Publications by Chris Brackley

School of Physics and Astronomy

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Transcription modulates chromatin dynamics and locus configuration sampling DOI
Giada Forte, Adam Buckle, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert and Chris A. Brackley, Nature Structural & Molecular Biology, 30, 9, p. 1275-1285 (2023)
Model for quorum-sensing mediated stochastic biofilm nucleation DOI
Patrick Sinclair, Chris A. Brackley, Martin Carballo-Pacheco and R. J. Allen, Physical Review Letters, 129, 19, p. 1-6 (2022)
A computational model for microbial colonisation of an antifouling surface DOI
Patrick Sinclair, Jennifer Longyear, Kevin Reynolds, Alistair A. Finnie, Chris Brackley, Martin Carballo Pacheco and Rosalind Allen, Frontiers in Microbiology, 13 (2022)
High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation DOI
Daniel Rico, Daniel Kent, Nefeli Karataraki, Aneta Mikulasova, Rolando Berlinguer-Palmini, Brian A Walker, Biola M Javierre, Lisa J. Russell and Chris A. Brackley, Genome Research, 32, 7, p. 1355-1366 (2022)
Simulating the chromatin mediated phase separation of model proteins with multiple domains DOI
Marco Ancona and Chris A. Brackley, Biophysical Journal, 121, 13, p. 2600-2612 (2022)
Predicting genome organisation and function with mechanistic modelling DOI
Michael Chiang, Chris A Brackley, Davide Marenduzzo and Nick Gilbert, Trends in Genetics, 38, 4, p. 364-378 (2022)
Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers DOI
Aneta Mikulasova, Daniel Kent, Marco Trevisan-Herraz, Nefeli Karataraki, Kent T.M. Fung, Cody Ashby, Agata Cieslak, Shmuel Yaccoby, Frits van Rhee, Chris A. Brackley et al., Genome Research, 2022, p. 1343-1354 (2021)
Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces DOI
C. A. Brackley, A. Lips, A. Morozov, W. C.K. Poon and D. Marenduzzo, Nature Communications, 12, 1, p. 1-6 (2021)
Complex small-world regulatory networks emerge from the 3D organisation of the human genome DOI
C. A. Brackley, N Gilbert, D. Michieletto, A Papantonis, M.C.F. Pereira, P. R. Cook and D. Marenduzzo, Nature Communications, 12, 1, p. 1-14 (2021)
Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling DOI
Yair A. G. Fosado, Davide Michieletto, Chris A. Brackley and Davide Marenduzzo, Proceedings of the National Academy of Sciences (PNAS), 118, 10, p. 1-6 (2021)
Polymer compaction and bridging-induced clustering of protein-inspired patchy particles DOI
C. A. Brackley, Journal of Physics: Condensed Matter, 32, 31 (2020)
Computational design of probes to detect bacterial genomes by multivalent binding DOI
Tine Curk, Chris Brackley, James D Farrell, Zhongyang Xing, Darshana Joshi, Susana Oliveira Lebre Direito, Urban Bren, Stefano Angioletti-Uberti, Jure Dobnikar, Erika Eiser et al., Proceedings of the National Academy of Sciences (PNAS) (2020)
Bridging-induced microphase separation: photobleaching experiments, chromatin domains, and the need for active reactions. DOI
Chris Brackley and Davide Marenduzzo, Briefings in functional genomics (2020)
Polymer Modeling Predicts Chromosome Reorganization in Senescence DOI
Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo and Tamir Chandra, Cell Reports, 28, 12, p. P3212-3223.e6 (2019)
Nucleosome positions alone can be used to predict domains in yeast chromosomes DOI
Oliver Wiese, Davide Marenduzzo and Chris Brackley, Proceedings of the National Academy of Sciences (PNAS) (2019)
Non-equilibrium effects of molecular motors on polymers DOI
Martina Foglino, E Locatelli, Chris Brackley, Davide Michieletto, C N Likos and Davide Marenduzzo, Soft Matter (2019)
capC-MAP: software for analysis of Capture-C data DOI
Adam Buckle, Davide Marenduzzo and Chris Brackley, Bioinformatics (2019)
Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling DOI
Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley, Giuseppe Gonnella and Davide Marenduzzo, Biophysical Journal (2019)
Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci DOI
Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo and Nick Gilbert, Molecular Cell, 72, 4, p. 786-797.e11 (2018)
HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types DOI
Anne Zirkel, Milos Nikolic, Konstantinos Sofiadis, Jan-Philipp Mallm, Chris A. Brackley, Henrike Gothe, Oliver Drechsel, Christian Becker, Janine Altmueller, Natasa Josipovic, Davide Marenduzzo et al., Molecular Cell, 70, 4, p. 730-744.e6 (2018)
Extrusion without a motor DOI
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook and D Marenduzzo, Nucleus, p. 1-10 (2018)
Nonequilibrium Chromosome Looping via Molecular Slip Links DOI
C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook and D. Marenduzzo, Physical Review Letters, 119, 13, p. 1-5 (2017)
Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains
Chris Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter Cook and Davide Marenduzzo, Biophysical Journal, 112, 6 (2017)
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei DOI
Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo and Argyris Papantonis, Molecular Systems Biology, 12, 12, p. 891 (2016)
Simulating topological domains in human chromosomes with a fitting-free model DOI
C A Brackley, D Michieletto, F Mouvet, J Johnson, S Kelly, P. R. Cook and D Marenduzzo, Nucleus, 7, 5, p. 453-461 (2016)
A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA DOI
Y. A. G. Fosado, D. Michieletto, J. Allan, C. Brackley, O. Henrich and D. Marenduzzo, Soft Matter, 12, 47, p. 9458-9470 (2016)
Stochastic Model of Supercoiling-Dependent Transcription DOI
C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella and D. Marenduzzo, Physical Review Letters, 117, 1 (2016)
Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains DOI
Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook and Davide Marenduzzo, Nucleic Acids Research, 44, 8, p. 3503–3512 (2016)
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models DOI
Chris A Brackley, Jill M Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R Hughes, Veronica J Buckle and Davide Marenduzzo, Genome Biology, 17, 1 (2016)
Community control in cellular protein production DOI
Frank S. Heldt, Chris A. Brackley, Celso Grebogi and Marco Thiel, Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 373, 2056 (2015)
A simple model for DNA bridging proteins and bacterial or human genomes DOI
J. Johnson, Chris Brackley, P. R. Cook and D. Marenduzzo, Journal of Physics: Condensed Matter, 27, 6 (2015)
Topological constraints strongly affect chromatin reconstitution in silico DOI
C. A. Brackley, James Allan, David Keszenman Pereyra and D. Marenduzzo, Nucleic Acids Research, 43, 1, p. 63-73 (2014)
Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS DOI
Chris Brackley, A. N. Morozov and D. Marenduzzo, The Journal of Chemical Physics, 140, 13 (2014)
Heterogeneous connectivity in neural fields DOI
Chris A. Brackley and Matthew S. Turner, Neural Fields: Theory and Applications, Springer-Verlag Berlin Heidelberg, p. 213-234 (2014)
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization DOI
Chris Brackley, Stephen Taylor, Argyris Papantonis, Peter R Cook and Davide Marenduzzo, Proceedings of the National Academy of Sciences (PNAS), 110, 38, p. E3605-11 (2013)
Intracellular Facilitated Diffusion DOI
Chris Brackley, M. E. Cates and D. Marenduzzo, Physical Review Letters, 111, 10 (2013)
Effect of DNA conformation on facilitated diffusion DOI
Chris Brackley, Michael Cates and Davide Marenduzzo, Biochemical Society Transactions, 41, p. 582-588 (2013)
Facilitated Diffusion on Mobile DNA DOI
Chris Brackley, M. E. Cates and D. Marenduzzo, Physical Review Letters, 109, 16 (2012)