Stephen G Oliver

Summary

Affiliation: University of Manchester
Country: UK

Publications

  1. ncbi request reprint A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    Chris F Taylor
    School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Nat Biotechnol 21:247-54. 2003
  2. pmc Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data
    Peter Li
    Manchester Centre for Integrative Systems Biology and School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
    BMC Bioinformatics 9:334. 2008
  3. pmc Functional genomics: lessons from yeast
    Stephen G Oliver
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Philos Trans R Soc Lond B Biol Sci 357:17-23. 2002
  4. ncbi request reprint The relative merits of the tetO2 and tetO7 promoter systems for the functional analysis of heterologous genes in yeast and a compilation of essential yeast genes with tetO2 promoter substitutions
    Jill A Wishart
    Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Yeast 23:325-31. 2006
  5. ncbi request reprint Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes
    Andrew H Sims
    School of Biological Sciences, University of Manchester, The Michael Smith Building, Manchester M13 9PT, UK
    Mycol Res 108:853-7. 2004
  6. pmc Growth control of the eukaryote cell: a systems biology study in yeast
    Juan I Castrillo
    Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    J Biol 6:4. 2007
  7. pmc A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network
    Gregory D Amoutzias
    Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
    BMC Syst Biol 1:34. 2007
  8. pmc All duplicates are not equal: the difference between small-scale and genome duplication
    Luke Hakes
    Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Genome Biol 8:R209. 2007
  9. ncbi request reprint Doxycycline, the drug used to control the tet-regulatable promoter system, has no effect on global gene expression in Saccharomyces cerevisiae
    Jill A Wishart
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
    Yeast 22:565-9. 2005
  10. pmc Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation
    Jian Wu
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, United Kingdom
    Proc Natl Acad Sci U S A 101:3148-53. 2004

Detail Information

Publications72

  1. ncbi request reprint A systematic approach to modeling, capturing, and disseminating proteomics experimental data
    Chris F Taylor
    School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Nat Biotechnol 21:247-54. 2003
    ..These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository...
  2. pmc Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data
    Peter Li
    Manchester Centre for Integrative Systems Biology and School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
    BMC Bioinformatics 9:334. 2008
    ..Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools...
  3. pmc Functional genomics: lessons from yeast
    Stephen G Oliver
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Philos Trans R Soc Lond B Biol Sci 357:17-23. 2002
    ..Finally, the prospects for elucidating the function of protozoan genes by using the methods pioneered with yeast, and even exploiting Saccharomyces itself, as a surrogate, are explored...
  4. ncbi request reprint The relative merits of the tetO2 and tetO7 promoter systems for the functional analysis of heterologous genes in yeast and a compilation of essential yeast genes with tetO2 promoter substitutions
    Jill A Wishart
    Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Yeast 23:325-31. 2006
    ..Subsequent efforts to generate a collection of tetracycline-regulatable strains have focused on the tetO2 promoter. These strains are available to the yeast community and can be used for functional genomics studies...
  5. ncbi request reprint Combining transcriptome data with genomic and cDNA sequence alignments to make confident functional assignments for Aspergillus nidulans genes
    Andrew H Sims
    School of Biological Sciences, University of Manchester, The Michael Smith Building, Manchester M13 9PT, UK
    Mycol Res 108:853-7. 2004
    ....
  6. pmc Growth control of the eukaryote cell: a systems biology study in yeast
    Juan I Castrillo
    Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    J Biol 6:4. 2007
    ..Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking...
  7. pmc A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network
    Gregory D Amoutzias
    Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
    BMC Syst Biol 1:34. 2007
    ..They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved...
  8. pmc All duplicates are not equal: the difference between small-scale and genome duplication
    Luke Hakes
    Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Genome Biol 8:R209. 2007
    ....
  9. ncbi request reprint Doxycycline, the drug used to control the tet-regulatable promoter system, has no effect on global gene expression in Saccharomyces cerevisiae
    Jill A Wishart
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, UK
    Yeast 22:565-9. 2005
    ..We have demonstrated that doxycycline has no significant effect on global transcription levels and will continue to use the tetO-regulatable promoter system for genetic studies...
  10. pmc Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation
    Jian Wu
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, United Kingdom
    Proc Natl Acad Sci U S A 101:3148-53. 2004
    ....
  11. ncbi request reprint Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures
    Daniela Delneri
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    Nat Genet 40:113-7. 2008
    ..This chromosome determines a yeast's mating type, and the concentration of haploinsufficient genes there may be a mechanism to prevent its loss...
  12. ncbi request reprint Use of expressed sequence tag analysis and cDNA microarrays of the filamentous fungus Aspergillus nidulans
    Andrew H Sims
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Fungal Genet Biol 41:199-212. 2004
    ..The profiles of genes showing statistically significant differential expression following the glucose up-shift are presented and an assessment of the quality and reproducibility of the A. nidulans arrays discussed...
  13. doi request reprint Conditional cell-wall mutants of Saccharomyces cerevisiae as delivery vehicles for therapeutic agents in vivo to the GI tract
    Walid A M Omara
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M139PT, UK
    J Biotechnol 147:136-43. 2010
    ..The greatest effects were seen with ANB1, TIR1, and MF(ALPHA)2), and we propose that their promoters have the potential to be used in vivo to achieve yeast lysis in the gut...
  14. 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...
  15. ncbi request reprint An improved tetO promoter replacement system for regulating the expression of yeast genes
    Kuangyu Yen
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Yeast 20:1255-62. 2003
    ..Altogether, the components of this new 'tool kit' greatly increase the efficiency of systematic promoter substitutions...
  16. pmc Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast
    Karin Lanthaler
    School of Chemistry, University of Manchester, Manchester, UK
    BMC Biol 9:70. 2011
    ..The recent recognition that drug uptake is mostly carrier-mediated raises the question of which drugs use which carriers...
  17. pmc Plasticity of genetic interactions in metabolic networks of yeast
    Richard Harrison
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
    Proc Natl Acad Sci U S A 104:2307-12. 2007
    ..Our work supports the view that functional redundancy may be more apparent than real, and it offers a unified framework for the evolution of environmental adaptation and mutational robustness...
  18. pmc Genotypic and physiological characterization of Saccharomyces boulardii, the probiotic strain of Saccharomyces cerevisiae
    Laura Edwards-Ingram
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK
    Appl Environ Microbiol 73:2458-67. 2007
    ..The contributions of the different genomic and phenotypic features of S. boulardii to its probiotic nature are discussed...
  19. pmc Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo
    Andrew H Sims
    Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
    Appl Environ Microbiol 71:2737-47. 2005
    ..The impact of overexpressing a secreted recombinant protein more closely resembles the unfolded-protein response in vivo...
  20. ncbi request reprint Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics
    Juan I Castrillo
    School of Biological Sciences, University of Manchester, 2205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    J Biochem Mol Biol 37:93-106. 2004
    ..g. plants, human)...
  21. pmc PEDRo: a database for storing, searching and disseminating experimental proteomics data
    Kevin Garwood
    Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    BMC Genomics 5:68. 2004
    ..However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets...
  22. ncbi request reprint GIMS: an integrated data storage and analysis environment for genomic and functional data
    Michael Cornell
    Department of Computer Science, University of Manchester, Manchester M13 9PL, UK
    Yeast 20:1291-306. 2003
    ..The GIMS database can be accessed remotely using a Java application that can be downloaded from http://img.cs.man.ac.uk/gims...
  23. ncbi request reprint Pedro: a configurable data entry tool for XML
    Kevin L Garwood
    Department of Computer Science, University of Manchester, UK
    Bioinformatics 20:2463-5. 2004
    ..The software also has the ability to import records from tab delimited text files and features various validation routines...
  24. pmc A kingdom-specific protein domain HMM library for improved annotation of fungal genomes
    Intikhab Alam
    School of Computer Science, University of Manchester, Kilburn Building, Manchester, UK
    BMC Genomics 8:97. 2007
    ....
  25. pmc Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness
    Anna Zakrzewska
    Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, Netherlands
    Mol Biol Cell 22:4435-46. 2011
    ..The reduction of growth rate, irrespective of the cause of this reduction, leads to redistribution of resources toward stress tolerance functions, thus preparing the cells for impending change...
  26. pmc Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network
    Gregory D Amoutzias
    Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
    BMC Genomics 7:107. 2006
    ..Specifically, bZIPs frequently have a role in mediating the response to oxidative stress, a crucial environmental signal that needs to be transduced to the gene regulatory network...
  27. pmc Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
    Kevin Garwood
    School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
    BMC Bioinformatics 7:532. 2006
    ..Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources...
  28. pmc From genomes to systems: the path with yeast
    Stephen G Oliver
    Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    Philos Trans R Soc Lond B Biol Sci 361:477-82. 2006
    ..More detailed modelling requires that 'natural' biological systems be identified. The combination of flux balance analysis with both genetics and metabolomics in the definition of metabolic systems is discussed...
  29. pmc ISPIDER Central: an integrated database web-server for proteomics
    Jennifer A Siepen
    Faculty of Life Sciences, University of Manchester, M13 9PT, UK
    Nucleic Acids Res 36:W485-90. 2008
    ..This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics...
  30. pmc Specificity in protein interactions and its relationship with sequence diversity and coevolution
    Luke Hakes
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, United Kingdom
    Proc Natl Acad Sci U S A 104:7999-8004. 2007
    ..e., within the same protein complex). This indicates that the observed correlated evolution of interacting proteins is due to similar constraints on evolutionary rate and not coevolution...
  31. ncbi request reprint The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
    Andrew R Jones
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    Nat Biotechnol 25:1127-33. 2007
    ..Such advances are important for transparent data management and mining in functional genomics and systems biology...
  32. pmc Effects of reciprocal chromosomal translocations on the fitness of Saccharomyces cerevisiae
    Isabelle Colson
    School of Biological Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
    EMBO Rep 5:392-8. 2004
    ..These results indicate that chromosomal translocations in Saccharomyces may have an adaptive significance, and lend support to a model of fixation by natural selection of reciprocal translocations in Saccharomyces species...
  33. ncbi request reprint Glutamic protease distribution is limited to filamentous fungi
    Andrew H Sims
    School of Biological Sciences, The Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
    FEMS Microbiol Lett 239:95-101. 2004
    ..A large number of coding regions for glutamic proteases were also found clustered together in the Phanerochaete chrysosporium genome, despite apparently being absent from three other species of Basidiomycota...
  34. ncbi request reprint Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae
    Andrew Hayes
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester, M13 9PT, United Kingdom
    Methods 26:281-90. 2002
    ..We use two experimental examples to illustrate the advantages of using this approach and then describe a specific application of this approach to investigate the effect of carbon and nitrogen limitation at the transcriptome level...
  35. ncbi request reprint Engineering evolution to study speciation in yeasts
    Daniela Delneri
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Nature 422:68-72. 2003
    ..This controlled comparison of the effect of chromosomal translocation on species barriers suggests a mechanism for the generation of redundancy in the S. cerevisiae genome...
  36. ncbi request reprint Metabolic footprinting and systems biology: the medium is the message
    Douglas B Kell
    School of Chemistry, University of Manchester, Faraday Building, PO Box 88, Sackville Street, Manchester M60 1QD, UK
    Nat Rev Microbiol 3:557-65. 2005
    ..Here, we review the principles, experimental approaches and scientific outcomes that have been obtained with this useful and convenient strategy...
  37. ncbi request reprint Using yeast to place human genes in functional categories
    Nianshu Zhang
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, UK
    Gene 303:121-9. 2003
    ....
  38. pmc Convergent evolution of gene networks by single-gene duplications in higher eukaryotes
    Gregory D Amoutzias
    School of Biological Sciences, University of Manchester, UK
    EMBO Rep 5:274-9. 2004
    ....
  39. pmc A model-based analysis of microarray experimental error and normalisation
    Yongxiang Fang
    School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK
    Nucleic Acids Res 31:e96. 2003
    ..If adaptive normalisation is combined with an effective dye bias identification method then there is no systematic difference between the outcomes of the two methods...
  40. ncbi request reprint An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry
    Juan I Castrillo
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Phytochemistry 62:929-37. 2003
    ..Examples of the application of this analytical strategy to specific yeast strains and single-ORF yeast deletion mutants generated through the EUROFAN programme are presented...
  41. ncbi request reprint Tools for the study of genome rearrangements in laboratory and industrial yeast strains
    Lesley Lockhart
    School of Biological Sciences, University of Manchester, 2 205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
    Yeast 19:441-8. 2002
    ..Using these plasmids as probes to hybridize a Southern blot from a pulsed-field gel electrophoresis separation of the 16 yeast chromosomes, it is possible to identify large chromosomal rearrangements such as reciprocal translocations...
  42. pmc Global phenotype screening and transcript analysis outlines the inhibitory mode(s) of action of two amphibian-derived, alpha-helical, cationic peptides on Saccharomyces cerevisiae
    C Oliver Morton
    Centre for Biomolecular Sciences, School of Biology, University of St Andrews, The North Haugh, St Andrews KY16 9ST, United Kingdom
    Antimicrob Agents Chemother 51:3948-59. 2007
    ..This implies that both peptides are able to pass through the cytoplasmic membrane of yeast cells and damage DNA, an inhibitory action that has not been previously attributed to either of these peptides...
  43. pmc Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi
    Michael J Cornell
    School of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
    Genome Res 17:1809-22. 2007
    ..These analyses have been collated in the e-Fungi data warehouse, providing an online resource for comparative genomic analysis of the fungi...
  44. pmc e-Fungi: a data resource for comparative analysis of fungal genomes
    Cornelia Hedeler
    School of Computer Science, The University of Manchester, Manchester, M13 9PL, UK
    BMC Genomics 8:426. 2007
    ..Furthermore, comparative analyses benefit from close integration of derived data sets that cluster genes or organisms in a way that eases the expression of requests that clarify points of similarity or difference between species...
  45. 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...
  46. pmc Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting
    Julie M Pratt
    Department of Veterinary Preclinical Sciences, University of Liverpool, Liverpool, UK
    Proteomics 2:157-63. 2002
    ..The method is tolerant to the extent of labelling, and as such, may be applicable to a range of single cell systems...
  47. ncbi request reprint Mapping pathways and phenotypes by systematic gene overexpression
    Richelle Sopko
    Department of Medical Genetics and Microbiology, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
    Mol Cell 21:319-30. 2006
    ..Large-scale application of this approach should provide a strategy for identifying target molecules regulated by specific signaling pathways...
  48. pmc Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis
    Darren M Soanes
    School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
    PLoS ONE 3:e2300. 2008
    ..The results demonstrate the potential of comparative genome analysis for exploring the evolution of eukaryotic microbial pathogenesis...
  49. 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
    ....
  50. 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
    ....
  51. doi request reprint Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek, 34342 Istanbul, Turkey
    Yeast 25:661-72. 2008
    ..Thus, Hap4p targets genes that are required for respiration and for fitness in nutrient-limited conditions. This suggests that Hap4p may enable cells to adapt to nutrient limitation as well as diauxy...
  52. ncbi request reprint Comparative assessment of large-scale data sets of protein-protein interactions
    Christian von Mering
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany
    Nature 417:399-403. 2002
    ..To measure their accuracy and potential as well as to identify biases, strengths and weaknesses, we compare the methods with each other and with a reference set of previously reported protein interactions...
  53. ncbi request reprint High-throughput classification of yeast mutants for functional genomics using metabolic footprinting
    Jess Allen
    Institute of Biological Sciences, Cledwyn Building, University of Wales, Aberystwyth, Aberystwyth SY23 3DD, UK
    Nat Biotechnol 21:692-6. 2003
    ..By using appropriate clustering and machine learning techniques, the latter based on genetic programming, we show that metabolic footprinting is an effective method to classify 'unknown' mutants by genetic defect...
  54. pmc SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences
    Paul E Boardman
    Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, PO Box 88, Manchester M60 1QD, UK
    Nucleic Acids Res 31:3572-5. 2003
    ....
  55. pmc Effect of dataset selection on the topological interpretation of protein interaction networks
    Luke Hakes
    Faculty of Life Sciences, The University of Manchester, Manchester, UK
    BMC Genomics 6:131. 2005
    ..Although a number of biological mechanisms have been proposed to account for these findings, the significance and influence of the specific datasets included in these studies has not been appreciated adequately...
  56. ncbi request reprint A common open representation of mass spectrometry data and its application to proteomics research
    Patrick G A Pedrioli
    Institute for Systems Biology, 1441 North 34 Street, Seattle, Washington 98103 8904, USA
    Nat Biotechnol 22:1459-66. 2004
    ..We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research...
  57. ncbi request reprint Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey
    Yeast 23:553-71. 2006
    ....
  58. pmc MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
    Irena Spasic
    School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
    BMC Bioinformatics 7:281. 2006
    ..The metabolomic data produced need to be structured and annotated in a machine-usable form to facilitate the exploration of the hidden links between the genes and their functions...
  59. pmc Cellular processes and pathways that protect Saccharomyces cerevisiae cells against the plasma membrane-perturbing compound chitosan
    Anna Zakrzewska
    Molecular Microbial Physiology, Swammerdam Institute of Life Sciences, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
    Eukaryot Cell 6:600-8. 2007
    ..We propose that global fitness analysis of yeast in combination with T-profiler is a powerful tool to identify specific cellular processes and pathways that are required for survival under stress conditions...
  60. ncbi request reprint Functional genomic hypothesis generation and experimentation by a robot scientist
    Ross D King
    Department of Computer Science, University of Wales, Aberystwyth SY23 3DB, UK
    Nature 427:247-52. 2004
    ....
  61. 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
    ....
  62. ncbi request reprint A proposed framework for the description of plant metabolomics experiments and their results
    Helen Jenkins
    Department of Computer Science, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, UK
    Nat Biotechnol 22:1601-6. 2004
    ..armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data...
  63. ncbi request reprint Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey
    Biotechnol Prog 23:320-6. 2007
    ..The FBA approach thereby enables identification of responsive pathways and so permits the elucidation of the genetic characteristics of strains in terms of expressed metabolite profiles...
  64. pmc Integrative investigation of metabolic and transcriptomic data
    Pinar Pir
    Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey
    BMC Bioinformatics 7:203. 2006
    ..At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods...
  65. ncbi request reprint Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae
    Zhikang Yin
    COGEME Proteome Research Facility 1, Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, UK
    Proteomics 4:2425-36. 2004
    ..cerevisiae, but were not significantly induced in C. albicans. These differences presumably reflect the contrasting niches of these relatively benign and pathogenic yeasts, respectively...
  66. pmc Discrimination of modes of action of antifungal substances by use of metabolic footprinting
    Jess Allen
    Department of Biological Sciences, University of Wales, Aberystwyth, UK
    Appl Environ Microbiol 70:6157-65. 2004
    ..Metabolic footprinting thus represents a rapid, convenient, and information-rich method for classifying the modes of action of antifungal substances...
  67. pmc Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex
    Laura C Edwards-Ingram
    Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology UMIST, Manchester M60 1QD, United Kingdom
    Genome Res 14:1043-51. 2004
    ..boulardii. We show that in addition to the phylogeny produced, we can identify and analyze individual ORF traits and interpret the results to give a detailed explanation of evolutionary events underlying the phylogeny...
  68. ncbi request reprint Chance and necessity in the evolution of minimal metabolic networks
    Csaba Pal
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69012 Heidelberg, Germany
    Nature 440:667-70. 2006
    ..We conclude that, at least for the particular cases considered here, gene content of an organism can be predicted with knowledge of its distant ancestors and its current lifestyle...
  69. ncbi request reprint Dynamics of protein turnover, a missing dimension in proteomics
    Julie M Pratt
    Department of Veterinary Preclinical Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingom
    Mol Cell Proteomics 1:579-91. 2002
    ....
  70. pmc Production of ethanol from starch by respiration-deficient recombinant Saccharomyces cerevisiae
    Ebru Toksoy Oner
    Marmara University, Faculty of Engineering, Department of Chemical Engineering, Goztepe 34722 Istanbul, Turkey
    Appl Environ Microbiol 71:6443-5. 2005
    ..In a comparison of ethanol fermentation performances with the parental respiration-sufficient WTPB-G strain, the NPB-G strain showed an increase of ca. 48% in both ethanol yield and ethanol productivity...
  71. ncbi request reprint Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
    Herman J Pel
    DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands
    Nat Biotechnol 25:221-31. 2007
    ..niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis...
  72. pmc Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complexes
    Fei Ling Lim
    Department of Biochemistry and Genetics, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
    Mol Cell Biol 23:450-61. 2003
    ..Thus, we discovered an important role for DNA bending by MADS-box proteins in the formation and function of eukaryotic transcription factor complexes...