Stephen G Oliver

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc Evaluation and properties of the budding yeast phosphoproteome
    Grigoris D Amoutzias
    Cambridge Systems Biology Centre and Dept Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Mol Cell Proteomics 11:M111.009555. 2012
  2. pmc Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae
    Michaela de Clare
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Biol 11:24. 2013
  3. pmc Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity
    Sara Holland
    School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Genome Biol 8:R268. 2007
  4. pmc Further developments towards a genome-scale metabolic model of yeast
    Paul D Dobson
    School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
    BMC Syst Biol 4:145. 2010
  5. pmc Data capture in bioinformatics: requirements and experiences with Pedro
    Daniel Jameson
    School of Chemistry, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
    BMC Bioinformatics 9:183. 2008
  6. pmc Information management for high content live cell imaging
    Daniel Jameson
    Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, Manchester, M1 7DN, UK
    BMC Bioinformatics 10:226. 2009
  7. ncbi request reprint Yeast cells with impaired drug resistance accumulate glycerol and glucose
    Duygu Dikicioglu
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
    Mol Biosyst 10:93-102. 2014
  8. pmc Synergistic effects of TOR and proteasome pathways on the yeast transcriptome and cell growth
    Nianshu Zhang
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Open Biol 3:120137. 2013
  9. pmc Nutrient control of eukaryote cell growth: a systems biology study in yeast
    Alex Gutteridge
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
    BMC Biol 8:68. 2010
  10. pmc The genetic control of growth rate: a systems biology study in yeast
    Pinar Pir
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Syst Biol 6:4. 2012

Collaborators

Detail Information

Publications26

  1. pmc Evaluation and properties of the budding yeast phosphoproteome
    Grigoris D Amoutzias
    Cambridge Systems Biology Centre and Dept Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Mol Cell Proteomics 11:M111.009555. 2012
    ..It appears that phosphoproteins constitute the raw material for pathway rewiring and adaptation at various evolutionary rates...
  2. pmc Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae
    Michaela de Clare
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Biol 11:24. 2013
    ..Since haploproficiency under nutrient-sufficient conditions is a novel phenotype, we sought here to characterise a subset of the yeast haploproficient genes which seem particularly relevant to human cancers...
  3. pmc Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity
    Sara Holland
    School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
    Genome Biol 8:R268. 2007
    ..Microarray-based screens of these heterozygotes are truly genome-wide as they include both essential and non-essential genes...
  4. pmc Further developments towards a genome-scale metabolic model of yeast
    Paul D Dobson
    School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
    BMC Syst Biol 4:145. 2010
    ....
  5. pmc Data capture in bioinformatics: requirements and experiences with Pedro
    Daniel Jameson
    School of Chemistry, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
    BMC Bioinformatics 9:183. 2008
    ....
  6. pmc Information management for high content live cell imaging
    Daniel Jameson
    Manchester Centre for Integrative Systems Biology, School of Chemistry, and Manchester Interdisciplinary Biocentre, University of Manchester, 131, Princess St, Manchester, M1 7DN, UK
    BMC Bioinformatics 10:226. 2009
    ..There is therefore a requirement for an information management solution that facilitates the indexing of experimental metadata and results of high content live cell imaging experiments...
  7. ncbi request reprint Yeast cells with impaired drug resistance accumulate glycerol and glucose
    Duygu Dikicioglu
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
    Mol Biosyst 10:93-102. 2014
    ....
  8. pmc Synergistic effects of TOR and proteasome pathways on the yeast transcriptome and cell growth
    Nianshu Zhang
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Open Biol 3:120137. 2013
    ..These data suggest that the proteasome and the TOR signalling pathway synergistically regulate a significant portion of the genome to coordinate cell growth and starvation response...
  9. pmc Nutrient control of eukaryote cell growth: a systems biology study in yeast
    Alex Gutteridge
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
    BMC Biol 8:68. 2010
    ....
  10. pmc The genetic control of growth rate: a systems biology study in yeast
    Pinar Pir
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Syst Biol 6:4. 2012
    ..It has not been determined whether the set of HFC genes is the same at all growth rates or whether it is the same in conditions of nutrient limitation or excess...
  11. pmc Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory
    Duygu Dikicioglu
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
    Biotechnol J 8:1017-34. 2013
    ..This review presents different methods and approaches undertaken toward improving our understanding and prediction of the growth phenotype of the yeast Saccharomyces cerevisiae as both a model and a production organism. ..
  12. pmc Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae
    Duygu Dikicioglu
    Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
    Appl Environ Microbiol 74:5809-16. 2008
    ....
  13. pmc The transcription activity of Gis1 is negatively modulated by proteasome-mediated limited proteolysis
    Nianshu Zhang
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
    J Biol Chem 285:6465-76. 2010
    ..Furthermore, we have revealed that the kinase activity of Rim15 is essential for this regulation...
  14. pmc Haploinsufficiency and the sex chromosomes from yeasts to humans
    Michaela de Clare
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, UK
    BMC Biol 9:15. 2011
    ..Haploinsufficiency is increasingly implicated in human disease, and so predicting this phenotype could provide insights into the genetic mechanisms behind many human diseases, including some cancers...
  15. doi request reprint Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast
    Nianshu Zhang
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Microbiology 155:1690-8. 2009
    ..In agreement with this, Rim15p is shown to act in parallel with Hog1p to defend cells against osmotic stress...
  16. pmc Canto: an online tool for community literature curation
    Kim M Rutherford
    Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA and Department of Genetics, Evolution and Environment, and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UKCambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA and Department of Genetics, Evolution and Environment, and UCL Cancer Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Bioinformatics 30:1791-2. 2014
    ..Availability: Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/)...
  17. doi request reprint Yeast systems biology: the challenge of eukaryotic complexity
    Juan I Castrillo
    Department of Biochemistry, Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB21GA, UK
    Methods Mol Biol 759:3-28. 2011
    ..Selected examples of the latest discoveries in eukaryote complexity and systems biology studies using yeast as a reference model and their applications in biotechnology and medicine are presented...
  18. doi request reprint JmjN interacts with JmjC to ensure selective proteolysis of Gis1 by the proteasome
    Zhenzhen Quan
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Microbiology 157:2694-701. 2011
    ..Together, these data suggest that JmjN and JmjC interact physically to form a structural unit that ensures the stability and appropriate transcription activity of Gis1...
  19. pmc Yeast-based automated high-throughput screens to identify anti-parasitic lead compounds
    Elizabeth Bilsland
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Open Biol 3:120158. 2013
    ..Finally, we demonstrate a 60 per cent success rate for our hit compounds in killing or severely inhibiting the growth of Trypanosoma brucei, the causative agent of African sleeping sickness...
  20. pmc Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids
    Annette A Alcasabas
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
    BMC Genomics 14:744. 2013
    ..These genes are termed HFC for high flux control. Such genes are overrepresented within pathways controlling the mitotic cell cycle...
  21. doi request reprint A metabolomic and multivariate statistical process to assess the effects of genotoxins in Saccharomyces cerevisiae
    Christopher M Titman
    Department of Biochemistry, University of Cambridge, Cambridge, UK
    Mol Biosyst 5:1913-24. 2009
    ..Finally, predictive models were built for distinguishing the genotoxic carcinogens from the control group according to the metabolic profile of the cell culture media...
  22. doi request reprint Phenomic and transcriptomic analyses reveal that autophagy plays a major role in desiccation tolerance in Saccharomyces cerevisiae
    Sooraj Ratnakumar
    Department of Chemical Engineering and Biotechnology, Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK
    Mol Biosyst 7:139-49. 2011
    ..Changes in nitrogen metabolism were evident during the drying process and parts of the environmental stress response were activated, repressing ribosome production and inducing genes for coping with oxidative and osmotic stress...
  23. ncbi request reprint A protocol for the subcellular fractionation of Saccharomyces cerevisiae using nitrogen cavitation and density gradient centrifugation
    Yuchong Wang
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, UK
    Yeast 31:127-35. 2014
    ..cerevisiae. We present an integrated protocol that is fast, facile, robust and efficient and that will enable 'omics' studies of the subcellular compartments of S. cerevisiae and other yeasts...
  24. pmc A prototrophic deletion mutant collection for yeast metabolomics and systems biology
    Michael Mülleder
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK
    Nat Biotechnol 30:1176-8. 2012
  25. pmc FYPO: the fission yeast phenotype ontology
    Midori A Harris
    Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Bioinformatics 29:1671-8. 2013
    ..To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast...
  26. pmc Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling
    Jacob G Bundy
    Department of Biochemistry, University of Cambridge, Cambridge, UK
    Genome Res 17:510-9. 2007
    ....