Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. PLoS Comput Biol. 2009;5:e1000257.
Article
PubMed
PubMed Central
Google Scholar
Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DCJ, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O’Donoghue K, Hester SS, Dunkley TPJ, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG. Growth control of the eukaryote cell: a systems biology study in yeast. J Biol. 2007;6:4.
Article
PubMed Central
Google Scholar
Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell. 2008;19:352–67.
Article
CAS
PubMed
PubMed Central
Google Scholar
Regenberg B, Grotkjaer T, Winther O, Fausbøll A, Akesson M, Bro C, Hansen LK, Brunak S, Nielsen J. Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol. 2006;7:R107.
Article
PubMed
PubMed Central
Google Scholar
Berry DB, Gasch AP. Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. Mol Biol Cell. 2008;19:4580–7.
Article
CAS
PubMed Central
Google Scholar
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000;11:4241–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lai L-C, Kissinger MT, Burke PV, Kwast KE. Comparison of the transcriptomic “stress response” evoked by antimycin A and oxygen deprivation in Saccharomyces cerevisiae. BMC Genomics. 2008;9:627.
Article
PubMed
PubMed Central
Google Scholar
Schürch A, Miozzari J, Hütter R. Regulation of tryptophan biosynthesis in Saccharomyces cerevisiae: mode of action of 5-methyl-tryptophan and 5-methyl-tryptophan-sensitive mutants. J Bacteriol. 1974;117:1131–40.
PubMed
PubMed Central
Google Scholar
Wolfner M, Yep D, Messenguy F, Fink GR. Integration of amino acid biosynthesis into the cell cycle of Saccharomyces cerevisiae. J Mol Biol. 1975;96:273–90.
Article
CAS
PubMed
Google Scholar
Jia MH, Larossa RA, Lee JM, Rafalski A, Derose E, Gonye G, Xue Z. Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol Genomics. 2000;3:83–92.
CAS
PubMed
Google Scholar
Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, Marton MJ. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol. 2001;21:4347–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hinnebusch AG. Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol. 2005;59:407–50.
Article
CAS
PubMed
Google Scholar
Wek SA, Zhu S, Wek RC. The histidyl-tRNA synthetase-related sequence in the eIF-2 alpha protein kinase GCN2 interacts with tRNA and is required for activation in response to starvation for different amino acids. Mol Cell Biol. 1995;15:4497–506.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu S, Sobolev AY, Wek RC. Histidyl-tRNA synthetase-related sequences in GCN2 protein kinase regulate in vitro phosphorylation of eIF-2. J Biol Chem. 1996;271:24989–94.
Article
CAS
PubMed
Google Scholar
Wek RC, Jackson BM, Hinnebusch AG. Juxtaposition of domains homologous to protein kinases and histidyl-tRNA synthetases in GCN2 protein suggests a mechanism for coupling GCN4 expression to amino acid availability. Proc Natl Acad Sci. 1989;86:4579–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dever TE, Feng L, Wek RC, Cigan AM, Donahue TF, Hinnebusch AG. Phosphorylation of initiation factor 2α by protein kinase GCN2 mediates gene-specific translational control of GCN4 in yeast. Cell. 1992;68:585–96.
Article
CAS
PubMed
Google Scholar
Tamari Z, Rosin D, Voichek Y, Barkai N. Coordination of gene expression and growth-rate in natural populations of budding yeast. PLoS One. 2014;9:e88801.
Article
PubMed
PubMed Central
Google Scholar
Gunther WR, Wang Y, Ji Y, Michaelis VK, Hunt ST, Griffin RG, Román-Leshkov Y. Sn-Beta zeolites with borate salts catalyse the epimerization of carbohydrates via an intramolecular carbon shift. Nat Commun. 2012;3:1109.
Article
PubMed
PubMed Central
Google Scholar
Granström TB, Takata G, Tokuda M, Izumori K. Izumoring. J Biosci Bioeng. 2004;97:89–94.
Article
PubMed
Google Scholar
Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ, Liti G, Moses A, Blomberg A. Trait variation in yeast is defined by population history. PLoS Genet. 2011;7:e1002111.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH. Functional discovery via a compendium of expression profiles. Cell. 2000;102:109–26.
Article
CAS
PubMed
Google Scholar
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N. Revealing modular organization in the yeast transcriptional network. Nat Genet. 2002;31:370–7.
CAS
PubMed
Google Scholar
Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell. 2001;12:323–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olsson L, Lindén T, Hahn-Hägerdal B. A rapid chromatographic method for the production of preparative amounts of xylulose. Enzyme Microb Technol. 1994;16:388–94.
Article
CAS
Google Scholar
Wenger JW, Schwartz K, Sherlock G. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae. PLoS Genet. 2010;6:e1000942.
Article
PubMed
PubMed Central
Google Scholar
Kivioja T, Vähärautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2012;9:72–4.
Article
CAS
Google Scholar