Andre S. Ribeiro
Andre S. Ribeiro
Tampere University
Verified email at tuni.fi - Homepage
Title
Cited by
Cited by
Year
A general modeling strategy for gene regulatory networks with stochastic dynamics
A Ribeiro, R Zhu, SA Kauffman
Journal of computational Biology 13 (9), 1630-1639, 2006
1452006
Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models
R Zhu, AS Ribeiro, D Salahub, SA Kauffman
Journal of Theoretical Biology 246 (4), 725-745, 2007
1362007
Noisy attractors and ergodic sets in models of gene regulatory networks
AS Ribeiro, SA Kauffman
Journal of theoretical biology 247 (4), 743-755, 2007
1192007
Mutual information in random Boolean models of regulatory networks
AS Ribeiro, SA Kauffman, J Lloyd-Price, B Samuelsson, JES Socolar
Physical Review E 77 (1), 011901, 2008
1072008
Stochastic and delayed stochastic models of gene expression and regulation
AS Ribeiro
Mathematical biosciences 223 (1), 1-11, 2010
862010
SGN Sim, a stochastic genetic networks simulator
AS Ribeiro, J Lloyd-Price
Bioinformatics 23 (6), 777-779, 2007
742007
Effects of transcriptional pausing on gene expression dynamics
T Rajala, A Häkkinen, S Healy, O Yli-Harja, AS Ribeiro
PLoS Comput Biol 6 (3), e1000704, 2010
662010
Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells
AB Muthukrishnan, M Kandhavelu, J Lloyd-Price, F Kudasov, ...
Nucleic acids research 40 (17), 8472-8483, 2012
582012
Delayed stochastic model of transcription at the single nucleotide level
AS Ribeiro, OP Smolander, T Rajala, A Häkkinen, O Yli-Harja
Journal of Computational Biology 16 (4), 539-553, 2009
582009
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli
A Häkkinen, AB Muthukrishnan, A Mora, JM Fonseca, AS Ribeiro
Bioinformatics 29 (13), 1708-1709, 2013
432013
Single-molecule dynamics of transcription of the lar promoter
M Kandhavelu, A Häkkinen, O Yli-Harja, AS Ribeiro
Physical Biology 9 (2), 026004, 2012
422012
Mytoe: automatic analysis of mitochondrial dynamics
E Lihavainen, J Mäkelä, JN Spelbrink, AS Ribeiro
Bioinformatics 28 (7), 1050-1051, 2012
412012
Stochastic sequence-level model of coupled transcription and translation in prokaryotes
J Mäkelä, J Lloyd-Price, O Yli-Harja, AS Ribeiro
BMC bioinformatics 12 (1), 121, 2011
402011
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps
M Kandhavelu*, H Mannerström*, A Gupta, A Häkkinen, J Lloyd-Price, ...
BMC systems biology 5 (1), 149, 2011
392011
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)
S Chowdhury, M Kandhavelu, O Yli-Harja, AS Ribeiro
BMC bioinformatics 14 (S10), S8, 2013
372013
Dissecting the stochastic transcription initiation process in live Escherichia coli
J Lloyd-Price, S Startceva, V Kandavalli, JG Chandraseelan, N Goncalves, ...
DNA Research 23 (3), 203-214, 2016
362016
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations
J Lloyd-Price, A Gupta, AS Ribeiro
Bioinformatics 28 (22), 3004-3005, 2012
352012
Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase
A Fukuoh, G Cannino, M Gerards, S Buckley, S Kazancioglu, F Scialo, ...
Molecular systems biology 10 (6), 734, 2014
342014
In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter
J Mäkelä, M Kandhavelu, SMD Oliveira, JG Chandraseelan, J Lloyd-Price, ...
Nucleic acids research 41 (13), 6544-6552, 2013
342013
Reversible disruption of neuronal mitochondria by ischemic and traumatic injury revealed by quantitative two-photon imaging in the neocortex of anesthetized mice
M Kislin, J Sword, IV Fomitcheva, D Croom, E Pryazhnikov, E Lihavainen, ...
Journal of Neuroscience 37 (2), 333-348, 2017
332017
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