Laboratory of Biosystem Dynamics (LBD)

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Recent Publications:

2018

  • L Martins, R Neeli-Venkata, SMD Oliveira, A Häkkinen, AS Ribeiro, and JM Fonseca (2018) SCIP: A Single-Cell Image Processor toolbox. Bioinformatics. In press. DOI: 10.1093/bioinformatics/bty505
  • R Neeli-Venkata, SMD Oliveira, L Martins, S Startceva, M Bahrudeen, JM Fonseca, M Minoia, and AS Ribeiro (2018) The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures. Physical Biology 15(5):056002. DOI: 10.1088/1478-3975/aac1cb.
  • NSM Goncalves, S Startceva, CSD Palma, MNM Bahrudeen, SMD Oliveira and AS Ribeiro (2018). Temperature-dependence of the single-cell kinetics of transcription activation in Escherichia coli. Physical Biology 15(2):026007. DOI:10.1088/1478-3975/aa9ddf.  PDF

2017

  • J. Mäkelä, V. Kandavalli and A.S. Ribeiro (2017) Rate-limiting steps in transcription dictate sensitivity to variability in cellular components. Scientific Reports 7:10588. DOI:10.1038/s41598-017-11257-2. PDF 
  • S Tripathi, J Lloyd-Price, AS Ribeiro, O Yli-Harja, M Dehmer, and F Emmert-Streib (2017) sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. BMC Bioinformatics 18:325. DOI 10.1186/s12859-017-1731-8 PDF
  • M Kislin, J Sword, I Fomitcheva, D Croom, E Pryazhnikov, E Lihavainen, D Toptunov, H Rauvala, AS Ribeiro, L Khiroug, and S Kirov (2017) Reversible disruption of the neuronal mitochondria by ischemic and traumatic injury revealed by quantitative two-photon imaging in the neocortex of anesthetized mice. The Journal of Neuroscience 37(2), 333-348. DOI: 10.1523/JNEUROSCI.1510-16.2017. PDF

2016

  • C Zimmer, A Häkkinen and AS Ribeiro (2016) Estimation of kinetic parameters of transcription from temporal single-RNA measurements. Math Biosciences. 271, 146–153. DOI: 10.1016/j.mbs.2015.10.001. PDF
  • SMD Oliveira, R Neeli-Venkata, N Goncalves, JA Santinha, L Martins, H Tran, J Mäkelä, A Gupta, M Barandas, A Häkkinen, J Lloyd-Price, JM Fonseca, and AS Ribeiro (2016) Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli. Mol. Microbiol. 99(4), 686–699. DOI: 10.1111/mmi.13257.  PDF
  • A Häkkinen and AS Ribeiro (2016) Identifying Rate Limiting Steps in Transcription from RNA Production Times in Live Cells. Bioinformatics. 32(9): 1346-1352. DOI: 10.1093/bioinformatics/btv744. PDF
  • R Neeli-Venkata, A Martikainen*, A Gupta*, N Gonçalves*, J Fonseca, and AS Ribeiro (2016) Robustness of the process of nucleoid exclusion of protein aggregates in Escherichia coli. Journal of Bacteriology. 198(6), 898-906. DOI: 10.1128/JB.00848-15.  PDF
  • J Lloyd-Price, S Startceva, V Kandavalli, JG Chandraseelan, N Goncalves, SMD Oliveira, A Häkkinen and AS Ribeiro (2016) Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Research. 23 (3): 203-214. DOI: 10.1093/dnares/dsw009.  PDF
  • VK Kandavalli, H Tran, and AS Ribeiro (2016) Effects of sigma factor competition on the in vivo kinetics of transcription initiation in Escherichia coli. BBA Gene Regulatory Mechanisms 1859, 1281-1288. PDF

For a audio presentation PRESS HERE

  • SMD Oliveira*, A Häkkinen*, J Lloyd-Price, H Tran,  VK Kandavalli, and AS Ribeiro (2016) Temperature-Dependent Model of Multi-Step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLOS Computational Biology 12(10):e1005174. doi: 10.1371/journal.pcbi.1005174.. *Equal contributions. PDF
  • AS Ribeiro (2016) Delays as regulators of the dynamics of genetic circuits. Markov Processes and Related Fields 22, 573-594. PDF
  • R Neeli-Venkata, S Starceva, T Annila, and AS Ribeiro (2016) Polar Localization of the Serine Chemoreceptor of Escherichia coli is Nucleoid Exclusion-Dependent. Biophysical Journal 111, 2512-2522. DOI: 10.1016/j.bpj.2016.10.024. (Get PDF of final article here)(pre-print here)

2015

  • A Gupta, J Lloyd-Price, and AS Ribeiro (2015) In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biology 1(2), 9-21. DOI: 10.3233/ISB-140462. PDF
  • A Häkkinen and AS Ribeiro (2015) Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. Bioinformatics 31(1), 69-75. DOI: 10.1093/bioinformatics/btu592. PDF
  • SMD Oliveira*, JG Chandraseelan*, A Häkkinen, NSM Goncalves, O. Yli-Harja, S. Startceva, and AS Ribeiro (2015) Single-cell kinetics of the Repressilator when implemented in a single-copy plasmid. Mol. BioSyst. 11, 1939-1945. *Equal contributions. DOI: 10.1039/C5MB00012B. PDF
  • E Lihavainen, M Kislin, D Toptunov, L Khiroug, AS Ribeiro (2015) Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue. Journal of Microscopy. 260(3), 338-51. DOI: 10.1111/jmi.12301. PDF
  • H Tran, SMD Oliveira, N Goncalves, and AS Ribeiro (2015) Kinetics of the cellular intake of a gene expression inducer at high concentrations. Molecular BioSystems, 11, 2579-2587. DOI: 10.1039/C5MB00244C. PDF

2014

  • A Häkkinen, M Kandhavelu, S Garasto, and AS Ribeiro (2014) Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinformatics (30(8), 1146-1153. PDF
  • A Gupta, J Lloyd-Price, SMD Oliveira, RN Venkata, and AS Ribeiro (2014) In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli. Biophysical Journal, 106(9), 1928-1937. PDF
  • J Lloyd-Price, H Tran, and AS Ribeiro (2014) Dynamics of small genetic circuits subject to stochastic partitioning in cell division. J. Theo. Biol. 356, 11-19. PDF
  • A Fukuoh*, G Cannino*, M Gerards, S Buckley, S Kazancioglu, F Scialo, E Lihavainen, AS Ribeiro, E Dufour and HT Jacobs (2014) Screen for mitochondrial DNA copy-number maintenance genes reveals essential role for ATP synthase. Mol. Syst. Biol. 10, 734.
  • A-B Muthukrishnan, A Martikainen, R Neeli-Venkata, and AS Ribeiro (2014) In vivo Transcription Kinetics of a Synthetic Gene Uninvolved in Stress-Response Pathways in Stressed Escherichia coli cells. PLoS ONE 9(9): e109005. PDF
  • AS Ribeiro, BA Eales, J Lloyd-Price, and FG Biddle (2014) Predictability and randomness of paw choices are critical elements in the behavioural plasticity of mouse paw preference. Animal Behavior 98, 167-176. PDF
                For a audio presentation PRESS HERE
  • A Gupta, J Lloyd-Price, SMD Oliveira, O Yli-Harja, A-B Muthukrishnan and AS Ribeiro (2014) Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking. Physical Biology 11(6):066005. PDF

2013

  • A.S. Ribeiro (2013) Kinetics of gene expression in live bacteria: from models to measurements, and back again. Canadian Journal of Chemistry, 91(7): 487-494.
  • A.S. Ribeiro, B.A. Eales, and F.G. Biddle (2013) Short-term and long-term memory deficits in handedness learning in mice with absent corpus callosum and reduced hippocampal commissure. Behavioural Brain Research 245, 145–151. Link PDF
  • . Mäkelä, M. Kandhavelu, S.M.D. Oliveira, J.G. Chandraseelan, J. Lloyd-Price, J. Peltonen, O. Yli-Harja and A.S. Ribeiro (2013) In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Res 41(13):6544-52. Link PDF
  • A. Häkkinen, A.-B. Muthukrishnan, A. Mora, J.M. Fonseca, and A.S. Ribeiro (2013) CellAging: A tool to study segregation and partitioning in division in cell lineages of Escherichia coli. Bioinformatics 29 (13): 1708-1709.Link
  • A Häkkinen, H Tran, B Ingalls, and AS Ribeiro (2013) Effects of multimerization on the temporal variability of protein complex abundance. BMC Systems Biology 7 (Sup. 1).Link
  • S Chowdhury, M Kandhavelu, O Yli-Harja, and AS Ribeiro (2013) Cell Segmentation by Multi-resolution Analysis and Maximum Likelihood Estimation (MAMLE). BMC Bioinformatics 14 (Sup. 10), S8.Link
  • T Annila, E Lihavainen, IJ Marques, DR Williams, O Yli-Harja and AS Ribeiro (2013) ZebIAT, an image analysis tool for registering zebra fish embryos and quantifying cancer metastasis. BMC Bioinformatics 14 (Sup. 10), S5.Link
  • A Häkkinen, H Tran, O Yli-Harja, and AS Ribeiro (2013) Effects of rate-limiting steps in transcription initiation on genetic filter motifs, PLoS ONE 8(8): e70439. Link
  • J Lloyd-Price and AS Ribeiro (2013) Bistability in a stochastic RNA-mediated gene network. Phys. Rev. E 88(3): 032714. Link
  • JG Chandraseelan, SMD Oliveira, I Potapov, A Häkkinen, M Kandhavelu, and AS Ribeiro (2013) Temperature dependence of the LacI-TetR-CI Repressilator. Mol. BioSyst. 9(12), 3117-23.

Previous, Selected Publications:

  • A. S. Ribeiro, R. Zhu, and S. A. Kauffman (2006) A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics. Journal of Computational Biology 13(9): 1630-1639. Link
    PDF: This is a copy of an article published in the Journal of Computational Biology © 2006 Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://online.liebertpub.com.
  • A. S. Ribeiro and J. Lloyd-Price, (2007) SGN Sim, a Stochastic Genetic Networks Simulator. Bioinformatics 23(6): 777-779. Link PDF
  • A. S. Ribeiro and S. A. Kauffman (2007) Noisy Attractors and Ergodic Sets in Models of Gene Regulatory Networks. Journal of Theoretical Biology 247(4): 743-755. Link PDF
  • A. S. Ribeiro (2007) Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions. Physical Review E 75(6): 061903. Link PDF
  • A. S. Ribeiro, D. Charlebois, J. Lloyd-Price (2007) CellLine, a stochastic cell lineage simulator. Bioinformatics 23(24): 3409-3411. Link PDF
  • A. S. Ribeiro, S. A. Kauffman, J. Lloyd-Price, B. Samuelsson, and J.E.S. Socolar (2008), Mutual Information in Random Boolean models of regulatory networks. Physical Review E 77(1): 011901. Link PDF
  • A. S. Ribeiro, J. Lloyd-Price, J. Kesseli, A. Häkkinen, and O. Yli-Harja (2008), Quantifying Local Structure Effects in Network Dynamics. Physical Review E 78(5): 056108. Link PDF
  • A. S. Ribeiro (2008) Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments. Physical Review E 78(6): 061902. Link PDF
  • A. S. Ribeiro, O.-P. Smolander, T. Rajala, A. Häkkinen and O. Yli-Harja (2009) Delayed stochastic model of transcription at the single nucleotide level. Journal of Computational Biology 16(4): 539-553. Link
    PDF: This is a copy of an article published in the Journal of Computational Biology © 2009 Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://online.liebertpub.com.
  • A. S. Ribeiro (2010) Stochastic and delayed stochastic models of gene expression and regulation. Mathematical Biosciences 223(1): 1-11. Link PDF
  • A. S. Ribeiro, A. Häkkinen, H. Mannerström, J. Lloyd-Price, and O. Yli-Harja (2010) Effects of the promoter open complex formation on gene expression dynamics. Physical Review E 81(1): 011912. Link PDF
  • A. S. Ribeiro, J. Lloyd-Price, B. Eales, and F. G. Biddle (2010) Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse. Adaptive Behavior 18(2): 116-131. Link PDF
  • T. Rajala, A. Häkkinen, S. Healy, O. Yli-Harja, and A. S. Ribeiro (2010) Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Computational Biology 6(3): e1000704. Link PDF
  • A. S. Ribeiro, B. A. Eales and F. G. Biddle (2011) Learning of paw preference in mice is strain dependent, gradual and based on short-term memory of previous reaches. Animal Behavior 81(1): 249-257. Link PDF
  • J. Mäkelä, J. Lloyd-Price, O. Yli-Harja, and A. S. Ribeiro (2011) Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinformatics 12: 121. Link PDF
  • O.-P. Smolander, M. Kandhavelu, H. Mannerström, E. Lihavainen, S. Kalaichelvan, S. Healy, O. Yli-Harja, M. Karp, and A. S. Ribeiro (2011) Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter. BMC Molecular Biology 12: 21. Link PDF
  • J. Mäkelä, H. Huttunen, M. Kandhavelu, O. Yli-Harja, and A. S. Ribeiro (2011) Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. Bioinformatics 27: 2714-2720. Link PDF
  • M. Kandhavelu, H. Mannerström, A. Gupta, A. Häkkinen, J. Lloyd-Price, O. Yli-Harja, and A. S. Ribeiro (2011) In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate limiting steps. BMC Systems Biology 5: 149. Link PDF
  • J. Lloyd-Price, M. Lehtivaara, M. Kandhavelu, S. Chowdhury, A.-B. Muthukrishnan, O. Yli-Harja and A. S. Ribeiro (2012) Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli. Molecular BioSystems 8(2): 565–571. Link PDF
  • J. Lloyd-Price, A. Häkkinen, M. Kandhavelu, I. J. Marques, S. Chowdhury, E. Lihavainen, O. Yli-Harja, and A. S. Ribeiro (2012) Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. Journal of Bacteriology 194(7): 1747–1752. Link PDF
  • E. Lihavainen, J. Mäkelä, J. N. Spelbrink, and A. S. Ribeiro (2012) Mytoe: Automatic analysis of mitochondrial dynamics. Bioinformatics 7(28): 1050-1051. Link PDF
  • M. Kandhavelu, A. Häkkinen, O. Yli-Harja, and A. S. Ribeiro (2012) Single-molecule dynamics of transcription of the lar promoter. Physical Biology 9(2), 026004. Link PDF
  • A.-B. Muthukrishnan, M. Kandhavelu, J. Lloyd-Price, F. Kudasov, S. Chowdhury, O. Yli-Harja, and A. S. Ribeiro (2012) Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells. Nucleic Acids Research 40(17): 8472-8483. Link PDF
  • F. Emmert-Streib, A. Häkkinen, and A. S. Ribeiro (2012) Detecting sequence dependent trandivional pauses from RNA and protein number time series. BMC Bioinformatics 13: 152. Link PDF
  • J. Lloyd-Price, A. Gupta, and A. S. Ribeiro (2012) Robustness and Information Propagation in Attractors of Random Boolean Networks. PLoS ONE 7(7): e42018. Link PDF
  • M. Kandhavelu, J. Lloyd-Price, A. Gupta, A.-B. Muthukrishnan, O. Yli-Harja, and A. S. Ribeiro (2012) Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter. FEBS Letters 586: 3870-3875. Link PDF