Andre S Ribeiro
Affiliation: Tampere University of Technology
Tripathi S, Lloyd Price J, Ribeiro A, Yli Harja O, Dehmer M, Emmert Streib F. sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinformatics. 2017;18:325 pubmed publisher
..sgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X. ..
Startceva S, Kandavalli V, Visa A, Ribeiro A. Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression. Biochim Biophys Acta Gene Regul Mech. 2018;: pubmed publisher
Oliveira S, Chandraseelan J, HÃ¤kkinen A, Goncalves N, Yli Harja O, Startceva S, et al
. Single-cell kinetics of a repressilator when implemented in a single-copy plasmid. Mol Biosyst. 2015;11:1939-45 pubmed publisher
..The SCR will be of use in future synthetic circuits, since it complements the array of tasks that the LCR can perform. ..
Tran H, Oliveira S, Gonçalves N, Ribeiro A. Kinetics of the cellular intake of a gene expression inducer at high concentrations. Mol Biosyst. 2015;11:2579-87 pubmed publisher
..7 minutes, strongly affecting cells' response time. The novel methodology followed here should aid the study of cellular intake mechanisms at the single-event level. ..
Neeli Venkata R, Martikainen A, Gupta A, GonÃ§alves N, Fonseca J, Ribeiro A. Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli. J Bacteriol. 2016;198:898-906 pubmed publisher
..We conclude that the energy-free process of the midcell exclusion of aggregates partially loses effectiveness under stressful conditions. ..
Lloyd Price J, Startceva S, Kandavalli V, Chandraseelan J, Gonçalves N, Oliveira S, et al
. Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Res. 2016;23:203-14 pubmed publisher
..The methods employed here should be of use to resolve the rate-limiting steps governing the in vivo dynamics of initiation of prokaryotic promoters, similar to established steady-state assays to resolve the in vitro dynamics. ..
Kandavalli V, Tran H, Ribeiro A. Effects of ? factor competition are promoter initiation kinetics dependent. Biochim Biophys Acta. 2016;1859:1281-8 pubmed publisher
..We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by ? factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation. ..
Neeli Venkata R, Startceva S, Annila T, Ribeiro A. Polar Localization of the Serine Chemoreceptor of Escherichia coli Is Nucleoid Exclusion-Dependent. Biophys J. 2016;111:2512-2522 pubmed publisher
..We conclude that nucleoid exclusion also contributes to the preference of Tsr clusters for polar localization. ..
Mäkelä J, Kandavalli V, Ribeiro A. Rate-limiting steps in transcription dictate sensitivity to variability in cellular components. Sci Rep. 2017;7:10588 pubmed publisher
..We conclude that cell-to-cell and consequent lineage-to-lineage variability in RNA and protein numbers are both promoter sequence-dependent and subject to regulation. ..