Enhancing yeast transcription analysis through integration of heterogeneous data

Current Genomics

Volumn 5, Issue 8, 2004, Pages 673-686

  Grotkjaer T ^a   Nielsen, J ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Cluster analysis; DNA microarray; Functional genomics; Mathematical modelling; Saccharomyces cerevisiae; Systems biology

Indexed keywords

MESSENGER RNA;

CELL CYCLE PARAMETERS; CLUSTER ANALYSIS; DATA ANALYSIS; DNA MICROARRAY; FUNGAL STRAIN; FUNGUS GROWTH; GENE AMPLIFICATION; GENETIC TRANSCRIPTION; GROWTH RATE; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; MOLECULAR MECHANICS; NONHUMAN; PROBABILITY; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REVIEW; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 10644285716     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389202043348472     Document Type: Review

References (100)

1. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W,, Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H., Oliver, S.G. Life with 6000 genes. Science 1996, 274 5287): 546, 563-567.
2. Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., Brown, E.L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 1996, 14(13): 1675-1680.
3. Aebersold, R., Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422(6928): 198-207.
4. Phizicky, E., Bastiaens, P.I., Zhu, H., Snyder, M., Fields, S. Protein analysis on a proteomic scale. Nature 2003, 422 6928): 208-215.
5. Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M.C., Berden, J.A., Brindle, K.M., Kell, D.B., Rowland, J.J., Westerhoff, H.V., v Dam, K., Oliver, S.G. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 2001, 19: 45-50.
6. Gombert, A.K., dos, Santos, M.M., Christensen, B., Nielsen, J. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 2001, 183(4): 1441-1451.
7. Szyperski, T. C-13-NMR, MS and metabolic flux balancing in biotechnology research. Q. Rev. Biophys. 1998, 31: 41-106.
8. Draghici, S. Statistical intelligence: effective analysis of high-density microarray data. Drug Discov. Today 2002, 7 11): S55-S63.
9. Cui, X., Churchill, G.A. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 2003, 4(4): 210.
10. Pan, W. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18(4): 546-554,
11. Benjamini, Y., Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. 1995, 57: 289-300.
12. Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 1998, 95(25): 14863-14868.
13. Kitano, H. Systems biology: a brief overview. Science 2002, 295(5560): 1662-1664.
14. Giaever, G. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418(6896): 387-391.
15. Tong, A.H.Y., Lesage, G., Bader, G.D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G.F., Brost, R.L., Chang, M., Chen, Y., Cheng, X., Chua, G., Friesen, H., Goldberg, D.S., Haynes, J., Humphries, C., He, G., Hussein, S., Ke, L., Krogan, N., Li, Z., Levinson, J.N., Lu, H., Menard, P., Munyana, C., Parsons, A.B., Ryan, O., Tonikian, R., Roberts, T., Sdicu, A.M., Shapiro, J., Sheikh, B., Suter, B., Wong, S.L., Zhang, L.V., Zhu, H., Burd, C.G., Munro, S., Sander, C., Rine, J., Greenblatt, J., Peter, M., Bretscher, A., Bell, G., Roth, F.P,, Brown, G.W., Andrews, B., Bussey, H., Boone, C. Global mapping of the yeast genetic interaction network. Science 2004, 303(5659): 808-813.
16. Castrillo, J.I., Oliver, S.G. Yeast as a touchstone in post-genomic Research.: strategies for integrative analysis in functional genomics. J. Biochem. Mol. Biol. 2004, 37: 93-106.
17. Goesmann, A., Linke, B., Rupp, O., Krause, L., Bartels, D., Dondrup, M., McHardy, A.C., Wilke, A., Puhler, A., Meyer, F. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. J. Biotechnol. 2003, 106(2-3): 157-167.
18. Ideker, T., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Eng, J.K., Bumgarner, R., Goodlett, D.R., Aebersold, R., Hood, L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292(5518 : 929-934.
19. Ideker, T., Ozier, O., Schwikowski, B., Siegel, A.F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002, 18 Suppl 1: S233-S240.
20. Segal, E., Wang, H., Koller, D. Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics 2003, 19 Suppl 1: 1264-1272.
21. Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., Friedman, N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 2003, 34(2): 166-176.
22. Bar-Joseph, Z., Gerber, G.K., Lee, T.I., Rinaldi, N.J., Yoo, J.Y., Robert, F., Gordon, D.B., Fraenkel, E., Jaakkola, T.S., Young, R.A., Gifford, D.K. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 2003, 21(11): 1337-1342.
23. Chen, K.C., Csikasz-Nagy, A., Gyorffy, B., Val, J., Novak, B., Tyson, J.J. Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol. Biol. Cell 2000, 11: 369-392.
24. Altman, R.B., Raychaudhuri, S. Whole-genome expression analysis: challenges beyond clustering. Curr. Opin. Struct. Biol. 2001, 11(3): 340-347.
25. Fodor, S.P., Rava, R.P., Huang, X.C., Pease, A.C., Holmes, C.P., Adams, CL. Multiplexed biochemical assays with biological chips. Nature 1993, 364(6437): 555-556.
26. Schena, M., Shalon, D., Davis, R.W., Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235): 467-470.
27. Eisen, M.B. Brown, P.O: DNA arrays for analysis of gene expression. Methods Enzymol. 1999, 303: 179-205.
28. Zhang, L., Miles, M.F., Aldape, K.D. A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol. 2003, 21(7): 818-821.
29. Churchill, G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 2002, 32 Suppl: 490-495.
30. Quackenbush, J. Microarray data normalization and transformation. Nat. Genet. 2002, 32 Suppl: 496-501.
31. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., Vingron, M, Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29(4): 365-371.
32. Gollub, J., Ball, C.A., Binkley, G., Demeter, J., Finkelstein, D.B., Hebert, J.M., Hernandez-Boussard, T., Jin, H., Kaloper, M., Matese, J.C,, Schroeder, M., Brown, P.O., Botstein, D., Sherlock, G. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 2003, 31: 94-96.
33. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., Chu, A.M., Connelly, C., Davis, K., Dietrich, F., Dow, S.W., Bakkoury, M.E., Foury, F., Friend, S.H., Gentalen, E., Giaever, G., Hegemann, J.H., Jones, T., Laub, M., Liao, H., Davis, R.W. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285(5429): 901-906.
34. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., Kidd, M.J., King, A.M., Meyer, M.R., Slade, D., Lum, P.Y., Stepaniants, S.B., Shoemaker, D.D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., Friend, S.H. Functional discovery via a compendium of expression profiles. Cell 2000, 102: 109-126.
35. Hayes, A., Zhang, N., Wu, J., Butler, P.R., Hauser, N.C., Hoheisel, J.D., Lim, F.L., Sharrocks, A.D., Oliver, S.G. Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae. Methods 2002, 26(3): 281-290.
36. DeRisi, J.L., Iyer, V.R., Brown, P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278(5338): 680-686.
37. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, PO., Herskowitz, I. The transcriptional program of sporulation in budding yeast. Science 1998, 282(5389): 699-705.
38. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E,, Landsman, D., Lockhart, D.J., Davis, R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 1998, 2: 65-73.
39. Nielsen, J., Villadsen, J., Lidén, G. Bioreaction engineering principles. New York: Kluwer Academic / Plenum Publishers, 2nd edition 2003.
40. Jones, D.L., Petty, J., Hoyle, D.C., Hayes, A., Ragni, E., Popolo, L., Oliver, S.G., Stateva, L.I. Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. Physiol. Genomics 2003, 16: 107-118.
41. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9(12): 3273-3297.
42. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D., Brown, P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 2000, 11(12): 4241-4257.
43. Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T.I., True, H.L., Lander, E.S., Young, R.A. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 2001, 12(2): 323-337.
44. Piper, M.D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J., Pronk, J.T. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 2002, 277(40): 37001-37008.
45. Boer, V.M., de Winde, J.H., Pronk, J.T., Piper, M.D.W. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus or sulfur. J. Biol. Chem. 2002, 278 5): 3265-3274.
46. Daran-Lapujade, P., Jansen, M.L., Daran, J,M., Gulik, W.V., Winde, J.H.D., Pronk, J.T. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae, a chemostat culture study. J. Biol. Chem. 2004, 279(10): 9125-9138.
47. ter Linde, J.J., Liang, H., Davis, R.W., Steensma, H.Y., van Dijken, J.P., Pronk, J.T. Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J. Bacteriol. 1999, 181(24): 7409-7413.
48. Wu, J., Zhang, N., Hayes, A., Panoutsopoulou, K., Oliver, S.G. Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation. Proc. Natl. Acad. Sci. USA 2004, 101(9): 3148-3153.
49. Li, C., Wong, W.H. Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 2001, 98: 31-36.
50. van de Peppel, J., Kemmeren, P., van Bakel, H., Radonjic, M., van Leenen, D., Holstege, F.C. Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep. 2003, 4(4): 387-393.
51. Tyson, C.B., Lord, P.G., Wheals, A.E. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J. Bacteriol. 1979, 138: 92-98.
52. Waldron, C., Lacroute, F. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J. Bacteriol. 1975, 122(3): 855-865.
53. Parada, G., Acevedo, F. On the relation of temperature and RNA content to the specific growth rate in Saccharomyces cerevisiae. Biotechnol. Bioeng. 1983, 25(11): 2785-2788.
54. Gasch, A.P. Yeast genomic expression studies using DNA microarrays. Methods Enzymol. 2002, 350: 393-414.
55. MacKay, D.J.C. Information Theory, Inference and Learning Algorithms. Cambridge: Cambridge University Press, 1st edition 2003
56. Gibbons, F.D., Roth, F.P. Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res. 2002, 12(10): 1574-1581.
57. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q, Kitareewan, S., Dmitrovsky, E., Lander, E.S., Golub, T.R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 1999, 96(6): 2907-2912.
58. Ghosh, D., Chinnaiyan, A.M. Mixture modelling of gene expression data from microarray experiments. Bioinformatics 2002, 18(2): 275-286.
59. McLachlan, G.J., Bean, R.W., Peel, D. A mixture model-based approach to the clustering of microarray expression data. Bioinformatics 2002, 18(3): 413-422.
60. Blatt, M., Wiseman, S., Domany, E. Superparamagnetic clustering of data. Phys. Rev. Lett. 1996, 76(18): 3251-3254.
61. Kaminski, N., Friedman, N. Practical approaches to analyzing results of microarray experiments. Am. J. Respir. Cell Mol. Biol. 2002, 27(2): 125-132.
62. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., Barkai, N. Revealing modular organization in the yeast transcriptional network. Nat. Genet. 2002, 31(4): 370-377.
63. Kitano, H. Systems biology: Toward system-level understanding of biological systems. In Foundations of systems biology, 1st edition. Edited by Kitano H, MIT Press 2001: 1-36.
64. Gygi, S.P., Rochon, Y., Franza, B.R., Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19(3): 1720-1730.
65. Futcher, B., Latter, G.I., Monardo, P., McLaughlin, C.S., Garrels, JI. A sampling of the yeast proteome. Mol. Cell Biol. 1999, 19(11): 7357-7368.
66. Fraenkel, D.G. The top genes: on the distance from transcript to function in yeast glycolysis. Curr. Opin. Microbiol. 2003, 6(2): 198-201.
67. ter Kuile, B.H., Westerhoff, H.V. Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 2001, 500(3): 169-171.
68. Ihmels, J., Levy, R., Barkai, N. Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat. Biotechnol. 2003.
69. van Helden, J., Andre, B., Collado-Vides, J. A web site for the computational analysis of yeast regulatory sequences. Yeast 2000, 16(2): 177-187.
70. Forster, J., Famili, I., Fu, P., Palsson, B.O., Nielsen, J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13(2): 244-253.
71. Duarte, N.C., Herrgard, M.J., Palsson, B. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 2004, 5(1): 63-73.
72. Stephanopoulos, G.N., Aristidou, A., Nielsen, J. Metabolic engineering principles and methodologies. San Diego: Academic Press, 1st edition 1998.
73. Forster, J., Famili, I., Palsson, B.O., Nielsen, J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS. 2003, 7(2): 193-202.
74. Famili, I., Forster, J., Nielsen, J., Palsson, B.O. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 2003,100(23): 13134-13139.
75. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., Bork, P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417 6887): 399-403.
76. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25: 25-29.
77. Dwight, S.S., Harris, M.A., Dolinski, K., Ball, C.A., Binkley, G., Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., Botstein, D., Cherry, J.M. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002, 30 69-72.
78. Ashburner, M., Ball, C.A., Blake, J.A. Creating the Gene Ontology Resource: design and implementation. Genome Res. 2001, 11(8): 1425-1433.
79. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, JS., O'Shea, EK. Global analysis of protein localization in budding yeast. Nature 2003, 425(6959): 686-691.
80. Ahuatzi, D., Herrero, P., de la, CT., Moreno, F. The glucose-regulated nuclear localization of hexokinase 2 in Saccharomyces cerevisiae is Mig1-dependent. J. Biol. Chem. 2004, 279(14): 14440-14446.
81. Mewes, H.W., Heumann, K., Kaps, A., Mayer, K., Pfeiffer, F., Stocker, S., Frishman, D. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 1999, 27: 44-48.
82. Troyanskaya, O.G., Dolinski, K., Owen, A.B., Altman, R.B., Botstein, D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl. Acad. Sci. USA 2003, 100(14): 8348-8353.
83. Fraser, C.M., Eisen, J.A., Salzberg, S.L. Microbial genome sequencing. Nature 2000, 406(6797): 799-803.
84. Friedman, N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303 (5659): 799-805.
85. Jensen, F.V. Bayesian networks and decision graphs, Volume 1 of Statistics for engineering and information science. New York: Springer-Verlag, 1st edition 2001.
86. Pearl, J. Probabilistic reasoning in intelligent systems: networks of plausible inference. San Mateo, CA: Morgan Kaufmann, 1st edition 1988.
87. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13(11): 2498-2504.
88. Ideker, T., Lauffenburger, D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol. 2003, 21(6): 255-262.
89. Zaslaver, A., Mayo, A.E., Rosenberg, R., Bashkin, P., Sberro, H., Tsalyuk, M., Surette, M.G., Alon, U. Just-in-time transcription program in metabolic pathways. Nat. Genet. 2004, 36(5): 486-491.
90. Klipp, E., Heinrich, R., Holzhutter, HG. Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities. Eur. J. Biochem. 2002, 269(22): 5406-5413.
91. Cross, F.R., Archambault, V., Miller, M., Klovstad, M. Testing a mathematical model of the yeast cell cycle. Mol. Biol. Cell 2002, 13: 52-70.
92. Chen, K.C., Calzone, L., Csikasz-Nagy, A., Cross, F.R., Novak, B., Tyson, J.J. Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 2004, 15(8): 3841-3862.
93. von Dassow, G., Meir, E., Munro, E.M., Odell, G.M. The segment polarity network is a robust developmental module. Nature 2000, 406(6792): 188-192.
94. Nielsen, J., Olsson, L. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology. FEMS Yeast Res. 2002, 2(2): 175-181.
95. Daran-Lapujade, P., Daran, J.M., Kotter, P., Petit, T., Piper, M.D.W., Pronk, J.T. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK113-7D using oligonucleotide microarrays. FEMS Yeast Res. 2003, 4 3): 259-269.
96. van Dijken, J.P., Bauer, J., Brambilla, L., Duboc, P., Francois, J.M., Gancedo, C., Giuseppin, M.L.F., Hejjnen, J.J., Hoare, M., Lange, H.C., Madden, E.A., Niederberger, P., Nielsen, J., Parrou, J.L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H.Y., Verrips, C.T., Vindeloev, J., Pronk, J.T. An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb. Technol. 2000, 26 9-10): 706-714.
97. Gaisne, M., Becam, A.M., Verdiere, J., Herbert, C.J. A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288C affects the complex regulatory gene HAP1 (CYP1). Curr. Genet. 1999, 36(4): 195-200.
98. Sherman, F. Getting started with yeast. Methods Enzymol. 2002, 350: 3-41.
99. Vanhalewyn, M., Dumortier, F., Debast, G., Colombo, S., Ma, P., Winderickx, J., Dijck, P.V., Thevelein, J.M. A mutation in Saccharomyces cerevisiae adenylate cyclase, Cyr1K1876M, specifically affects glucose- and acidification-induced cAMP signalling and not the basal cAMP level. Mol. Microbiol. 1999, 33(2): 363-376.
100. Cornell, M., Paton, N.W., Hedeler, C., Kirby, P., Delneri, D., Hayes, A., Oliver, S.G. GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast 2003, 20(15): 1291-1306.