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Results: 1 to 20 of 23

1.

Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking.

Gupta A, Lloyd-Price J, Oliveira SM, Yli-Harja O, Muthukrishnan AB, Ribeiro AS.

Phys Biol. 2014 Nov 10;11(6):066005. doi: 10.1088/1478-3975/11/6/066005.

PMID:
25382420
[PubMed - in process]
2.

In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins.

Gupta A, Lloyd-Price J, Ribeiro AS.

In Silico Biol. 2014 Oct 13. [Epub ahead of print]

PMID:
25318468
[PubMed - as supplied by publisher]
3.

In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli.

Gupta A, Lloyd-Price J, Neeli-Venkata R, Oliveira SM, Ribeiro AS.

Biophys J. 2014 May 6;106(9):1928-37. doi: 10.1016/j.bpj.2014.03.035.

PMID:
24806925
[PubMed - indexed for MEDLINE]
4.

Dynamics of small genetic circuits subject to stochastic partitioning in cell division.

Lloyd-Price J, Tran H, Ribeiro AS.

J Theor Biol. 2014 Sep 7;356:11-9. doi: 10.1016/j.jtbi.2014.04.018. Epub 2014 Apr 23.

PMID:
24768865
[PubMed - in process]
5.

Bistability in a stochastic RNA-mediated gene network.

Lloyd-Price J, Ribeiro AS.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Sep;88(3):032714. Epub 2013 Sep 23.

PMID:
24125301
[PubMed - indexed for MEDLINE]
6.

In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter.

Mäkelä J, Kandhavelu M, Oliveira SM, Chandraseelan JG, Lloyd-Price J, Peltonen J, Yli-Harja O, Ribeiro AS.

Nucleic Acids Res. 2013 Jul;41(13):6544-52. doi: 10.1093/nar/gkt350. Epub 2013 May 3.

PMID:
23644285
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Effects of gene length on the dynamics of gene expression.

Ribeiro AS, Häkkinen A, Lloyd-Price J.

Comput Biol Chem. 2012 Dec;41:1-9. doi: 10.1016/j.compbiolchem.2012.10.002. Epub 2012 Oct 22.

PMID:
23142668
[PubMed - indexed for MEDLINE]
8.

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter.

Kandhavelu M, Lloyd-Price J, Gupta A, Muthukrishnan AB, Yli-Harja O, Ribeiro AS.

FEBS Lett. 2012 Nov 2;586(21):3870-5. doi: 10.1016/j.febslet.2012.09.014. Epub 2012 Sep 24.

PMID:
23017207
[PubMed - indexed for MEDLINE]
Free Article
9.

SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations.

Lloyd-Price J, Gupta A, Ribeiro AS.

Bioinformatics. 2012 Nov 15;28(22):3004-5. doi: 10.1093/bioinformatics/bts556. Epub 2012 Sep 26.

PMID:
23014631
[PubMed - indexed for MEDLINE]
Free Article
10.

Robustness and information propagation in attractors of Random Boolean Networks.

Lloyd-Price J, Gupta A, Ribeiro AS.

PLoS One. 2012;7(7):e42018. doi: 10.1371/journal.pone.0042018. Epub 2012 Jul 30.

PMID:
22860048
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells.

Muthukrishnan AB, Kandhavelu M, Lloyd-Price J, Kudasov F, Chowdhury S, Yli-Harja O, Ribeiro AS.

Nucleic Acids Res. 2012 Sep 1;40(17):8472-83. Epub 2012 Jun 22.

PMID:
22730294
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time.

Lloyd-Price J, Häkkinen A, Kandhavelu M, Marques IJ, Chowdhury S, Lihavainen E, Yli-Harja O, Ribeiro AS.

J Bacteriol. 2012 Apr;194(7):1747-52. doi: 10.1128/JB.06500-11. Epub 2012 Jan 27.

PMID:
22287517
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Dynamics of a genetic toggle switch at the nucleotide and codon levels.

Potapov I, Lloyd-Price J, Yli-Harja O, Ribeiro AS.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031903. Epub 2011 Sep 1. Erratum in: Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec;84(6 Pt 2):069903.

PMID:
22060399
[PubMed - indexed for MEDLINE]
14.

Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli.

Lloyd-Price J, Lehtivaara M, Kandhavelu M, Chowdhury S, Muthukrishnan AB, Yli-Harja O, Ribeiro AS.

Mol Biosyst. 2012 Feb;8(2):565-71. doi: 10.1039/c1mb05100h. Epub 2011 Nov 3.

PMID:
22048277
[PubMed - indexed for MEDLINE]
15.

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps.

Kandhavelu M, Mannerström H, Gupta A, Häkkinen A, Lloyd-Price J, Yli-Harja O, Ribeiro AS.

BMC Syst Biol. 2011 Sep 25;5:149. doi: 10.1186/1752-0509-5-149.

PMID:
21943372
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Stochastic sequence-level model of coupled transcription and translation in prokaryotes.

Mäkelä J, Lloyd-Price J, Yli-Harja O, Ribeiro AS.

BMC Bioinformatics. 2011 Apr 26;12:121. doi: 10.1186/1471-2105-12-121.

PMID:
21521517
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Diversity of temporal correlations between genes in models of noisy and noiseless gene networks.

Ribeiro AS, Lloyd-Price J, Chowdhury S, Yli-Harja O.

Biosystems. 2011 May-Jun;104(2-3):136-44. doi: 10.1016/j.biosystems.2011.02.003. Epub 2011 Feb 26.

PMID:
21356270
[PubMed - indexed for MEDLINE]
18.

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.

BMC Syst Biol. 2010 Oct 26;4:143. doi: 10.1186/1752-0509-4-143.

PMID:
20977725
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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

Ribeiro AS, Häkkinen A, Mannerström H, Lloyd-Price J, Yli-Harja O.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jan;81(1 Pt 1):011912. Epub 2010 Jan 22.

PMID:
20365404
[PubMed - indexed for MEDLINE]
20.

Quantifying local structure effects in network dynamics.

Ribeiro AS, Lloyd-Price J, Kesseli J, Häkkinen A, Yli-Harja O.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Nov;78(5 Pt 2):056108. Epub 2008 Nov 24.

PMID:
19113191
[PubMed]
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