Kyriakidou P, Chaliotis A, Van de Peer Y, Oliver SG, Amoutzias GD (2017) Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. GigaScience doi:10.1093/gigascience/giw015
CaoL, Tang Y, Quan, Oliver SG, Zhang N (2016) Chronological lifespan in yeast is dependent on the accumulation of storage carbohydrates mediated by Yak1, Mck1 and Rim15 kinases PLoS Genet 12: e1006458.
FidanerIB, Cankorur-CetinkayaA, DikiciogluD, KirdarB, Ali AT, Oliver SG (2016) CLUSTERnGO: A user-defined non-linear modelling platform for two-stage clustering of time-series data. Bioinformatics 32, 388-397.
BilslandE, BeanDM, DevaneyE, OliverSG (2016) Yeast-based high-throughput screens to identify novel compounds active against Brugia malayi. PLoS Neglected Tropical Diseases 10: e000401.
Aubrey W, Riley MC, Young M, King RD, Oliver SG, Clare A (2015) A tool for multiple targeted genome deletions that is precise, scar-free, and suitable for automation. PLoS ONE 10: e0142494.
Quan Z, Cao L, Tang Y, Yan Y, Oliver SG, Zhang N (2015) The yeast GSK-3 homologue Mck1 is a key controller of quiescence entry and chronological lifespan. PLos Genetics 11: e1005282. (17 pages)
DikiciogluD, KırdarB, OliverSG (2015) Biomass composition: the “elephant in the room” of metabolic modelling. Metabolomics 11, 1690-1701.
Binder BJ, Sundstrom JF, Gardner JM, Jiranek V, Oliver SG (2015) Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies. PLoS Comp Biol 11: e1004070. (15 pages)
Williams K, Bilsland E, Sparkes A, Aubrey W, Young M, Soldatova LN, De Grave K, Ramon J, de Clare M, Sirawaraporn W, Oliver SG, King RD (2015) Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases. J Roy Soc Interface 12: 20141289. (9 pages)
ChughM, ScheurerC, SaxS, BilslandE, van SchalkwykDA, WichtKJ, HofmannN, Sharma A, BashyamS, SinghS, OliverSG, EganTJ, MalhotraP, SutherlandCJ, BeckH-P, WittlinS, SpangenbergT, Ding XC (2015) Identification and deconvolution of antimalarial compounds cross-resistance signals using multidrug-resistant Plasmodium falciparum strains. Antimicrob Agents Chemother 59: 1110-1118.
Gene Ontology Forum; PomBase, University of Cambridge (Cambridge, UK): Harris MA, Oliver SG, Rutherford K, Wood V (2015) Nuc Acids Res 43: D1049–D1056.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V (2015) PomBase 2015: Updates to the fission yeast database. Nuc Acids Res 43: D656-D661.
Ben Binder (Adelaide), Kevin Brindle, Jules Griffin (CSBC), Vlad Jiranek (Adelaide), Douglas Kell (Manchester), Ross King (Manchester), Talyan Cemgil (Istanbul), Betul Kirdar (Istanbul), Kathryn Lilley (CSBC), Pedro Mendes (Manchester) Balàzs Papp (Szeged), Nianshu Zhang (CSBC) plus former colleagues in Manchester.