Publications

2024

• S Dash, R Jagadeesan, ISC Baptista, V Chauhan, V Kandavalli, SMD Oliveira and AS Ribeiro (2023) A library of reporters of the global regulators of gene expression in Escherichia coli. mSystems, e00065-24. DOI: 10.1128/msystems.00065-24

2023

• V Chauhan, ISC Baptista, R Jagadeesan, S Dash, and AS Ribeiro (2023) Transcription attenuation in synthetic promoters in tandem formation. bioRxiv. DOI: 2023.12.05.569149v1

• R Jagadeesan, S Dash, C Palma, ISC Baptista, V Chauhan, J Mäkelä, and AS Ribeiro (2023) Dynamics of bacterial operons during genome-wide stresses. bioRxiv, DOI:2023.08. 24.554578.

• V Gobbo, P Turkki, CSD Palma, V Parihar, E Vernè, S Spriano, AS Ribeiro, VP Hytönen, and J Massera (2023) Surface modification of silicate, borosilicate, and phosphate bioactive glasses to improve/control protein adsorption: PART II. Ceramics International 49 (8), 12856-12865.

2022

• S Dash*, CSD Palma*, ISC Baptista, BLB Almeida, MNM Bahrudeen, V Chauhan, R Jagadeesan and AS Ribeiro (2022) Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Research 50(15) 8512–8528. DOI: 10.1093/nar/gkac643. *Equal contributions. 

• B Almeida, MNM Bahrudeen*, V Chauhan*, S Dash*, V Kandavalli, A Häkkinen, J Lloyd-Price, CSD Palma, ISC Baptista, A Gupta, J Kesseli, E Dufour, O-P Smolander, M Nykter, P Auvinen, HT Jacobs, SMD Oliveira, and AS Ribeiro (2022) The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Research 50(12), 6801–6819. DOI: 10.1093/nar/gkac540. *Equal contributions.

• ISC Baptista*, V Kandavalli*, V Chauhan, MNM Bahrudeen, BLB Almeida, CSD Palma, S Dash, and AS Ribeiro (2022) Sequence-dependent model of genes with dual σ factor preference, BBA Gene Regulatory Mechanisms 1865(3), 194812. DOI: 10.1016/j.bbagrm.2022.194812. *Equal contributions.

• V Chauhan*, MNM Bahrudeen*, CSD Palma, ISC Baptista, BLB Almeida, S Dash, V Kandavalli, and AS Ribeiro (2022). Analytical kinetic model of native tandem promoters in E. coli. PLOS Computational Biology 18(1): e1009824. DOI: 10.1371/journal.pcbi.1009824. *Equal contributions.

Prior to 2022 (2018 to 2021)

• NB Hyunh, CSD Palma, R Rahikainen, A Mishra, L Azizi, E Verne, S Ferraris, VP Hytönen, AS Ribeiro, and J Massera (2021) Surface Modification of Bioresorbable Phosphate Glasses for Controlled Protein Adsorption. ACS Biomaterials Science and Engineering 7(9), 4483−4493. DOI: 10.1021/acsbiomaterials.1c00735. 

• ISC Baptista and AS Ribeiro (2020) Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli. BioSystems 193–194, 104154. (invited review article). DOI: 10.1016/j.biosystems.2020.104154. 

• CSD Palma, V Kandavalli, MNM Bahrudeen, M Minoia, V Chauhan and AS Ribeiro (2020) Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. BBA - Gene Regulatory Mechanisms, 1863(5), 194515. doi: 10.1016/j.bbagrm.2020.194515. 

• I Baptista, V Chauhan, B Almeida, V Kandavalli and AS Ribeiro (2020) Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli. In: Duménil G., van Teeffelen S. (eds) Physical Microbiology. Advances in Experimental Medicine and Biology, 1267. Springer, 59-80. DOI: https://doi.org/10.1007/978-3-030-46886-6_4.

• A Häkkinen, SMD Oliveira, R Neeli-Venkata, and AS Ribeiro (2019) Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. Journal of the Royal Society Interface. In press. DOI: 10.1101/842484 

• MNM Bahrudeen*, V Chauhan*, CSD Palma, SMD Oliveira, VK Kandavalli, and AS Ribeiro (2019) Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry. Journal of Microbiological Methods 166, 105745. DOI: 10.1016/j.mimet.2019.105745. *Equal contributions.

• SMD Oliveira, NSM Goncalves, VK Kandavalli, L Martins, R Neeli-Venkata, J Reyelt, JM Fonseca, J Lloyd-Price, H Kranz, and AS Ribeiro (2019) Chromosome and plasmid-borne PLacO3O1 promoters differ in sensitivity to critically low temperatures. Scientific Reports 9:4486. DOI: 10.1038/s41598-019-39618-z 

• S Startceva, VK Kandavalli, A Visa, and AS Ribeiro (2019) Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1862(2), 119–128. DOI: 10.1016/j.bbagrm.2018.12.005

• MK Prajapat, AS Ribeiro (2018) Added value of autoregulation and multi-step kinetics of transcription initiation. R. Soc. Open Sci. 5: 181170. DOI: 10.1098/rsos.181170.

• L Martins, R Neeli-Venkata, SMD Oliveira, A Häkkinen, AS Ribeiro, and JM Fonseca (2018) SCIP: A Single-Cell Image Processor toolbox. Bioinformatics 34(24), 4318–4320. 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. 

Previous, Selected Publications ( - 2018):

• 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

• A. S. Ribeiro and J. Lloyd-Price, (2007) SGN Sim, a Stochastic Genetic Networks Simulator. Bioinformatics 23(6): 777-779. Link

• 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

• 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

• A. S. Ribeiro (2010) Stochastic and delayed stochastic models of gene expression and regulation. Mathematical Biosciences 223(1): 1-11. Link

• 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

• 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

• E. Lihavainen, J. Mäkelä, J. N. Spelbrink, and A. S. Ribeiro (2012) Mytoe: Automatic analysis of mitochondrial dynamics. Bioinformatics 7(28): 1050-1051. Link

• 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

• 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

• 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, M Kandhavelu, S Garasto, and AS Ribeiro (2014) Estimation of fluorescence-tagged RNA numbers from spot intensities. Bioinformatics (30(8), 1146-1153.

• 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.

• 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.

• 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.

• 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.

• 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. 

• 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.

• 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.

• 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.

• 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.