Publications

2025

• R Jagadeesan, S Dash, CSD Palma, ISC Baptista, V Chauhan, J Mäkelä, and AS Ribeiro (2025) Dynamics of bacterial operons during genome-wide stresses. Science Advances 11 (20), eadl3570. DOI: 10.1126/sciadv.adl3570.

• Baptista ISC, Dash S, Arsh AM, Kandavalli V, Scandolo CM, Sanders BC, and Ribeiro AS (2025) Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses. PLoS Comput Biol 21(2): e1012817. https://doi.org/10.1371/journal.pcbi.1012817

2024

• V Chauhan, ISC Baptista, A Arsh, R Jagadeesan, S Dash, and AS Ribeiro (2024) Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation. Biochemistry 63(16), 2009–2022. DOI: 10.1021/acs.biochem.4c00012.

• 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

• 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.

Selected Publications Prior to 2022

• 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. 

• 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 

• 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

• 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

• 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. 

• 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.

• 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.