Yli-Harja O - Search Results

1

Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time.

Martins L, Mäkelä J, Häkkinen A, Kandhavelu M, Yli-Harja O, Fonseca JM, Ribeiro AS. Martins L, et al. J Theor Biol. 2012 May 21;301:83-94. doi: 10.1016/j.jtbi.2012.02.015. Epub 2012 Feb 20. J Theor Biol. 2012. PMID: 22370562

2

Quantifying local structure effects in network dynamics.

Ribeiro AS, Lloyd-Price J, Kesseli J, Häkkinen A, Yli-Harja O. Ribeiro AS, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Nov;78(5 Pt 2):056108. doi: 10.1103/PhysRevE.78.056108. Epub 2008 Nov 24. Phys Rev E Stat Nonlin Soft Matter Phys. 2008. PMID: 19113191

3

Delayed stochastic model of transcription at the single nucleotide level.

Ribeiro AS, Smolander OP, Rajala T, Häkkinen A, Yli-Harja O. Ribeiro AS, et al. J Comput Biol. 2009 Apr;16(4):539-53. doi: 10.1089/cmb.2008.0153. J Comput Biol. 2009. PMID: 19361326

4

Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch.

Ribeiro AS, Dai X, Yli-Harja O. Ribeiro AS, et al. J Theor Biol. 2009 Sep 7;260(1):66-76. doi: 10.1016/j.jtbi.2009.05.025. Epub 2009 Jun 6. J Theor Biol. 2009. PMID: 19501103

5

Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources.

Dai X, Yli-Harja O, Ribeiro AS. Dai X, et al. Bioinformatics. 2009 Sep 15;25(18):2362-8. doi: 10.1093/bioinformatics/btp411. Epub 2009 Jul 1. Bioinformatics. 2009. PMID: 19570801

6

Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch.

Dai X, Healy S, Yli-Harja O, Ribeiro AS. Dai X, et al. J Theor Biol. 2009 Dec 7;261(3):441-8. doi: 10.1016/j.jtbi.2009.08.024. Epub 2009 Aug 25. J Theor Biol. 2009. PMID: 19712686 Review.

7

Effects of transcriptional pausing on gene expression dynamics.

Rajala T, Häkkinen A, Healy S, Yli-Harja O, Ribeiro AS. Rajala T, et al. PLoS Comput Biol. 2010 Mar 12;6(3):e1000704. doi: 10.1371/journal.pcbi.1000704. PLoS Comput Biol. 2010. PMID: 20300642 Free PMC article.

8

Effects of the promoter open complex formation on gene expression dynamics.

Ribeiro AS, Häkkinen A, Mannerström H, Lloyd-Price J, Yli-Harja O. Ribeiro AS, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan;81(1 Pt 1):011912. doi: 10.1103/PhysRevE.81.011912. Epub 2010 Jan 22. Phys Rev E Stat Nonlin Soft Matter Phys. 2010. PMID: 20365404

9

Dynamical effects of transcriptional pause-prone sites.

Ribeiro AS, Häkkinen A, Healy S, Yli-Harja O. Ribeiro AS, et al. Comput Biol Chem. 2010 Jun;34(3):143-8. doi: 10.1016/j.compbiolchem.2010.04.003. Epub 2010 May 9. Comput Biol Chem. 2010. PMID: 20537588

10

Information propagation within the Genetic Network of Saccharomyces cerevisiae.

Chowdhury S, Lloyd-Price J, Smolander OP, Baici WC, Hughes TR, Yli-Harja O, Chua G, Ribeiro AS. Chowdhury S, et al. BMC Syst Biol. 2010 Oct 26;4:143. doi: 10.1186/1752-0509-4-143. BMC Syst Biol. 2010. PMID: 20977725 Free PMC article.

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