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Items: 1 to 20 of 380

1.

Genome-wide system analysis reveals stable yet flexible network dynamics in yeast.

Gustafsson M, Hörnquist M, Björkegren J, Tegnér J.

IET Syst Biol. 2009 Jul;3(4):219-28. doi: 10.1049/iet-syb.2008.0112.

PMID:
19640161
2.

The properties of hub proteins in a yeast-aggregated cell cycle network and its phase sub-networks.

Wu X, Guo J, Zhang DY, Lin K.

Proteomics. 2009 Oct;9(20):4812-24. doi: 10.1002/pmic.200900053.

PMID:
19743420
3.

Few crucial links assure checkpoint efficiency in the yeast cell-cycle network.

Stoll G, Rougemont J, Naef F.

Bioinformatics. 2006 Oct 15;22(20):2539-46. Epub 2006 Aug 7.

PMID:
16895923
4.

Genomic analysis of regulatory network dynamics reveals large topological changes.

Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M.

Nature. 2004 Sep 16;431(7006):308-12.

5.

Integrated analysis of multiple data sources reveals modular structure of biological networks.

Lu H, Shi B, Wu G, Zhang Y, Zhu X, Zhang Z, Liu C, Zhao Y, Wu T, Wang J, Chen R.

Biochem Biophys Res Commun. 2006 Jun 23;345(1):302-9. Epub 2006 Apr 27.

PMID:
16690033
6.

Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.

Chen HC, Lee HC, Lin TY, Li WH, Chen BS.

Bioinformatics. 2004 Aug 12;20(12):1914-27. Epub 2004 Mar 25.

PMID:
15044243
7.

Detecting biological associations between genes based on the theory of phase synchronization.

Kim CS, Riikonen P, Salakoski T.

Biosystems. 2008 May;92(2):99-113. doi: 10.1016/j.biosystems.2007.12.006. Epub 2008 Jan 11.

PMID:
18289772
8.

Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.

Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, Charnock-Jones DS, Print C, Miyano S.

Bioinformatics. 2008 Apr 1;24(7):932-42. doi: 10.1093/bioinformatics/btm639. Epub 2008 Feb 21.

PMID:
18292116
9.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203. doi: 10.1186/1471-2105-9-203.

10.
11.

Connectivity in the yeast cell cycle transcription network: inferences from neural networks.

Hart CE, Mjolsness E, Wold BJ.

PLoS Comput Biol. 2006 Dec 22;2(12):e169. Epub 2006 Oct 30.

12.

Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae.

Cokus S, Rose S, Haynor D, Grønbech-Jensen N, Pellegrini M.

BMC Bioinformatics. 2006 Aug 16;7:381.

13.

Stability of functions in Boolean models of gene regulatory networks.

Rämö P, Kesseli J, Yli-Harja O.

Chaos. 2005 Sep;15(3):34101.

PMID:
16252995
14.

Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network.

Lau KY, Ganguli S, Tang C.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):051907. Epub 2007 May 9.

PMID:
17677098
15.

Modular organization of protein interaction networks.

Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH.

Bioinformatics. 2007 Jan 15;23(2):207-14. Epub 2006 Nov 8. Erratum in: Bioinformatics. 2007 Apr 1;23(7):916.

PMID:
17092991
16.

Proteome survey reveals modularity of the yeast cell machinery.

Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G.

Nature. 2006 Mar 30;440(7084):631-6. Epub 2006 Jan 22.

PMID:
16429126
17.

Understanding signaling in yeast: Insights from network analysis.

Arga KY, Onsan ZI, Kirdar B, Ulgen KO, Nielsen J.

Biotechnol Bioeng. 2007 Aug 1;97(5):1246-58.

PMID:
17252576
18.

Robustness and adaptation reveal plausible cell cycle controlling subnetwork in Saccharomyces cerevisiae.

Huang JY, Huang CW, Kao KC, Lai PY.

Gene. 2013 Apr 10;518(1):35-41. doi: 10.1016/j.gene.2012.11.088. Epub 2012 Dec 27.

PMID:
23274654
19.

Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity.

Braunewell S, Bornholdt S.

J Theor Biol. 2007 Apr 21;245(4):638-43. Epub 2006 Nov 21.

PMID:
17204290
20.

Identification of transcription factor cooperativity via stochastic system model.

Chang YH, Wang YC, Chen BS.

Bioinformatics. 2006 Sep 15;22(18):2276-82. Epub 2006 Jul 14.

PMID:
16844711

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