Papers: 2021-present
Peter Cook thanks those that helped make these papers
[Notes highlighting properties of loops and transcription factories]
Soitu, C., Panea, M., Castrejón-Pita, A.A., Cook, P.R., and Walsh, E.J. (2021). Creating wounds in cell monolayers using micro-jets. Biomicrofluidics 15, 014108. [PubMed] [journal] [pdf]
Brackley, C.A., Gilbert, N., Michieletto, D., Papantonis, A., Pereira, M.C.F., Cook, P.R., and Marenduzzo, D. (2021). Complex small-world regulatory networks emerge from the 3D organisation of the human genome. Nat. Commun. 12, 5756. [PubMed] [journal] [pdf] [Bursty transcription, complex small-world regulatory networks, reconciling results from Yamanaka and GWAS]
Deroy, C., Nebuloni, F., Cook, P.R., and Walsh, E.J. (2021). Microfluidics on standard Petri dishes for bioscientists. Small Methods 2021, 2100724. [PubMed] [journal] [pdf]
Deroy, C., Storvall-Kurtz-N., Nebuloni, F., Soitu, C., Cook, P.R., and Walsh, E.J. (2021). Predicting flows through microfluidic circuits with fluid walls. Microsystems & Nanoengineering 7, 93. [PubMed] [journal] [pdf]
Deroy, C, Wheeler, J.H.R., Rumianek, A.N., Cook, P.R., Durham, W.H., Foster, K.R., and Walsh, E.J., (2022). Reconfigurable microfluidic circuits for isolating and retrieving cells of interest. ACS Appl. Mater. Interfaces. 14, 25209-25219. [PubMed] [journal] [pdf]
Deroy, C., Rumianek, A.N., Wheeler, J.H.R., Nebuloni, F., Cook, P.R., Greaves, D.R., and Walsh, E.J. (2022). Assaying macrophage chemotaxis using fluid-walled microfluidics. Adv. Mater. Technol. 7, 2200279. [journal] [pdf]
Nebuloni, F., Morgan, J., Walsh E.J., and Cook, P.R. (2023). A platform for modular assembly and feeding of micro-organoids on standard Petri dishes. Biology Open 12, bio059825. [PubMed] [journal] [pdf]
Nebuloni, F., Cook, P.R., and Walsh, E.J. (2023). Flows in fluid-walled conduits driven by Laplace pressure. J. Fluid Mech. 969, A28. [journal] [pdf]
Forte, G., Boteva, L., Conforto, F., Gilbert, N., Cook, P.R., and Marenduzzo, D. (2023). Bridging condensins mediate compaction of mitotic chromosomes. J. Cell Biol, 223, e202209113. [PubMed] [journal] [pdf]
Nebuloni, F., Deroy, C., Cook, P.R., and Walsh, E.J. (2024). Stable diffusion gradients in microfluidic conduits bounded by fluid walls. Microsystems & Nanoengineering 10, 79. [journal] [pdf]
Nebuloni, F., Do, Q.B., Cook, P.R., Walsh, E.J., and Wade-Martins, R. (2024). A fluid-walled microfluidic platform for human neuron microcircuits and directed axotomy. Lab Chip 24, 3252-3264. [PubMed] [journal] [pdf]
Forte, G., Buonomo, S., Cook, P. R., Gilbert, N., Marenduzzo, D., and Orlandini, E. (2024). Modeling the 3D spatiotemporal organization of chromatin replication. PRX Life 2, 033014. [journal] [pdf]
Negro, G., Semeraro, M., Cook, P.R., and Marenduzzo, D. (2024), A unified-field theory of genome organization and gene regulation. iScience 27, 111218. [PubMed] [journal] [pdf] [A mini-review of the pan-genomic model, plus a simple equation enabling prediction of how often a promoter fires]
Semeraro, M., Negro, G., Forte, G., Suma, A., Gonnella, G., Cook, P.R., and Marenduzzo D. (2025). Cluster size determines morphology of transcription factories in human cells. eLife 14, RP103955. [journal] [pdf] [Non-specific binding of transcription factors drives emergence of a myriad of different factory types]