Andre S Ribeiro
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Explore the profile of Andre S Ribeiro including associated specialties, affiliations and a list of published articles.
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Recent Articles
11.
Palma C, Kandavalli V, Bahrudeen M, Minoia M, Chauhan V, Dash S, et al.
Biochim Biophys Acta Gene Regul Mech
. 2020 Mar;
1863(5):194515.
PMID: 32113983
Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of...
12.
Hakkinen A, Oliveira S, Neeli-Venkata R, Ribeiro A
J R Soc Interface
. 2019 Dec;
16(161):20190507.
PMID: 31822223
Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a...
13.
Bahrudeen M, Chauhan V, Palma C, Oliveira S, Kandavalli V, Ribeiro A
J Microbiol Methods
. 2019 Oct;
166:105745.
PMID: 31654657
Estimating the statistics of single-cell RNA numbers has become a key source of information on gene expression dynamics. One of the most informative methods of in vivo single-RNA detection is...
14.
Oliveira S, Goncalves N, Kandavalli V, Martins L, Neeli-Venkata R, Reyelt J, et al.
Sci Rep
. 2019 Mar;
9(1):4486.
PMID: 30872616
Temperature shifts trigger genome-wide changes in Escherichia coli's gene expression. We studied if chromosome integration impacts on a gene's sensitivity to these shifts, by comparing the single-RNA production kinetics of...
15.
Prajapat M, Ribeiro A
R Soc Open Sci
. 2018 Dec;
5(11):181170.
PMID: 30564410
Bacterial gene expression regulation occurs mostly during transcription, which has two main rate-limiting steps: the close complex formation, when the RNA polymerase binds to an active promoter, and the subsequent...
16.
Startceva S, Kandavalli V, Visa A, Ribeiro A
Biochim Biophys Acta Gene Regul Mech
. 2018 Dec;
1862(2):119-128.
PMID: 30557610
Genetic circuits change the status quo of cellular processes when their protein numbers cross thresholds. We investigate the regulation of RNA and protein threshold crossing propensities in Escherichia coli. From...
17.
Martins L, Neeli-Venkata R, Oliveira S, Hakkinen A, Ribeiro A, Fonseca J
Bioinformatics
. 2018 Jun;
34(24):4318-4320.
PMID: 29931314
Summary: Each cell is a phenotypically unique individual that is influenced by internal and external processes, operating in parallel. To characterize the dynamics of cellular processes one needs to observe...
18.
Neeli-Venkata R, Oliveira S, Martins L, Startceva S, Bahrudeen M, Fonseca J, et al.
Phys Biol
. 2018 May;
15(5):056002.
PMID: 29717708
Cell division in Escherichia coli is morphologically symmetric due to, among other things, the ability of these cells to place the Z-ring at midcell. Studies have reported that, at sub-optimal...
19.
Goncalves N, Startceva S, Palma C, Bahrudeen M, Oliveira S, Ribeiro A
Phys Biol
. 2017 Nov;
15(2):026007.
PMID: 29182518
From in vivo single-cell, single-RNA measurements of the activation times and subsequent steady-state active transcription kinetics of a single-copy Lac-ara-1 promoter in Escherichia coli, we characterize the intake kinetics of...
20.
Makela J, Kandavalli V, Ribeiro A
Sci Rep
. 2017 Sep;
7(1):10588.
PMID: 28878283
Cell-to-cell variability in cellular components generates cell-to-cell diversity in RNA and protein production dynamics. As these components are inherited, this should also cause lineage-to-lineage variability in these dynamics. We conjectured...