Publications

2024

• J. Mäkelä*, A. Papagiannakis*, W.H. Lin, M.C. Lanz, S. Glenn, M. Swaffer, M. Swaffer, G.K. Marinov, J.M. Skotheim, C. Jacobs-Wagner (2024) Genome concentration limits cell growth and modulates proteome composition in Escherichia coli. bioRxiv, doi:10.1101/2024.02.26.582181        
  *equal contribution                          

2023

• R. Jagadeesan, S. Dash, C.S.D. Palma, I.S.C. Baptista, V. Chauhan, J. Mäkelä, A.S. Ribeiro (2023) Dynamics of bacterial operons during genome-wide stresses. bioRxiv, doi:10.1101/2023.08.24.554578

2021

• ​​​​J.P. Prince, J.R. Bolla, G.L.M. Fisher, J. Mäkelä, C.V. Robinson, L.K.  Arciszewska, D.J. Sherratt (2021) Acyl Carrier Protein binding to the Escherichia coli MukB coiled coil activates MukB ATPase and is required for in vivo MukBEF function. Nature Communications 12, 6721
• G.L.M. Fisher, J.R. Bolla, K.V. Rajasekar, J. Mäkelä, R. Baker, M. Zhou, J. Prince, M. Stracy, C.V. Robinson, L.K. Arciszewska, D.J. Sherratt (2021) Competitive binding of MatP and topoisomerase IV to the MukB dimerization hinge. eLife, 10:e70444
• J. Mäkelä*, S. Uphoff, D.J. Sherratt* (2021) Non-random segregation of sister chromosomes by Escherichia coli MukBEF. PNAS, 118(33): e2022078118
  *corresponding authors

2020

• J. Mäkelä and D.J. Sherratt (2020) SMC complexes organize the bacterial chromosome by lengthwise compaction. Current Genetics, 66:895–899
• J. Mäkelä and D.J. Sherratt (2020) Organization of the Escherichia coli chromosome by a MukBEF axial core. Molecular Cell, 78(2):250-260

2019

• K.V. Rajasekar, R. Baker, G.L.M. Fisher, J.R. Bolla, J. Mäkelä, M. Tang, K. Zawadzka, O. Koczy, F. Wagner, C.V. Robinson, L.K. Arciszewska, D.J. Sherratt (2019) Dynamic architecture of the Escherichia coli structural maintenance of chromosomes (SMC) complex, MukBEF. Nucleic Acids Research, 47(18):9696-9707
• A. Hofmann*, J. Mäkelä*, D.J. Sherratt, D. Heermann, S.M. Murray (2019) Self-organised segregation of bacterial chromosomal origins. eLife, 8:e46564          
  *equal contribution
• N. Banaz*, J. Mäkelä*, S. Uphoff (2019) Choosing the right label for single-molecule tracking in live bacteria: Side-by-side comparison of photoactivatable fluorescent protein and Halo tag dyes. Journal of Physics D: Applied Physics, 52:064002            
  *equal contribution

Older selected articles

• J. Mäkelä, V. Kandavalli, A.S. Ribeiro (2017) Rate-limiting steps in transcription dictate sensitivity to variability in cellular components. Scientific Reports, 7:10588
• S.M.D. Oliveira, R. Neeli-Venkata, N. Goncalves, J.A. Santinha, L. Martins, H. Tran, J. Mäkelä, A. Gupta, M. Barandas, A. Häkkinen, J. Lloyd-Price, J.M. Fonseca, A.S. Ribeiro (2016) Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli. Molecular Microbiology, 99(4):686–699
• L. Kong, K.L. Aho, K. Granberg, R. Lund, L. Järvenpää, J. Seppälä, P. Gokhale, K. Leinonen, L. Hahne, J. Mäkelä, K. Laurila, H. Pukkila, E. Närvä, O. Yli-Harja, P.W. Andrews, M. Nykter, R. Lahesmaa, C. Roos, R. Autio (2013) ESTOOLS Data@Hand, a human gene expression data analysis resource for the stem cell research community. Nature Methods, 10:814-815
• J. Mäkelä, M. Kandhavelu, S. Oliveira, J. Chandraseelan, J. Lloyd-Price, J. Peltonen, O. Yli-Harja, A.S. Ribeiro (2013) In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Research, 41(13):6544-6552
• E. Lihavainen, J. Mäkelä, J.N. Spelbrink, A.S. Ribeiro (2012) Mytoe: Automatic analysis of mitochondrial dynamics. Bioinformatics, 28(7):1050-1051
• J. Mäkelä, H. Huttunen, M. Kandhavelu, O. Yli-Harja, 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(19):2714-2720
• J. Mäkelä, J. Lloyd-Price, O. Yli-Harja, A.S. Ribeiro (2011) Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinformatics, 12:121