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For: Muthukrishnan AB, Kandhavelu M, Lloyd-Price J, Kudasov F, Chowdhury S, Yli-Harja O, Ribeiro AS. Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells. Nucleic Acids Res 2012;40:8472-83. [PMID: 22730294 PMCID: PMC3458540 DOI: 10.1093/nar/gks583] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Chauhan V, Baptista ISC, Arsh AM, Jagadeesan R, Dash S, Ribeiro AS. Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation. Biochemistry 2024. [PMID: 38997112 DOI: 10.1021/acs.biochem.4c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
2
Ma M, Szavits-Nossan J, Singh A, Grima R. Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction. Math Biosci 2024;373:109204. [PMID: 38710441 DOI: 10.1016/j.mbs.2024.109204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
3
Szavits-Nossan J, Grima R. Solving stochastic gene-expression models using queueing theory: A tutorial review. Biophys J 2024;123:1034-1057. [PMID: 38594901 PMCID: PMC11079947 DOI: 10.1016/j.bpj.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 02/12/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]  Open
4
Stevanovic M, Teuber Carvalho JP, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures. Phys Biol 2024;21:036002. [PMID: 38412523 PMCID: PMC10988634 DOI: 10.1088/1478-3975/ad2d64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/25/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
5
Stevanovic M, Carvalho JPT, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance to metabolism explains emergence of heterogeneity during drug exposures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558994. [PMID: 37790326 PMCID: PMC10542528 DOI: 10.1101/2023.09.22.558994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
6
Weidemann DE, Holehouse J, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. SCIENCE ADVANCES 2023;9:eadh5138. [PMID: 37556551 PMCID: PMC10411910 DOI: 10.1126/sciadv.adh5138] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
7
Weidemann DE, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531283. [PMID: 36945401 PMCID: PMC10028819 DOI: 10.1101/2023.03.06.531283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
8
Öcal K, Gutmann MU, Sanguinetti G, Grima R. Inference and uncertainty quantification of stochastic gene expression via synthetic models. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022;19:20220153. [PMID: 35858045 PMCID: PMC9277240 DOI: 10.1098/rsif.2022.0153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
9
Stevanovic M, Boukéké-Lesplulier T, Hupe L, Hasty J, Bittihn P, Schultz D. Nutrient Gradients Mediate Complex Colony-Level Antibiotic Responses in Structured Microbial Populations. Front Microbiol 2022;13:740259. [PMID: 35572643 PMCID: PMC9093743 DOI: 10.3389/fmicb.2022.740259] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022]  Open
10
Reuter A, Virolle C, Goldlust K, Berne-Dedieu A, Nolivos S, Lesterlin C. Direct visualisation of drug-efflux in liveEscherichia colicells. FEMS Microbiol Rev 2020;44:782-792. [DOI: 10.1093/femsre/fuaa031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022]  Open
11
Häkkinen A, Oliveira SMD, Neeli-Venkata R, Ribeiro AS. Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. J R Soc Interface 2019;16:20190507. [PMID: 31822223 DOI: 10.1098/rsif.2019.0507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
12
Choubey S, Kondev J, Sanchez A. Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells. Biophys J 2019;114:2072-2082. [PMID: 29742401 DOI: 10.1016/j.bpj.2018.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/18/2018] [Accepted: 03/29/2018] [Indexed: 11/25/2022]  Open
13
Durante-Rodríguez G, de Lorenzo V, Nikel PI. A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli. ACS Synth Biol 2018;7:2686-2697. [PMID: 30346720 DOI: 10.1021/acssynbio.8b00345] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Multiscale effects of heating and cooling on genes and gene networks. Proc Natl Acad Sci U S A 2018;115:E10797-E10806. [PMID: 30341217 PMCID: PMC6233105 DOI: 10.1073/pnas.1810858115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
15
Choubey S. Nascent RNA kinetics: Transient and steady state behavior of models of transcription. Phys Rev E 2018;97:022402. [PMID: 29548128 DOI: 10.1103/physreve.97.022402] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Indexed: 11/07/2022]
16
Schultz D, Palmer AC, Kishony R. Regulatory Dynamics Determine Cell Fate following Abrupt Antibiotic Exposure. Cell Syst 2017;5:509-517.e3. [PMID: 29102611 DOI: 10.1016/j.cels.2017.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/26/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023]
17
van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017;8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023]  Open
18
Jong WSP, Vikström D, Houben D, van den Berg van Saparoea HB, de Gier JW, Luirink J. Application of an E. coli signal sequence as a versatile inclusion body tag. Microb Cell Fact 2017;16:50. [PMID: 28320377 PMCID: PMC5359840 DOI: 10.1186/s12934-017-0662-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 03/10/2017] [Indexed: 12/18/2022]  Open
19
Desponds J, Tran H, Ferraro T, Lucas T, Perez Romero C, Guillou A, Fradin C, Coppey M, Dostatni N, Walczak AM. Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos. PLoS Comput Biol 2016;12:e1005256. [PMID: 27942043 PMCID: PMC5152799 DOI: 10.1371/journal.pcbi.1005256] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/19/2016] [Indexed: 12/21/2022]  Open
20
Oliveira SMD, Häkkinen A, Lloyd-Price J, Tran H, Kandavalli V, Ribeiro AS. Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLoS Comput Biol 2016;12:e1005174. [PMID: 27792724 PMCID: PMC5085040 DOI: 10.1371/journal.pcbi.1005174] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/23/2016] [Indexed: 11/19/2022]  Open
21
Effects of σ factor competition are promoter initiation kinetics dependent. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016;1859:1281-8. [DOI: 10.1016/j.bbagrm.2016.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 01/29/2023]
22
Gupta A, Lloyd-Price J, Ribeiro AS. In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biol 2016;12:9-21. [PMID: 25318468 PMCID: PMC4923715 DOI: 10.3233/isb-140462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
23
Lloyd-Price J, Startceva S, Kandavalli V, Chandraseelan JG, Goncalves N, Oliveira SMD, Häkkinen A, Ribeiro AS. Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Res 2016;23:203-14. [PMID: 27026687 PMCID: PMC4909308 DOI: 10.1093/dnares/dsw009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/11/2016] [Indexed: 02/01/2023]  Open
24
Häkkinen A, Ribeiro AS. Characterizing rate limiting steps in transcription from RNA production times in live cells. Bioinformatics 2016;32:1346-52. [PMID: 26722120 DOI: 10.1093/bioinformatics/btv744] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/15/2015] [Indexed: 11/13/2022]  Open
25
Viswanathan A, Anufrieva O, Sala A, Yli-Harja O, Kandhavelu M. Phase-dependent dynamics of the lac promoter under nutrient stress. Res Microbiol 2016;167:451-61. [PMID: 27106257 DOI: 10.1016/j.resmic.2016.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/04/2016] [Accepted: 04/04/2016] [Indexed: 11/26/2022]
26
Oliveira SMD, Neeli-Venkata R, Goncalves NSM, Santinha JA, Martins L, Tran H, Mäkelä J, Gupta A, Barandas M, Häkkinen A, Lloyd-Price J, Fonseca JM, Ribeiro AS. Increased cytoplasm viscosity hampers aggregate polar segregation inEscherichia coli. Mol Microbiol 2015;99:686-99. [DOI: 10.1111/mmi.13257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2015] [Indexed: 12/11/2022]
27
Zimmer C, Häkkinen A, Ribeiro AS. Estimation of kinetic parameters of transcription from temporal single-RNA measurements. Math Biosci 2015;271:146-53. [PMID: 26522167 DOI: 10.1016/j.mbs.2015.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/07/2015] [Accepted: 10/01/2015] [Indexed: 11/27/2022]
28
Tran H, Oliveira SMD, Goncalves N, Ribeiro AS. Kinetics of the cellular intake of a gene expression inducer at high concentrations. MOLECULAR BIOSYSTEMS 2015. [PMID: 26223179 DOI: 10.1039/c5mb00244c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
29
Mitarai N, Semsey S, Sneppen K. Dynamic competition between transcription initiation and repression: Role of nonequilibrium steps in cell-to-cell heterogeneity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015;92:022710. [PMID: 26382435 DOI: 10.1103/physreve.92.022710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 06/05/2023]
30
Häkkinen A, Ribeiro AS. Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinformatics 2015;31:69-75. [PMID: 25189780 DOI: 10.1093/bioinformatics/btu592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
31
Gupta A, Lloyd-Price J, Neeli-Venkata R, Oliveira SMD, Ribeiro AS. In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli. Biophys J 2014;106:1928-37. [PMID: 24806925 DOI: 10.1016/j.bpj.2014.03.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 10/25/2022]  Open
32
Gupta A, Lloyd-Price J, Oliveira SMD, Yli-Harja O, Muthukrishnan AB, Ribeiro AS. Robustness of the division symmetry inEscherichia coliand functional consequences of symmetry breaking. Phys Biol 2014;11:066005. [DOI: 10.1088/1478-3975/11/6/066005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
33
Muthukrishnan AB, Martikainen A, Neeli-Venkata R, Ribeiro AS. In vivo transcription kinetics of a synthetic gene uninvolved in stress-response pathways in stressed Escherichia coli cells. PLoS One 2014;9:e109005. [PMID: 25268540 PMCID: PMC4182640 DOI: 10.1371/journal.pone.0109005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/29/2014] [Indexed: 11/27/2022]  Open
34
Xiao S, Zhang JY, Wu J, Wu RY, Xia Y, Zheng KW, Hao YH, Zhou X, Tan Z. Formation of DNA:RNA Hybrid G-Quadruplexes of Two G-Quartet Layers in Transcription: Expansion of the Prevalence and Diversity of G-Quadruplexes in Genomes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
35
Xiao S, Zhang JY, Wu J, Wu RY, Xia Y, Zheng KW, Hao YH, Zhou X, Tan Z. Formation of DNA:RNA hybrid G-quadruplexes of two G-quartet layers in transcription: expansion of the prevalence and diversity of G-quadruplexes in genomes. Angew Chem Int Ed Engl 2014;53:13110-4. [PMID: 25267250 DOI: 10.1002/anie.201407045] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/17/2014] [Indexed: 01/04/2023]
36
Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014;114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
37
Hakkinen A, Kandhavelu M, Garasto S, Ribeiro AS. Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinformatics 2014;30:1146-1153. [DOI: 10.1093/bioinformatics/btt766] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/25/2013] [Indexed: 11/14/2022]  Open
38
Häkkinen A, Tran H, Yli-Harja O, Ingalls B, Ribeiro AS. Effects of multimerization on the temporal variability of protein complex abundance. BMC SYSTEMS BIOLOGY 2013;7 Suppl 1:S3. [PMID: 24267954 PMCID: PMC3750523 DOI: 10.1186/1752-0509-7-s1-s3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
39
Lloyd-Price J, Ribeiro AS. Bistability in a stochastic RNA-mediated gene network. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013;88:032714. [PMID: 24125301 DOI: 10.1103/physreve.88.032714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/10/2013] [Indexed: 06/02/2023]
40
Häkkinen A, Tran H, Yli-Harja O, Ribeiro AS. Effects of rate-limiting steps in transcription initiation on genetic filter motifs. PLoS One 2013;8:e70439. [PMID: 23940576 PMCID: PMC3734270 DOI: 10.1371/journal.pone.0070439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/18/2013] [Indexed: 11/19/2022]  Open
41
Ribeiro AS. Kinetics of gene expression in bacteria — From models to measurements, and back again. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
42
Mäkelä J, Kandhavelu M, Oliveira SMD, Chandraseelan JG, Lloyd-Price J, Peltonen J, Yli-Harja O, Ribeiro AS. In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Res 2013;41:6544-52. [PMID: 23644285 PMCID: PMC3711423 DOI: 10.1093/nar/gkt350] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
43
Chandraseelan JG, Oliveira SMD, Häkkinen A, Tran H, Potapov I, Sala A, Kandhavelu M, Ribeiro AS. Effects of temperature on the dynamics of the LacI-TetR-CI repressilator. MOLECULAR BIOSYSTEMS 2013;9:3117-23. [DOI: 10.1039/c3mb70203k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
44
Ribeiro AS, Häkkinen A, Lloyd-Price J. Effects of gene length on the dynamics of gene expression. Comput Biol Chem 2012;41:1-9. [PMID: 23142668 DOI: 10.1016/j.compbiolchem.2012.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 10/11/2012] [Accepted: 10/11/2012] [Indexed: 01/06/2023]
45
Lloyd-Price J, Gupta A, Ribeiro AS. SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. ACTA ACUST UNITED AC 2012;28:3004-5. [PMID: 23014631 DOI: 10.1093/bioinformatics/bts556] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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