Nuclear Structure and Function Research Group

Melnik, S., Caudron-Herger, M., Brant, L., Carr, I.M., Rippe, K., Cook, P.R., and Papantonis, A. (2016). Isolation of the protein and RNA content of active sites of transcription from mammalian cells. Nat. Protoc. 11, 553-565. [PubMed] [pdf]

Larkin, J.D., and Cook, P.R. (2016). Super-resolution measurement of distance between transcription sites using RNA FISH with intronic probes. Methods 98, 150-157. [PubMed] [pdf]

Brackley, C.A., Johnson, J., Kelly, S., Cook, P.R., and Marenduzzo, D. (2016). Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains. Nucleic Acids Res. 44, 3503-3512. [PubMed] [pdf]

Walsh, E., Feuerborn, A., Cook, P.R. (2016). Formation of droplet interface bilayers in a Teflon tube. Sci. Rep. 6, 34355. [PubMed] [pdf]

Kolovos, P., Georgomanolis, T., Koeferle, A., Larkin, J.D., Brant, L., Nikolicæ, M., Gusmao, E.G., Zirkel, A., Knoch, T.A., van Ijcken, W.F., Cook, P.R., Costa, I.G., Grosveld, F.G., and Papantonis, A. (2016). Binding of nuclear factor kB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res. 26, 1478-1489. [PubMed] [pdf]

Brackley, C.A., Michieletto, D., Mouvet, F., Johnson, J., Kelly, S., Cook, P.R., and Marenduzzo, D. (2016). Simulating topological domains in human chromosomes with a fitting-free model. Nucleus 7, 453-461. [PubMed] [pdf]

Prastowo, A., Feuerborn, A., Cook, P.R., and Walsh, E.J. (2016). Biocompatibility of fluids for multiphase drops-in-drops microfluidics. Biomed. Microdevices 18, 114. [PubMed] [pdf]

Brackley, C.A., Liebchen, B., Michieletto, D., Mouvet, F., Cook, P.R., and Marenduzzo, D. (2017). Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains. Biophys. J. 112, 1085-1093. [PubMed] [pdf]

Brackley, C.A., Johnson, J., Michieletto, D., Morozov, A.N., Nicodemi, M., Cook, P.R., and Marenduzzo, D. (2017). Non-equilibrium chromosome looping via molecular slip-links. Phys. Rev. Lett. 119, 138101. [PubMed] [pdf]

Walsh, E.J., Feuerborn, A., Wheeler, J.H.R., Tan, A.N., Durham, W.M., Foster, K.R., and Cook, P.R. (2017). Microfluidics with fluid walls. Nat. Commun. 8, 816. [PubMed] [journal] [pdf] [pdf with embedded movies]

Brackley, C.A., Johnson, J., Michieletto, D., Morozov, A.N., Nicodemi, M., Cook, P.R., and Marenduzzo, D. (2018). Extrusion without a motor: a new take on the loop extrusion model of genome organization. Nucleus 9, 95-103. [PubMed] [pdf]

Michieletto, D., Chiang, M., Colì, D., Papantonis, A., Orlandini, E., Cook, P.R., and Marenduzzo, D. (2018). Shaping epigenetic memory via genomic bookmarking. Nucl. Acids Res. 46, 83-93. [PubMed] [pdf]

Soitu, C., Feuerborn, A., Tan, A.N., Walker, H., Walsh, P.A., Castrejon-Pita, A.A., Cook, P.R., and Walsh, E.J. (2018). Microfluidic chambers using fluid walls for cell biology. Proc. Natl. Acad. Sci. USA 115, E5926-E5933. [PubMed] [journal] [pdf] [pdf with embedded movies]

Cook, P.R., and Marenduzzo, D. (2018). Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations. Nucl. Acids Res. 46, 9895-9906. [PubMed] [journal] [pdf].

Soitu, C., Feuerborn, A., Deroy, C., Castrejón-Pita, A.A., Cook, P.R., and Walsh. E.J. (2019). Raising fluid walls around living cells. Sci. Adv. 5, eaav8002. [PubMed] [journal] [pdf] [pdf with embedded movies]

Soitu, C., Deroy, C., Castrejón-Pita, A.A., Cook, P.R., and Walsh, E.J. (2020). Using fluid walls for single-cell cloning provides assurance in monoclonality. SLAS Technol. 25, 267-275. [PubMed] [journal] [pdf] [pdf with embedded movies]

Soitu, C., Stovall-Kurtz, N., Deroy, C., Castrejón-Pita, A.A., Cook, P.R., and Walsh, E.J. (2020). Jet-printing microfluidic devices on demand. Advanced Science 7, 2001854. [PubMed] [journal] [pdf]

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]

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]

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