Research output per year
Research output per year
- 40 results
Search results
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2024
Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer
Davidson, B. S. A., Arcila-Galvis, J. E., Trevisan-Herraz, M., Mikulasova, A., Brackley, C. A., Russell, L. J. & Rico, D., 30 Jul 2024, In: Frontiers in Cell and Developmental Biology. 12, p. 1-15 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin
Sacristan, C., Samejima, K., Ruiz, L. A., Deb, M., Lambers, M. L. A., Buckle, A., Brackley, C. A., Robertson, D., Hori, T., Webb, S., Kiewisz, R., Bepler, T., van Kwawegen, E., Risteski, P., Vukušić, K., Tolić, I. M., Müller-Reichert, T., Fukagawa, T., Gilbert, N., Marenduzzo, D., & 2 others, 6 Jun 2024, In: Cell. 187, 12, p. 3006-3023.e26 45 p.Research output: Contribution to journal › Article › peer-review
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2023
Transcription modulates chromatin dynamics and locus configuration sampling
Forte, G., Buckle, A., Boyle, S., Marenduzzo, D., Gilbert, N. & Brackley, C. A., 3 Aug 2023, In: Nature Structural & Molecular Biology. 30, 9, p. 1275-1285 23 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2022
Model for quorum-sensing mediated stochastic biofilm nucleation
Sinclair, P., Brackley, C. A., Carballo-Pacheco, M. & Allen, R. J., 4 Nov 2022, In: Physical Review Letters. 129, 19, p. 1-6 6 p., 198102.Research output: Contribution to journal › Article › peer-review
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A computational model for microbial colonisation of an antifouling surface
Sinclair, P., Longyear, J., Reynolds, K., Finnie, A. A., Brackley, C., Carballo Pacheco, M. & Allen, R., 27 Sept 2022, In: Frontiers in Microbiology. 13, 920014.Research output: Contribution to journal › Article › peer-review
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High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation
Rico, D., Kent, D., Karataraki, N., Mikulasova, A., Berlinguer-Palmini, R., Walker, B. A., Javierre, B. M., Russell, L. J. & Brackley, C. A., 21 Jul 2022, In: Genome Research. 32, 7, p. 1355-1366 12 p.Research output: Contribution to journal › Article › peer-review
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Simulating the chromatin mediated phase separation of model proteins with multiple domains
Ancona, M. & Brackley, C. A., 5 Jul 2022, In: Biophysical Journal. 121, 13, p. 2600-2612 13 p.Research output: Contribution to journal › Article › peer-review
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Predicting genome organisation and function with mechanistic modelling
Chiang, M., Brackley, C. A., Marenduzzo, D. & Gilbert, N., 1 Apr 2022, In: Trends in Genetics. 38, 4, p. 364-378 15 p.Research output: Contribution to journal › Review article › peer-review
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2021
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
Mikulasova, A., Kent, D., Trevisan-Herraz, M., Karataraki, N., Fung, K. T. M., Ashby, C., Cieslak, A., Yaccoby, S., van Rhee, F., Zangari, M., Thanendrarajan, S., Schinke, C., Morgan, G. J., Asnafi, V., Spicuglia, S., Brackley, C. A., Corcoran, A. E., Hambleton, S., Walker, B. A., Rico, D., & 1 others, 21 Dec 2021, (E-pub ahead of print) In: Genome Research. 2022, p. 1343-1354 7 p., 32.Research output: Contribution to journal › Article › peer-review
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Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces
Brackley, C. A., Lips, A., Morozov, A., Poon, W. C. K. & Marenduzzo, D., 24 Nov 2021, In: Nature Communications. 12, 1, p. 1-6 6 p., 6812.Research output: Contribution to journal › Article › peer-review
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Complex small-world regulatory networks emerge from the 3D organisation of the human genome
Brackley, C. A., Gilbert, N., Michieletto, D., Papantonis, A., Pereira, M. C. F., Cook, P. R. & Marenduzzo, D., 1 Oct 2021, In: Nature Communications. 12, 1, p. 1-14 14 p., 5756.Research output: Contribution to journal › Article › peer-review
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Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling
Fosado, Y. A. G., Michieletto, D., Brackley, C. A. & Marenduzzo, D., 1 Mar 2021, In: Proceedings of the National Academy of Sciences (PNAS). 118, 10, p. 1-6 6 p., e1905215118.Research output: Contribution to journal › Article › peer-review
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2020
Polymer compaction and bridging-induced clustering of protein-inspired patchy particles
Brackley, C. A., 6 May 2020, In: Journal of Physics: Condensed Matter. 32, 31Research output: Contribution to journal › Article › peer-review
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Computational design of probes to detect bacterial genomes by multivalent binding
Curk, T., Brackley, C., Farrell, J. D., Xing, Z., Joshi, D., Oliveira Lebre Direito, S., Bren, U., Angioletti-Uberti, S., Dobnikar, J., Eiser, E., Frenkel, D. & Allen, R., 2 Apr 2020, In: Proceedings of the National Academy of Sciences (PNAS). 201918274 .Research output: Contribution to journal › Article › peer-review
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Bridging-induced microphase separation: photobleaching experiments, chromatin domains, and the need for active reactions.
Brackley, C. & Marenduzzo, D., 23 Jan 2020, In: Briefings in functional genomics.Research output: Contribution to journal › Article › peer-review
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2019
Polymer Modeling Predicts Chromosome Reorganization in Senescence
Chiang, M., Michieletto, D., Brackley, C. A., Rattanavirotkul, N., Mohammed, H., Marenduzzo, D. & Chandra, T., 17 Sept 2019, In: Cell Reports. 28, 12, p. P3212-3223.e6Research output: Contribution to journal › Article › peer-review
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Nucleosome positions alone can be used to predict domains in yeast chromosomes
Wiese, O., Marenduzzo, D. & Brackley, C., 15 Aug 2019, In: Proceedings of the National Academy of Sciences (PNAS).Research output: Contribution to journal › Article › peer-review
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Non-equilibrium effects of molecular motors on polymers
Foglino, M., Locatelli, E., Brackley, C., Michieletto, D., Likos, C. N. & Marenduzzo, D., 11 Jul 2019, In: Soft Matter.Research output: Contribution to journal › Article › peer-review
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capC-MAP: software for analysis of Capture-C data
Buckle, A., Marenduzzo, D. & Brackley, C., 7 Jun 2019, In: Bioinformatics.Research output: Contribution to journal › Article › peer-review
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Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling
Ancona, M., Bentivoglio, A., Brackley, C. A., Gonnella, G. & Marenduzzo, D., 26 Apr 2019, (E-pub ahead of print) In: Biophysical Journal. 9 p.Research output: Contribution to journal › Article › peer-review
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2018
Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci
Buckle, A., Brackley, C. A., Boyle, S., Marenduzzo, D. & Gilbert, N., Nov 2018, In: Molecular Cell. 72, 4, p. 786-797.e11 23 p.Research output: Contribution to journal › Article › peer-review
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HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types
Zirkel, A., Nikolic, M., Sofiadis, K., Mallm, J-P., Brackley, C. A., Gothe, H., Drechsel, O., Becker, C., Altmueller, J., Josipovic, N., Georgomanolis, T., Brant, L., Franzen, J., Koker, M., Gusmao, E. G., Costa, I. G., Ullrich, R. T., Wagner, W., Roukos, V., Nuernberg, P., & 3 others, 17 May 2018, In: Molecular Cell. 70, 4, p. 730-744.e6 21 p.Research output: Contribution to journal › Article › peer-review
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Extrusion without a motor: a new take on the loop extrusion model of genome organization
Brackley, C. A., Johnson, J., Michieletto, D., Morozov, A. N., Nicodemi, M., Cook, P. R. & Marenduzzo, D., 18 Jan 2018, In: Nucleus. p. 1-10 10 p.Research output: Contribution to journal › Article › peer-review
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2017
Nonequilibrium Chromosome Looping via Molecular Slip Links
Brackley, C. A., Johnson, J., Michieletto, D., Morozov, A. N., Nicodemi, M., Cook, P. R. & Marenduzzo, D., 29 Sept 2017, In: Physical Review Letters. 119, 13, p. 1-5 5 p., 138101.Research output: Contribution to journal › Article › peer-review
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Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains
Brackley, C., Liebchen, B., Michieletto, D., Mouvet, F., Cook, P. & Marenduzzo, D., 28 Mar 2017, In: Biophysical Journal. 112, 6Research output: Contribution to journal › Article › peer-review
Open Access -
2016
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei
Brant, L., Georgomanolis, T., Nikolic, M., Brackley, C. A., Kolovos, P., van Ijcken, W., Grosveld, F. G., Marenduzzo, D. & Papantonis, A., 9 Dec 2016, In: Molecular Systems Biology. 12, 12, p. 891Research output: Contribution to journal › Article › peer-review
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Simulating topological domains in human chromosomes with a fitting-free model
Brackley, C. A., Michieletto, D., Mouvet, F., Johnson, J., Kelly, S., Cook, P. R. & Marenduzzo, D., 14 Nov 2016, In: Nucleus. 7, 5, p. 453-461 9 p.Research output: Contribution to journal › Article › peer-review
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A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
Fosado, Y. A. G., Michieletto, D., Allan, J., Brackley, C., Henrich, O. & Marenduzzo, D., 8 Nov 2016, In: Soft Matter. 12, 47, p. 9458-9470Research output: Contribution to journal › Article › peer-review
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Stochastic Model of Supercoiling-Dependent Transcription
Brackley, C. A., Johnson, J., Bentivoglio, A., Corless, S., Gilbert, N., Gonnella, G. & Marenduzzo, D., 27 Jun 2016, In: Physical Review Letters. 117, 1, 018101.Research output: Contribution to journal › Article › peer-review
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Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains
Brackley, C. A., Johnson, J., Kelly, S., Cook, P. R. & Marenduzzo, D., 5 May 2016, In: Nucleic Acids Research. 44, 8, p. 3503–3512 10 p.Research output: Contribution to journal › Article › peer-review
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Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
Brackley, C. A., Brown, J. M., Waithe, D., Babbs, C., Davies, J., Hughes, J. R., Buckle, V. J. & Marenduzzo, D., 31 Mar 2016, In: Genome Biology. 17, 1, 59.Research output: Contribution to journal › Article › peer-review
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2015
Community control in cellular protein production: Consequences for amino acid starvation
Heldt, F. S., Brackley, C. A., Grebogi, C. & Thiel, M., 13 Dec 2015, In: Philosophical Transactions A: Mathematical, Physical and Engineering Sciences. 373, 2056, 20150107.Research output: Contribution to journal › Article › peer-review
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A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction
Johnson, J., Brackley, C., Cook, P. R. & Marenduzzo, D., 18 Feb 2015, In: Journal of Physics: Condensed Matter. 27, 6, 7 p., 064119.Research output: Contribution to journal › Article › peer-review
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2014
Topological constraints strongly affect chromatin reconstitution in silico
Brackley, C. A., Allan, J., Keszenman Pereyra, D. & Marenduzzo, D., 1 Oct 2014, In: Nucleic Acids Research. 43, 1, p. 63-73 11 p.Research output: Contribution to journal › Article › peer-review
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Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS
Brackley, C., Morozov, A. N. & Marenduzzo, D., 7 Apr 2014, In: The Journal of Chemical Physics. 140, 13, 10 p., 135103.Research output: Contribution to journal › Article › peer-review
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Heterogeneous connectivity in neural fields: A stochastic approach
Brackley, C. A. & Turner, M. S., 1 Mar 2014, Neural Fields: Theory and Applications. Springer, p. 213-234 22 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter
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2013
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization
Brackley, C., Taylor, S., Papantonis, A., Cook, P. R. & Marenduzzo, D., 17 Sept 2013, In: Proceedings of the National Academy of Sciences (PNAS). 110, 38, p. E3605-11Research output: Contribution to journal › Article › peer-review
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Intracellular Facilitated Diffusion: Searchers, Crowders, and Blockers
Brackley, C., Cates, M. E. & Marenduzzo, D., 3 Sept 2013, In: Physical Review Letters. 111, 10, 5 p., 108101.Research output: Contribution to journal › Article › peer-review
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Effect of DNA conformation on facilitated diffusion
Brackley, C., Cates, M. & Marenduzzo, D., Apr 2013, In: Biochemical Society Transactions. 41, p. 582-588 7 p.Research output: Contribution to journal › Article › peer-review
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2012
Facilitated Diffusion on Mobile DNA: Configurational Traps and Sequence Heterogeneity
Brackley, C., Cates, M. E. & Marenduzzo, D., 17 Oct 2012, In: Physical Review Letters. 109, 16, 5 p., 168103.Research output: Contribution to journal › Article › peer-review
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