Zobrazit více v PubMed
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., et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 1998;2:65–73.
PubMed
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;9:3273–3297.
PubMed
PMC
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;95:14863–14868.
PubMed
PMC
Chu S., DeRisi J., Eisen M., Mulholland J., Botstein D., Brown P.O., Herskowitz I. The transcriptional program of sporulation in budding yeast. Science. 1998;282:699–705.
PubMed
Holter N.S., Maritan A., Cieplak M., Fedoroff N.V., Banavar J.R. Dynamic modeling of gene expression data. Proc. Natl Acad. Sci. USA. 2001;98:1693–1698.
PubMed
PMC
Holter N.S., Mitra M., Maritan A., Cieplak M., Banavar J.R., Fedoroff N.V. Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl Acad. Sci. USA. 2000;97:8409–8414.
PubMed
PMC
Alter O., Brown P.O., Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA. 2000;97:10101–10106.
PubMed
PMC
Iyer R., Iverson T.M., Accardi A., Miller C. A biological role for prokaryotic ClC chloride channels. Nature. 2002;419:715–718.
PubMed
Simon I., Barnett J., Hannett N., Harbison C.T., Rinaldi N.J., Volkert T.L., Wyrick J.J., Zeitlinger J., Gifford D.K., Jaakkola T.S., et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 2001;106:697–708.
PubMed
Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002;298:799–804.
PubMed
Chen K.C., Wang T.Y., Tseng H.H., Huang C.Y., Kao C.Y. A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics. 2005;21:2883–2890.
PubMed
Chen H.C., Lee H.C., Lin T.Y., Li W.H., Chen B.S. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics. 2004;20:1914–1927.
PubMed
Sasik R., Iranfar N., Hwa T., Loomis W.F. Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. Bioinformatics. 2002;18:61–66.
PubMed
Woolf P.J., Wang Y. A fuzzy logic approach to analyzing gene expression data. Physiol. Genomics. 2000;3:9–15.
PubMed
Nachman I., Regev A., Friedman N. Inferring quantitative models of regulatory networks from expression data. Bioinformatics. 2004;20:I248–I256.
PubMed
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., et al. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 2003;21:1337–1342.
PubMed
Wang W., Cherry J.M., Nochomovitz Y., Jolly E., Botstein D., Li H. Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc. Natl Acad. Sci. USA. 2005;102:1998–2003.
PubMed
PMC
Makita Y., De Hoon M.J., Ogasawara N., Miyano S., Nakai K. Bayesian joint prediction of associated transcription factors in Bacillus subtilis. Pac. Symp. Biocomput. 2005:507–518.
PubMed
Vohradsky J. Neural network model of gene expression. FASEB J. 2001;15:846–854.
PubMed
Vohradsky J. Neural model of the genetic network. J. Biol. Chem. 2001;276:36168–36173.
PubMed
Vu T.T., Vohradsky J. Genexp-a genetic network simulation environment. Bioinformatics. 2002;18:1400–1401.
PubMed
Bar-Joseph Z. Analyzing time series gene expression data. Bioinformatics. 2004;20:2493–2503.
PubMed
de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 2002;9:67–103.
PubMed
Matsuno H., Doi A., Nagasaki M., Miyano S. Hybrid Petri net representation of gene regulatory network. Pac. Symp. Biocomp. 2000:341–352.
PubMed
McAdams H.H., Shapiro L. Circuit simulation of genetic networks. Science. 1995;269:650–656.
PubMed
McAdams H.H., Arkin A. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct. 1998;27:199–224.
PubMed
Dembele D., Kastner P. Fuzzy C-means method for clustering microarray data. Bioinformatics. 2003;19:973–980.
PubMed
Gasch A.P., Eisen M.B. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol. 2002;3:research0059.1–research0059.22.
PubMed
PMC
Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., Church G.M. Systematic determination of genetic network architecture. Nature Genet. 1999;22:281–285.
PubMed
Alter O., Brown P.O., Botstein D. Generalized singular value decomposition for comparative analysis of genome-scale expression datasets of two different organisms. Proc. Natl Acad. Sci. USA. 2003;100:3351–3356.
PubMed
PMC
Iyer V.R., Horak C.E., Scafe C.S., Botstein D., Snyder M., Brown P.O. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001;409:533–538.
PubMed