TY - JOUR AU - Kacser, H. AU - Burns, J. A. PY - 1973 DA - 1973// TI - The control of flux JO - Symp Soc Exp Biol VL - 27 ID - Kacser1973 ER - TY - JOUR AU - Warner, J. R. PY - 1999 DA - 1999// TI - The economics of ribosome biosynthesis in yeast JO - Trends Biochem Sci VL - 24 ID - Warner1999 ER - TY - JOUR AU - Fingar, D. C. AU - Blenis, J. PY - 2004 DA - 2004// TI - Target of rapamycin (TOR): an integrator of nutrient and growth factor signals and coordinator of cell growth and cell cycle progression JO - Oncogene VL - 23 ID - Fingar2004 ER - TY - BOOK PY - 2004 DA - 2004// TI - Cell Growth: Control of Cell Size. Monograph 42 PB - Cold Spring Harbor Laboratory Press CY - New York ID - ref4 ER - TY - CHAP AU - Jorgensen, P. AU - Tyers, M. AU - Warner, J. R. ED - Hall, M. N. ED - Raff, M. ED - Thomas, G. PY - 2004 DA - 2004// TI - Forging the factory: ribosome synthesis and growth control in budding yeast BT - Cell Growth: Control of Cell Size. Monograph 42 PB - Cold Spring Harbor Laboratory Press CY - New York ID - Jorgensen2004 ER - TY - JOUR AU - Manning, B. D. AU - Cantley, L. C. PY - 2004 DA - 2004// TI - Sizing up a growing field JO - Nature VL - 431 ID - Manning2004 ER - TY - JOUR AU - Hartwell, L. H. AU - Weinert, T. A. PY - 1989 DA - 1989// TI - Checkpoints: controls that ensure the order of cell cycle events JO - Science VL - 246 ID - Hartwell1989 ER - TY - JOUR AU - Spellman, P. T. AU - Sherlock, G. AU - Zhang, M. Q. AU - Iyer, V. R. AU - Anders, K. AU - Eisen, M. B. AU - Brown, P. O. AU - Botstein, D. AU - Futcher, B. PY - 1998 DA - 1998// TI - Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiaeby microarray hybridization JO - Mol Biol Cell VL - 9 ID - Spellman1998 ER - TY - JOUR AU - Jorgensen, P. AU - Nishikawa, J. L. AU - Breitkreutz, B. J. AU - Tyers, M. PY - 2002 DA - 2002// TI - Systematic identification of pathways that couple cell growth and division in yeast JO - Science VL - 297 ID - Jorgensen2002 ER - TY - JOUR AU - Jorgensen, P. AU - Tyers, M. PY - 2004 DA - 2004// TI - How cells coordinate growth and division JO - Curr Biol VL - 14 ID - Jorgensen2004 ER - TY - JOUR AU - Mager, W. H. AU - Planta, R. J. PY - 1991 DA - 1991// TI - Coordinate expression of ribosomal protein genes in yeast as a function of cellular growth rate JO - Mol Cell Biochem VL - 104 ID - Mager1991 ER - TY - JOUR AU - Kraakman, L. S. AU - Griffioen, G. AU - Zerp, S. AU - Groeneveld, P. AU - Thevelein, J. M. AU - Mager, W. H. AU - Planta, R. J. PY - 1993 DA - 1993// TI - Growth-related expression of ribosomal protein genes in Saccharomyces cerevisiae JO - Mol Gen Genet VL - 239 ID - Kraakman1993 ER - TY - JOUR AU - Planta, R. J. PY - 1997 DA - 1997// TI - Regulation of ribosome synthesis in yeast JO - Yeast VL - 13 ID - Planta1997 ER - TY - JOUR AU - Hayes, A. AU - Zhang, N. AU - Wu, J. AU - Butler, P. R. AU - Hauser, N. C. AU - Hoheisel, J. D. AU - Lim, F. L. AU - Sharrocks, A. D. AU - Oliver, S. G. PY - 2002 DA - 2002// TI - Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae JO - Methods VL - 26 ID - Hayes2002 ER - TY - JOUR AU - van Uden, N. PY - 1968 DA - 1968// TI - Yield and maintenance analysis in the chemostat; a tool for metabolic studies of growing cells JO - Arch Mikrobiol VL - 62 ID - van Uden1968 ER - TY - JOUR AU - Hoskisson, P. A. AU - Hobbs, G. PY - 2005 DA - 2005// TI - Continuous culture - making a comeback? JO - Microbiology VL - 151 ID - Hoskisson2005 ER - TY - JOUR AU - Ferenci, T. PY - 2006 DA - 2006// TI - A cultural divide on the use of chemostats JO - Microbiology VL - 152 ID - Ferenci2006 ER - TY - JOUR AU - Boer, V. M. AU - de Winde, J. H. AU - Pronk, J. T. AU - Piper, M. D. PY - 2003 DA - 2003// TI - The genome-wide transcriptional responses of Saccharomyces cerevisiaegrown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur JO - J Biol Chem VL - 278 ID - Boer2003 ER - TY - JOUR AU - Wu, J. AU - Zhang, N. AU - Hayes, A. AU - Panoutsopoulou, K. AU - Oliver, S. G. PY - 2004 DA - 2004// TI - Global analysis of nutrient control of gene expression in Saccharomyces cerevisiaeduring growth and starvation JO - Proc Natl Acad Sci USA VL - 101 ID - Wu2004 ER - TY - JOUR AU - Kolkman, A. AU - Daran-Lapujade, P. AU - Fullaondo, A. AU - Olsthoorn, M. M. AU - Pronk, J. T. AU - Slijper, M. AU - Heck, A. J. PY - 2006 DA - 2006// TI - Proteome analysis of yeast response to various nutrient limitations JO - Mol Syst Biol VL - 2 ID - Kolkman2006 ER - TY - JOUR AU - Beilharz, T. H. AU - Preiss, T. PY - 2004 DA - 2004// TI - Translational profiling: the genome-wide measure of the nascent proteome JO - Brief Funct Genomic Proteomic VL - 3 ID - Beilharz2004 ER - TY - JOUR AU - Arava, Y. AU - Wang, Y. AU - Storey, J. D. AU - Liu, C. L. AU - Brown, P. O. AU - Herschlag, D. PY - 2003 DA - 2003// TI - Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae JO - Proc Natl Acad Sci USA VL - 100 ID - Arava2003 ER - TY - JOUR AU - Arava, Y. AU - Boas, F. E. AU - Brown, P. O. AU - Herschlag, D. PY - 2005 DA - 2005// TI - Dissecting eukaryotic translation and its control by ribosome density mapping JO - Nucleic Acids Res VL - 33 ID - Arava2005 ER - TY - JOUR AU - Mata, J. AU - Marguerat, S. AU - Bähler, J. PY - 2005 DA - 2005// TI - Post-transcriptional control of gene expression: a genome-wide perspective JO - Trends Biochem Sci VL - 30 ID - Mata2005 ER - TY - JOUR AU - Kahn, D. AU - Westerhoff, H. V. PY - 1991 DA - 1991// TI - Control theory of regulatory cascades JO - J Theor Biol VL - 153 ID - Kahn1991 ER - TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Systems biology: a brief overview JO - Science VL - 295 ID - Kitano2002 ER - TY - JOUR AU - Nurse, P. PY - 2003 DA - 2003// TI - Systems biology: understanding cells JO - Nature VL - 424 ID - Nurse2003 ER - TY - CHAP AU - Castrillo, J. I. AU - Oliver, S. G. ED - Esser, K. PY - 2006 DA - 2006// TI - Metabolomics and systems biology in Saccharomyces cerevisiae BT - Fungal Genomics. The Mycota PB - Springer-Verlag CY - Berlin ID - Castrillo2006 ER - TY - JOUR AU - Kell, D. B. PY - 2006 DA - 2006// TI - Metabolomics, modelling and machine learning in systems biology: towards an understanding of the languages of cells. The 2005 Theodor Bucher Lecture JO - FEBS J VL - 273 ID - Kell2006 ER - TY - JOUR AU - Bjornsti, M. A. AU - Houghton, P. J. PY - 2004 DA - 2004// TI - The TOR pathway: a target for cancer therapy JO - Nat Rev Cancer VL - 4 ID - Bjornsti2004 ER - TY - CHAP AU - Guertin, D. A. AU - Kim, D. -. H. AU - Sabatini, D. M. ED - Hall, M. N. ED - Raff, M. ED - Thomas, G. PY - 2004 DA - 2004// TI - Growth control through the mTOR network BT - Cell Growth: Control of Cell Size. Monograph 42 PB - Cold Spring Harbor Laboratory Press CY - New York ID - Guertin2004 ER - TY - CHAP AU - Loewith, R. AU - Hall, M. N. ED - Hall, M. N. ED - Raff, M. ED - Thomas, G. PY - 2004 DA - 2004// TI - TOR signalling in yeast: Temporal and spatial control of cell growth BT - Cell Growth: Control of Cell Size. Monograph 42 PB - Cold Spring Harbor Laboratory Press CY - New York ID - Loewith2004 ER - TY - STD TI - Thomas G, Sabatini DM, Hall MN, Eds: TOR: target of rapamycin. Curr Top Microbiol Immunol 279. 2004, New York: Springer-Verlag ID - ref33 ER - TY - JOUR AU - Ross, P. L. AU - Huang, Y. N. AU - Marchese, J. N. AU - Williamson, B. AU - Parker, K. AU - Hattan, S. AU - Khainovski, N. AU - Pillai, S. AU - Dey, S. AU - Daniels, S. PY - 2004 DA - 2004// TI - Multiplexed protein quantitation in Saccharomyces cerevisiaeusing amine-reactive isobaric tagging reagents JO - Mol Cell Proteomics VL - 3 ID - Ross2004 ER - TY - JOUR AU - Shadforth, I. P. AU - Dunkley, T. P. AU - Lilley, K. S. AU - Bessant, C. PY - 2005 DA - 2005// TI - i-Tracker: for quantitative proteomics using iTRAQ JO - BMC Genomics VL - 6 ID - Shadforth2005 ER - TY - JOUR AU - Oliver, S. G. PY - 1997 DA - 1997// TI - From gene to screen with yeast JO - Curr Opin Genet Dev VL - 7 ID - Oliver1997 ER - TY - JOUR AU - Allen, J. AU - Davey, H. M. AU - Broadhurst, D. AU - Heald, J. K. AU - Rowland, J. J. AU - Oliver, S. G. AU - Kell, D. B. PY - 2003 DA - 2003// TI - High-throughput classification of yeast mutants for functional genomics using metabolic footprinting JO - Nat Biotechnol VL - 21 ID - Allen2003 ER - TY - JOUR AU - Kell, D. B. AU - Brown, M. AU - Davey, H. M. AU - Dunn, W. B. AU - Spasic, I. AU - Oliver, S. G. PY - 2005 DA - 2005// TI - Metabolic footprinting and systems biology: the medium is the message JO - Nat Rev Microbiol VL - 3 ID - Kell2005 ER - TY - JOUR AU - Nielsen, J. AU - Oliver, S. PY - 2005 DA - 2005// TI - The next wave in metabolome analysis JO - Trends Biotechnol VL - 23 ID - Nielsen2005 ER - TY - JOUR AU - Storey, J. D. PY - 2002 DA - 2002// TI - A direct approach to false discovery rates JO - J R Stat Soc Ser B VL - 64 ID - Storey2002 ER - TY - JOUR AU - Giaever, G. AU - Chu, A. M. AU - Ni, L. AU - Connelly, C. AU - Riles, L. AU - Veronneau, S. AU - Dow, S. AU - Lucau-Danila, A. AU - Anderson, K. AU - Andre, B. PY - 2002 DA - 2002// TI - Functional profiling of the Saccharomyces cerevisiaegenome JO - Nature VL - 418 ID - Giaever2002 ER - TY - STD TI - Saccharomyces Genome Database (SGD). [http://www.yeastgenome.org] UR - http://www.yeastgenome.org ID - ref42 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 ID - Ashburner2000 ER - TY - STD TI - GoMiner tool. [http://discover.nci.nih.gov/gominer] UR - http://discover.nci.nih.gov/gominer ID - ref44 ER - TY - STD TI - GenMAPP tool. [http://www.genmapp.org] UR - http://www.genmapp.org ID - ref45 ER - TY - JOUR AU - Ferenci, T. PY - 1999 DA - 1999// TI - Regulation by nutrient limitation JO - Curr Opin Microbiol VL - 2 ID - Ferenci1999 ER - TY - CHAP AU - Ohsumi, Y. ED - Hall, M. N. ED - Raff, M. ED - Thomas, G. PY - 2004 DA - 2004// TI - Autophagy: reversing cell growth BT - Cell Growth, Control of Cell Size. Monograph 42 PB - Cold Spring Harbor Laboratory Press CY - New York ID - Ohsumi2004 ER - TY - JOUR AU - Kamada, Y. AU - Sekito, T. AU - Ohsumi, Y. PY - 2004 DA - 2004// TI - Autophagy in yeast: a TOR-mediated response to nutrient starvation JO - Curr Top Microbiol Immunol VL - 279 ID - Kamada2004 ER - TY - JOUR AU - Gasch, A. P. AU - Spellman, P. T. AU - Kao, C. M. AU - Carmel-Harel, O. AU - Eisen, M. B. AU - Storz, G. AU - Botstein, D. AU - Brown, P. O. PY - 2000 DA - 2000// TI - Genomic expression programs in the response of yeast cells to environmental changes JO - Mol Biol Cell VL - 11 ID - Gasch2000 ER - TY - JOUR AU - Gasch, A. P. AU - Werner-Washburne, M. PY - 2002 DA - 2002// TI - The genomics of yeast responses to environmental stress and starvation JO - Funct Integr Genomics VL - 2 ID - Gasch2002 ER - TY - STD TI - Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, et al: Fungal BLAST and model organism BLASTP best hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005, D374-D377. 33 Database ID - ref51 ER - TY - STD TI - SGD model organism BLASTP best hits. [http://db.yeastgenome.org/cgi-bin/bestHits] UR - http://db.yeastgenome.org/cgi-bin/bestHits ID - ref52 ER - TY - JOUR AU - Krogan, N. J. AU - Cagney, G. AU - Yu, H. AU - Zhong, G. AU - Guo, X. AU - Ignatchenko, A. AU - Li, J. AU - Pu, S. AU - Datta, N. AU - Tikuisis, A. P. PY - 2006 DA - 2006// TI - Global landscape of protein complexes in the yeast Saccharomyces cerevisiae JO - Nature VL - 440 ID - Krogan2006 ER - TY - JOUR AU - Barbet, N. C. AU - Schneider, U. AU - Helliwell, S. B. AU - Stansfield, I. AU - Tuite, M. F. AU - Hall, M. N. PY - 1996 DA - 1996// TI - TOR controls translation initiation and early G1 progression in yeast JO - Mol Biol Cell VL - 7 ID - Barbet1996 ER - TY - JOUR AU - Dorrello, N. V. AU - Peschiaroli, A. AU - Guardavaccaro, D. AU - Colburn, N. H. AU - Sherman, N. E. AU - Pagano, M. PY - 2006 DA - 2006// TI - S6K1- and βTRCP-mediated degradation of PDCD4 promotes protein translation and cell growth JO - Science VL - 314 ID - Dorrello2006 ER - TY - JOUR AU - Li, H. AU - Tsang, C. K. AU - Watkins, M. AU - Bertram, P. G. AU - Zheng, X. F. PY - 2006 DA - 2006// TI - Nutrient regulates Tor1 nuclear localization and association with rDNA promoter JO - Nature VL - 442 ID - Li2006 ER - TY - JOUR AU - Kuruvilla, F. G. AU - Shamji, A. F. AU - Schreiber, S. L. PY - 2001 DA - 2001// TI - Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors JO - Proc Natl Acad Sci USA VL - 98 ID - Kuruvilla2001 ER - TY - JOUR AU - Marion, R. M. AU - Regev, A. AU - Segal, E. AU - Barash, Y. AU - Koller, D. AU - Friedman, N. AU - O'Shea, E. K. PY - 2004 DA - 2004// TI - Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression JO - Proc Natl Acad Sci USA VL - 101 ID - Marion2004 ER - TY - JOUR AU - Martin, D. E. AU - Soulard, A. AU - Hall, M. N. PY - 2004 DA - 2004// TI - TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1 JO - Cell VL - 119 ID - Martin2004 ER - TY - JOUR AU - Schawalder, S. B. AU - Kabani, M. AU - Howald, I. AU - Choudhury, U. AU - Werner, M. AU - Shore, D. PY - 2004 DA - 2004// TI - Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1 JO - Nature VL - 432 ID - Schawalder2004 ER - TY - JOUR AU - Hardwick, J. S. AU - Kuruvilla, F. G. AU - Tong, J. K. AU - Shamji, A. F. AU - Schreiber, S. L. PY - 1999 DA - 1999// TI - Rapamycin-modulated transcription defines the subset of nutrient-sensitive signalling pathways directly controlled by the Tor proteins JO - Proc Natl Acad Sci USA VL - 96 ID - Hardwick1999 ER - TY - JOUR AU - Preiss, T. AU - Baron-Benhamou, J. AU - Ansorge, W. AU - Hentze, M. W. PY - 2003 DA - 2003// TI - Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock JO - Nat Struct Biol VL - 10 ID - Preiss2003 ER - TY - JOUR AU - Reinke, A. AU - Anderson, S. AU - McCaffery, J. M. AU - Yates, J. AU - Aronova, S. AU - Chu, S. AU - Fairclough, S. AU - Iverson, C. AU - Wedaman, K. P. AU - Powers, T. PY - 2004 DA - 2004// TI - TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae JO - J Biol Chem VL - 279 ID - Reinke2004 ER - TY - JOUR AU - Daran-Lapujade, P. AU - Jansen, M. L. AU - Daran, J. M. AU - van Gulik, W. AU - de Winde, J. H. AU - Pronk, J. T. PY - 2004 DA - 2004// TI - Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study JO - J Biol Chem VL - 279 ID - Daran-Lapujade2004 ER - TY - JOUR AU - Tian, Q. AU - Stepaniants, S. B. AU - Mao, M. AU - Weng, L. AU - Feetham, M. C. AU - Doyle, M. J. AU - Yi, E. C. AU - Dai, H. AU - Thorsson, V. AU - Eng, J. PY - 2004 DA - 2004// TI - Integrated genomic and proteomic analyses of gene expression in mammalian cells JO - Mol Cell Proteomics VL - 3 ID - Tian2004 ER - TY - JOUR AU - Gygi, S. P. AU - Rochon, Y. AU - Franza, B. R. AU - Aebersold, R. PY - 1999 DA - 1999// TI - Correlation between protein and mRNA abundance in yeast JO - Mol Cell Biol VL - 19 ID - Gygi1999 ER - TY - JOUR AU - Pradet-Balade, B. AU - Boulme, F. AU - Beug, H. AU - Mullner, E. W. AU - Garcia-Sanz, J. A. PY - 2001 DA - 2001// TI - Translation control: bridging the gap between genomics and proteomics? JO - Trends Biochem Sci VL - 26 ID - Pradet-Balade2001 ER - TY - JOUR AU - Greenbaum, D. AU - Jansen, R. AU - Gerstein, M. PY - 2002 DA - 2002// TI - Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts JO - Bioinformatics VL - 18 ID - Greenbaum2002 ER - TY - JOUR AU - Greenbaum, D. AU - Colangelo, C. AU - Williams, K. AU - Gerstein, M. PY - 2003 DA - 2003// TI - Comparing protein abundance and mRNA expression levels on a genomic scale JO - Genome Biol VL - 4 ID - Greenbaum2003 ER - TY - JOUR AU - Thomas, D. AU - Surdin-Kerjan, Y. PY - 1991 DA - 1991// TI - The synthesis of the two S-adenosyl-methionine synthetases is differently regulated in Saccharomyces cerevisiae JO - Mol Gen Genet VL - 226 ID - Thomas1991 ER - TY - JOUR AU - Griffin, T. J. AU - Gygi, S. P. AU - Ideker, T. AU - Rist, B. AU - Eng, J. AU - Hood, L. AU - Aebersold, R. PY - 2002 DA - 2002// TI - Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae JO - Mol Cell Proteomics VL - 1 ID - Griffin2002 ER - TY - JOUR AU - Brengues, M. AU - Teixeira, D. AU - Parker, R. PY - 2005 DA - 2005// TI - Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies JO - Science VL - 310 ID - Brengues2005 ER - TY - JOUR AU - Ciechanover, A. PY - 2005 DA - 2005// TI - Proteolysis: from the lysosome to ubiquitin and the proteasome JO - Nat Rev Mol Cell Biol VL - 6 ID - Ciechanover2005 ER - TY - JOUR AU - Pratt, J. M. AU - Petty, J. AU - Riba-Garcia, I. AU - Robertson, D. H. AU - Gaskell, S. J. AU - Oliver, S. G. AU - Beynon, R. J. PY - 2002 DA - 2002// TI - Dynamics of protein turnover, a missing dimension in proteomics JO - Mol Cell Proteomics VL - 1 ID - Pratt2002 ER - TY - JOUR AU - Messenguy, F. AU - Feller, A. AU - Crabeel, M. AU - Pierard, A. PY - 1983 DA - 1983// TI - Control-mechanisms acting at the transcriptional and post-transcriptional levels are involved in the synthesis of the arginine pathway carbamoylphosphate synthase of yeast JO - EMBO J VL - 2 ID - Messenguy1983 ER - TY - JOUR AU - Fang, P. AU - Wang, Z. AU - Sachs, M. S. PY - 2000 DA - 2000// TI - Evolutionarily conserved features of the arginine attenuator peptide provide the necessary requirements for its function in translational regulation JO - J Biol Chem VL - 275 ID - Fang2000 ER - TY - JOUR AU - Gaba, A. AU - Jacobson, A. AU - Sachs, M. S. PY - 2005 DA - 2005// TI - Ribosome occupancy of the yeast CPA1upstream open reading frame termination codon modulates nonsense-mediated mRNA decay JO - Mol Cell VL - 20 ID - Gaba2005 ER - TY - JOUR AU - Zhang, Z. AU - Dietrich, F. S. PY - 2005 DA - 2005// TI - Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae JO - Curr Genet VL - 48 ID - Zhang2005 ER - TY - JOUR AU - Oliver, S. G. PY - 2002 DA - 2002// TI - Functional genomics: lessons from yeast JO - Philos Trans R Soc Lond B Biol Sci VL - 357 ID - Oliver2002 ER - TY - JOUR AU - Pir, P. AU - Kirdar, B. AU - Hayes, A. AU - Onsan, Z. Y. AU - Ulgen, K. O. AU - Oliver, S. G. PY - 2006 DA - 2006// TI - Integrative investigation of metabolic and transcriptomic data JO - BMC Bioinformatics VL - 7 ID - Pir2006 ER - TY - JOUR AU - Patil, K. R. AU - Nielsen, J. PY - 2005 DA - 2005// TI - Uncovering transcriptional regulation of metabolism by using metabolic network topology JO - Proc Natl Acad Sci USA VL - 102 ID - Patil2005 ER - TY - JOUR AU - Thomas, D. AU - Surdin-Kerjan, Y. PY - 1997 DA - 1997// TI - Metabolism of sulfur amino acids in Saccharomyces cerevisiae JO - Microbiol Mol Biol Rev VL - 61 ID - Thomas1997 ER - TY - JOUR AU - Thomas, D. AU - Becker, A. AU - Surdin-Kerjan, Y. PY - 2000 DA - 2000// TI - Reverse methionine biosynthesis from S-adenosylmethionine in eukaryotic cells JO - J Biol Chem VL - 275 ID - Thomas2000 ER - TY - JOUR AU - Magasanik, B. AU - Kaiser, C. A. PY - 2002 DA - 2002// TI - Nitrogen regulation in Saccharomyces cerevisiae JO - Gene VL - 290 ID - Magasanik2002 ER - TY - JOUR AU - Csete, M. AU - Doyle, J. PY - 2004 DA - 2004// TI - Bow ties, metabolism and disease JO - Trends Biotechnol VL - 22 ID - Csete2004 ER - TY - JOUR AU - Purnelle, B. AU - Coster, F. AU - Goffeau, A. PY - 1994 DA - 1994// TI - The sequence of a 36 kb segment on the left arm of yeast chromosome X identifies 24 open reading frames including NUC1, PRP21 (SPP91), CDC6, CRY2, the gene for S24, a homologue to the aconitase gene ACO1and two homologues to chromosome III genes JO - Yeast VL - 10 ID - Purnelle1994 ER - TY - JOUR AU - Palmieri, L. AU - Agrimi, G. AU - Runswick, M. J. AU - Fearnley, I. M. AU - Palmieri, F. AU - Walker, J. E. PY - 2001 DA - 2001// TI - Identification in Saccharomyces cerevisiaeof two isoforms of a novel mitochondrial transporter for 2-oxoadipate and 2-oxoglutarate JO - J Biol Chem VL - 276 ID - Palmieri2001 ER - TY - JOUR AU - Mitchell, A. P. AU - Magasanik, B. PY - 1984 DA - 1984// TI - Three regulatory systems control production of glutamine synthetase in Saccharomyces cerevisiae JO - Mol Cell Biol VL - 4 ID - Mitchell1984 ER - TY - BOOK AU - Bender, D. A. PY - 1985 DA - 1985// TI - Amino Acid Metabolism PB - Sons CY - Chichester ID - Bender1985 ER - TY - CHAP AU - Hinnebusch, A. G. ED - Jones, E. W. ED - Pringle, J. R. ED - Broach, J. R. PY - 1992 DA - 1992// TI - General and pathway-specific regulatory mechanisms controlling the synthesis of amino acid biosynthetic enzymes in Saccharomyces cerevisiae BT - The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression PB - Cold Spring Harbor Laboratory Press CY - New York ID - Hinnebusch1992 ER - TY - JOUR AU - Stanbrough, M. AU - Rowen, D. W. AU - Magasanik, B. PY - 1995 DA - 1995// TI - Role of the GATA factors Gln3p and Nil1p of Saccharomyces cerevisiaein the expression of nitrogen-regulated genes JO - Proc Natl Acad Sci USA VL - 92 ID - Stanbrough1995 ER - TY - JOUR AU - Crespo, J. L. AU - Powers, T. AU - Fowler, B. AU - Hall, M. N. PY - 2002 DA - 2002// TI - The TOR-controlled transcription activators GLN3, RTG1, and RTG3 are regulated in response to intracellular levels of glutamine JO - Proc Natl Acad Sci USA VL - 99 ID - Crespo2002 ER - TY - BOOK AU - Chen, X. AU - Blumenthal, R. M. PY - 1999 DA - 1999// TI - S-Adenosylmethionine-dependent Methyl-transferases: Structures and Functions PB - World Scientific Publishing CY - Singapore ID - Chen1999 ER - TY - BOOK AU - Clarke, S. G. AU - Tamanoi, F. PY - 2006 DA - 2006// TI - Protein Methyltransferases. The Enzymes PB - Elsevier/Academic Press CY - San Diego ID - Clarke2006 ER - TY - JOUR AU - Loenen, W. A. PY - 2006 DA - 2006// TI - S-Adenosylmethionine: jack of all trades and master of everything? JO - Biochem Soc Trans VL - 34 ID - Loenen2006 ER - TY - JOUR AU - Farooqui, J. Z. AU - Lee, H. W. AU - Kim, S. AU - Paik, W. K. PY - 1983 DA - 1983// TI - Studies on compartmentation of S-adenosyl-L-methionine in Saccharomyces cerevisiaeand isolated rat hepatocytes JO - Biochim Biophys Acta VL - 757 ID - Farooqui1983 ER - TY - JOUR AU - Kumar, A. AU - Agarwal, S. AU - Heyman, J. A. AU - Matson, S. AU - Heidtman, M. AU - Piccirillo, S. AU - Umansky, L. AU - Drawid, A. AU - Jansen, R. AU - Liu, Y. PY - 2002 DA - 2002// TI - Subcellular localization of the yeast proteome JO - Genes Dev VL - 16 ID - Kumar2002 ER - TY - STD TI - Yeast GFP fusion localization database. [http://yeastgfp.ucsf.edu] UR - http://yeastgfp.ucsf.edu ID - ref98 ER - TY - STD TI - BioGRID database. [http://www.thebiogrid.org] UR - http://www.thebiogrid.org ID - ref99 ER - TY - JOUR AU - Gavin, A. C. AU - Aloy, P. AU - Grandi, P. AU - Krause, R. AU - Boesche, M. AU - Marzioch, M. AU - Rau, C. AU - Jensen, L. J. AU - Bastuck, S. AU - Dumpelfeld, B. PY - 2006 DA - 2006// TI - Proteome survey reveals modularity of the yeast cell machinery JO - Nature VL - 440 ID - Gavin2006 ER - TY - JOUR AU - Ünlü, M. AU - Morgan, M. E. AU - Minden, J. S. PY - 1997 DA - 1997// TI - Difference gel electrophoresis: a single gel method for detecting changes in protein extracts JO - Electrophoresis VL - 18 ID - Ünlü1997 ER - TY - JOUR AU - Karp, N. A. AU - Kreil, D. P. AU - Lilley, K. S. PY - 2004 DA - 2004// TI - Determining a significant change in protein expression with DeCyder during a pairwise comparison using two-dimensional difference gel electrophoresis JO - Proteomics VL - 4 ID - Karp2004 ER - TY - JOUR AU - Cherest, H. AU - Thomas, D. AU - Surdin-Kerjan, Y. PY - 2000 DA - 2000// TI - Polyglutamylation of folate coenzymes is necessary for methionine biosynthesis and maintenance of intact mitochondrial genome in Saccharomyces cerevisiae JO - J Biol Chem VL - 275 ID - Cherest2000 ER - TY - JOUR AU - Suliman, H. S. AU - Sawyer, G. M. AU - Appling, D. R. AU - Robertus, J. D. PY - 2005 DA - 2005// TI - Purification and properties of cobalamin-independent methionine synthase from Candida albicans and Saccharomyces cerevisiae JO - Arch Biochem Biophys VL - 441 ID - Suliman2005 ER - TY - JOUR AU - Shane, B. AU - Cichowicz, D. J. PY - 1983 DA - 1983// TI - Folylpoly-gamma-glutamate synthetases: properties and regulation JO - Adv Exp Med Biol VL - 163 ID - Shane1983 ER - TY - CHAP AU - White, R. J. ED - Hall, M. N. ED - Raff, M. ED - Thomas, G. PY - 2004 DA - 2004// TI - Control of rRNA and tRNA production is closely related to cell growth BT - Cell Growth; Control of Cell Size. Monograph 42 PB - Cold Spring Harbor Laboratory Press CY - New York ID - White2004 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1999 DA - 1999// TI - A computational screen for methylation guide snoRNAs in yeast JO - Science VL - 283 ID - Lowe1999 ER - TY - JOUR AU - Tschochner, H. AU - Hurt, E. PY - 2003 DA - 2003// TI - Pre-ribosomes on the road from the nucleolus to the cytoplasm JO - Trends Cell Biol VL - 13 ID - Tschochner2003 ER - TY - JOUR AU - Schwer, B. AU - Saha, N. AU - Mao, X. AU - Chen, H. W. AU - Shuman, S. PY - 2000 DA - 2000// TI - Structure-function analysis of yeast mRNA cap methyltransferase and high-copy suppression of conditional mutants by AdoMet synthase and the ubiquitin conjugating enzyme Cdc34p JO - Genetics VL - 155 ID - Schwer2000 ER - TY - JOUR AU - ter Kuile, B. H. AU - Westerhoff, H. V. PY - 2001 DA - 2001// TI - Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway JO - FEBS Lett VL - 500 ID - ter Kuile2001 ER - TY - JOUR AU - Rossell, S. AU - van der Weijden, C. C. AU - Kruckeberg, A. L. AU - Bakker, B. M. AU - Westerhoff, H. V. PY - 2005 DA - 2005// TI - Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae JO - FEMS Yeast Res VL - 5 ID - Rossell2005 ER - TY - JOUR AU - Rossell, S. AU - van der Weijden, C. C. AU - Lindenbergh, A. AU - van Tuijl, A. AU - Francke, C. AU - Bakker, B. M. AU - Westerhoff, H. V. PY - 2006 DA - 2006// TI - Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae JO - Proc Natl Acad Sci USA VL - 103 ID - Rossell2006 ER - TY - JOUR AU - Powers, T. AU - Dilova, I. AU - Chen, C. Y. AU - Wedaman, K. PY - 2004 DA - 2004// TI - Yeast TOR signaling: a mechanism for metabolic regulation JO - Curr Top Microbiol Immunol VL - 279 ID - Powers2004 ER - TY - JOUR AU - Di Ventura, B. AU - Lemerle, C. AU - Michalodimitrakis, K. AU - Serrano, L. PY - 2006 DA - 2006// TI - From in vivo to in silicobiology and back JO - Nature VL - 443 ID - Di Ventura2006 ER - TY - JOUR AU - Lee, W. AU - St Onge, R. P. AU - Proctor, M. AU - Flaherty, P. AU - Jordan, M. I. AU - Arkin, A. P. AU - Davis, R. W. AU - Nislow, C. AU - Giaever, G. PY - 2005 DA - 2005// TI - Genome-wide requirements for resistance to functionally distinct DNA-damaging agents JO - PLoS Genet VL - 1 ID - Lee2005 ER - TY - JOUR AU - Murata, Y. AU - Homma, T. AU - Kitagawa, E. AU - Momose, Y. AU - Sato, M. S. AU - Odani, M. AU - Shimizu, H. AU - Hasegawa-Mizusawa, M. AU - Matsumoto, R. AU - Mizukami, S. PY - 2006 DA - 2006// TI - Genome-wide expression analysis of yeast response during exposure to 4 degrees C JO - Extremophiles VL - 10 ID - Murata2006 ER - TY - BOOK AU - Fell, D. PY - 1997 DA - 1997// TI - Understanding the Control of Metabolism PB - Portland Press CY - London ID - Fell1997 ER - TY - JOUR AU - Hornberg, J. J. AU - Binder, B. AU - Bruggeman, F. J. AU - Schoeberl, B. AU - Heinrich, R. AU - Westerhoff, H. V. PY - 2005 DA - 2005// TI - Control of MAPK signalling: from complexity to what really matters JO - Oncogene VL - 24 ID - Hornberg2005 ER - TY - BOOK AU - Wagner, A. PY - 2005 DA - 2005// TI - Robustness and Evolvability in Living Systems. Princeton Studies in Complexity PB - Princeton University Press CY - Princeton, NJ ID - Wagner2005 ER - TY - JOUR AU - Baganz, F. AU - Hayes, A. AU - Marren, D. AU - Gardner, D. C. J. AU - Oliver, S. G. PY - 1997 DA - 1997// TI - Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae JO - Yeast VL - 13 ID - Baganz1997 ER - TY - STD TI - dChip software. [http://www.dchip.org] UR - http://www.dchip.org ID - ref121 ER - TY - STD TI - RMAExpress software. [http://rmaexpress.bmbolstad.com/] UR - http://rmaexpress.bmbolstad.com/ ID - ref122 ER - TY - STD TI - ArrayExpress public repository. [http://www.ebi.ac.uk/arrayexpress] UR - http://www.ebi.ac.uk/arrayexpress ID - ref123 ER - TY - STD TI - Matlab software. [http://www.mathworks.co.uk] UR - http://www.mathworks.co.uk ID - ref124 ER - TY - STD TI - GeneSpring software. [http://www.chem.agilent.com] UR - http://www.chem.agilent.com ID - ref125 ER - TY - STD TI - maxdView software. [http://bioinf.man.ac.uk/microarray/maxd] UR - http://bioinf.man.ac.uk/microarray/maxd ID - ref126 ER - TY - JOUR AU - Boehm, A. AU - Galvin, R. AU - Sickmann, A. PY - 2004 DA - 2004// TI - Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing JO - BMC Bioinformatics VL - 5 ID - Boehm2004 ER - TY - STD TI - i-Tracker software. [http://www.dasi.org.uk/download/itracker.htm] UR - http://www.dasi.org.uk/download/itracker.htm ID - ref128 ER - TY - STD TI - Genome Annotating Proteomic Pipeline (GAPP)system. [http://www.gapp.info] UR - http://www.gapp.info ID - ref129 ER - TY - STD TI - PRIDE proteomics repository. [http://www.ebi.ac.uk/pride] UR - http://www.ebi.ac.uk/pride ID - ref130 ER - TY - JOUR AU - Castrillo, J. I. AU - Hayes, A. AU - Mohammed, S. AU - Gaskell, S. J. AU - Oliver, S. G. PY - 2003 DA - 2003// TI - An optimised protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry JO - Phytochemistry VL - 62 ID - Castrillo2003 ER - TY - STD TI - Manchester Centre for Integrative Systems Biology. [http://www.mcisb.org/] UR - http://www.mcisb.org/ ID - ref132 ER - TY - JOUR AU - Spasic, I. AU - Dunn, W. B. AU - Velarde, G. AU - Tseng, A. AU - Jenkins, H. AU - Hardy, N. AU - Oliver, S. G. AU - Kell, D. B. PY - 2006 DA - 2006// TI - MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics JO - BMC Bioinformatics VL - 7 ID - Spasic2006 ER - TY - JOUR AU - Jenkins, H. AU - Hardy, N. AU - Beckmann, M. AU - Draper, J. AU - Smith, A. R. AU - Taylor, J. AU - Fiehn, O. AU - Goodacre, R. AU - Bino, R. J. AU - Hall, R. PY - 2004 DA - 2004// TI - A proposed framework for the description of plant metabolomics experiments and their results JO - Nat Biotechnol VL - 22 ID - Jenkins2004 ER - TY - STD TI - Consortium for the Functional Genomics of Microbial Eukaryotes, COGEME. [http://www.manchester.ac.uk/cogeme] UR - http://www.manchester.ac.uk/cogeme ID - ref135 ER - TY - STD TI - Cell Designer. [http://www.celldesigner.org] UR - http://www.celldesigner.org ID - ref136 ER - TY - STD TI - Adobe Illustrator. [http://www.adobe.com/products/illustrator] UR - http://www.adobe.com/products/illustrator ID - ref137 ER -