Publications

Below is a (hopefully up to date) list of my papers in roughly reverse order of publication, with links to published and pre-print versions where possible.

You can also find my papers on Google Scholar and the Edinburgh Research Explorer.

• G. Forte, A. Buckle, S. Boyle, D. Marenduzzo, N. Gilbert, and C. A. Brackley "Transcription modulates chromatin dynamics and locus configuration sampling" Nature Structural & Molecular Biology https://doi.org/10.1038/s41594-023-01059-8 (2023) url bioRxiv

• M. Chiang, C. A. Brackley, C. Naughton, R-S. Nozawa, C. Battaglia, D. Marenduzzo, N. Gilbert "Gene structure heterogeneity drives transcription noise within human chromosomes" Under review (2022) bioRxiv

• C. Sacristan, K. Samejima, L. Andrade Ruiz, M. L. A. Lambers, A. Buckle, C. A. Brackley, D. Robertson, T. Hori, S. Webb, T. Fukagawa, N. Gilbert, D. Marenduzzo, W. C. Earnshaw, G. J. P. L. Kops "Condensin reorganizes centromeric chromatin during mitotic entry into a bipartite structure stabilized by cohesin" Cell Accepted (2024) bioRxiv

• P. Sinclair, C. A. Brackley, M. Carballo Pacheco, and R. J Allen "A model for quorum-sensing mediated stochastic biofilm nucleation" Physical Review Letters 129 198102 (2022) url bioRxiv

• P. Sinclair, J. Longyear, K. Reynolds, A. A. Finnie, C. A. Brackley, M. Carballo-Pacheco, and R. J. Allen "A computational model for microbial colonisation of an antifouling surface" Frontiers in Microbiology 13 920014 (2022) url postprint

• D. Rico, D. Kent, N. Karataraki, A. Mikulasova,  R. Berlinguer-Palmini, B. A. Walker, B. M. Javierre, L. J. Russell, and C. A Brackley "High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights on proto-oncogene deregulation" Genome Research  32 1355-1366  (2022) url  bioRxiv

• M. Ancona and C. A. Brackley "Simulating the chromatin mediated phase separation of model proteins with multiple domains" Biophysical Journal 121  2600-2612 (2022) url arXiv

• M. Chiang, C. A. Brackley, D. Marenduzzo, and N. Gilbert "Predicting genome organisation and function with mechanistic modelling" Trends in Genetics 38 364  (2022) url

• A. Mikulasova, et al "Epigenomic translocation of H3K4me3 broad domains following super-enhancer hijacking" Genome Research 32 1343-1354 (2022) url bioRxiv 

• Y. A. G. Fosado, D. Michieletto, C. A. Brackley, and D. Marenduzzo "Twin Supercoiling Domain: Action at a Distance in Transcriptional Dynamics" Proc. Natl. Acad. Sci. USA 118 e1905215118 (2021) arXiv url

• C. A. Brackley, A. Lips, A. Morozov, W. C. K. Poon, and D. Marenduzzo "Electrostatic inactivation of RNA viruses at air-water and liquid-liquid interfaces" Nature Communications 12 6812 (2021) url arXiv

• C. A. Brackley, N. Gilbert, D. Michieletto, A. Papantonis, M. C. Pereira, P. R. Cook, and D. Marenduzzo "Complex small-world regulatory networks emerge from the 3D organisation of the human genome" Nature Communications 12 1-14 (2021) url  bioRxiv

• C. A. Brackley, D. Marenduzzo, and N. Gilbert "Mechanistic modeling of chromatin folding to understand function" Nature Methods 17 643-643 (2020) url

• T. Curk, C. A. Brackley, J. D. Farrell, Z. Xing, D. Joshi, S. Direito, U. Bren, S. Angioletti-Uberti, J. Dobnikar, E. Eiser, D. Frenkel, and R. J. Allen "Computational design of probes to detect bacterial genomes by multivalent binding" Proc. Natl. Acad. Sci. USA 117 8719-8726 (2020) url

• C. A. Brackley and D. Marenduzzo "Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions" Briefings in Functional Genomics 19 111-118 (2020) url

• C. A. Brackley "Polymer compaction and bridging-induced clustering of protein-inspired patchy particles" Journal of Physics: Condensed Matter 32 314002 (2020) url arXiv

• A Bonato, CA Brackley, J Johnson, D Michieletto, D Marenduzzo "Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins" Soft Matter 16 2406-2414 (2020) url bioRxiv

• O. Wiese, D. Marenduzzo, and C. A. Brackley "Nucleosome positions alone determine micro-domains in yeast chromosomes" Proc. Natl. Acad. Sci. USA 116 17307-17315 (2019) url bioRxiv

• M. Chiang, D. Michieletto, C. A. Brackley, N. Rattanavirotkul, H. Mohammed, D. Marenduzzo, and T. Chandra "Lamina and Heterochromatin Mediate Nuclear Organisation in Growing, Senescent and Progeroid Cells" Cell Reports 28 3212-3223.e6 (2019) url bioRxiv

• M. Foglino, E. Locatelli, D. Michieletto, C. A. Brackley, C. N. Likos and D. Marenduzzo "Non-Equilibrium Effects of Molecular Motors on Polymers" Soft Matter (2019) url

• A. Buckle, N. Gilbert, D. Marenduzzo, and C. A. Brackley "capC-MAP : A Software Package for Analysis of Capture-C data"  Bioinformatics (2019) url bioRxiv software manual

• C. A. Brackley, M. C. Pereira, J. Johnson, D. Michieletto, and D. Marenduzzo "Predictive Models for 3D Chromosome Organization: The Transcription Factor an d Diffusive Loop Extrusion Models" in Modeling the 3D Conformation of Genomes, ed. G. Tiana and L. Giorgetti CRC Press (2019) url

• A. Buckle, C. A. Brackley, S. Boyle, D. Marenduzzo and N. Gilbert "Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci" Molecular Cell 72 1-12 (2018) url bioRxiv

• M. Ancona, A. Bentivoglio, C. A. Brackley, G. Gonnella, and D. Marenduzzo "Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling" Biophysical Journal 117 369-376 (2019) url arxiv

• A. Zirkel, M. Nikolic K. Sofiadis J-P. Mallm C. A. Brackley ... A. Papantonis "HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types" Molecular Cell 70 1-15 (2018) url

• M. C. F. Pereira, C. A. Brackley, D. Michieletto, C. Annunziatella, S. Bianco, A. M. Chiariello, M. Nicodemi, and D. Marenduzzo "Complementary chromosome folding by transcription factors and cohesin" Submitted (2018) biorXiv

• A. Bentivoglio, M. Ancona, C. A. Brackley, G. Gonnella, and D. Marenduzzo "Non-equilibrium phase transition in a model for supercoiling-dependent DNA transcription", Soft Matter, 14 3632 (2018) url

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

• C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo "Non-equilibrium chromosome looping via molecular slip-links", Physical Review Letters, 119 138101 (2017) url arXiv 

• C. A. Brackley, B. Liebchen, D. Michieletto, F. L. Mouvet, P. R Cook and D. Marenduzzo "Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains" Biophysical Journal, 28 1085 (2017) url arXiv

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

• L. Brant, T. Georgomanolis, M. Nikolic, C. A. Brackley, P. Kolovos, W. van Ijcken, F. G. Grosveld, D. Marenduzzo, and A. Papantonis "Exploiting native forces to capture chromosome conformation in mammalian cell nuclei" Molecular Systems Biology 12 891 (2016) url

• M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori, D. Marenduzzo and E. Orlandini "Entropic elasticity and dynamics of the bacterial chromosome: a simulation study" Journal of Chemical Physics, 147, 044908 (2017) url arXiv

• Y. A. G. Fosado, D. Michieletto, J. Allan, C. Brackley, O. Henrich and D. Marenduzzo "A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA" Soft Matter, 12 9458 (2016) url arXiv

• C. A. Brackley, J. Johnson, S. Kelly, P. R. Cook and D. Marenduzzo "Binding of bivalent transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and domains" Nucleic Acids Research 44 3503 (2016) url arXiv

• C. A. Brackley, J. M. Brown, D. Waithe, C. Babbs, J. Davies, J. R. Hughes, V. J. Buckle and D. Marenduzzo "Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models" Genome Biology 17 1 (2016) url arXiv

• C. A. Brackley, J. Johnson, S. Corless, N. Gilbert, G. Gonnella, and D. Marenduzzo "A stochastic model of supercoiling-dependent transcription" Physical Review Letters, 117 018101 (2016) url arxiv

• F. S. Heldt, C. A. Brackley, C. Grebogi and M. Thiel "Community control in cellular protein production: consequences for amino acid starvation" Phil. Trans. R. Soc. A 373 20150107 (2015) url arXiv

• C. A. Brackley, J. Allan, D. Keszenman-Pereyra and D. Marenduzzo "Topological constraints strongly affect chromatin reconstitution in silico" Nucleic Acids Research 43 63 (2015) url

• J. Johnson, C. A. Brackley, P. R. Cook and D.Marenduzzo "A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction." J. Phys. Cond. Matt. 27 064119 (2015) url

• C. A. Brackley, A. N. Morozov and D. Marenduzzo "Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS" J. Chem. Phys. 140 135103 (2014) url  arXiv source code

• C. A. Brackley and M. S. Turner "Heterogeneous Connectivity in Neural Fields: A Stochastic Approach" in Neural Fields:  Theory and Applications, ed. S. Coombes et al., Springer-Verlag Berlin Heidelberg (2014) url

• C. A. Brackley, S. Taylor, A. Papantonis , P. R. Cook, and D. Marenduzzo "Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization" Proc. Natl. Acad. Sci. USA  110 E3605 (2013) url

• C. A. Brackley, M. E. Cates and D. Marenduzzo "Intracellular facilitated diffusion: searchers, crowders and blockers" Phys. Rev. Lett. 111 108101 (2013) url  arXiv

• C. A. Brackley, M. E. Cates and D. Marenduzzo "Effect of DNA conformation on facilitated diffusion" Biochem. Soc. Trans. 41 582 (2013) url  pdf

• C. A. Brackley, M. E. Cates and D. Marenduzzo "Facilitated diffusion on mobile DNA: Configurational traps and sequence heterogeneity" Phys. Rev. Lett. 109 168103 (2012) url  arXiv

• C. A. Brackley, L. Ciandrini, and M.C. Romano "Multiple exclusion processes with limited reservoirs of particles and fuel-carriers." J. Stat. Mech. P03002 (2012) url  arXiv

• C. A. Brackley, D. Broomhead, M. C. Romano and M. Thiel "A Max-Plus Model of Ribosome Dynamics During mRNA Translation." J. Theor. Biol. 303 128 (2012) url  arXiv

• C. A. Brackley, M. C. Romano and M. Thiel "The Dynamics of Supply and Demand in mRNA Translation" PLoS Comput. Biol. 7 e1002203 (2011) url

• C.A. Brackley et al. "Introduction to Focus Issue:Dynamics in Systems Biology" Chaos 20 045101 (2010) url

• C. A. Brackley M. C. Romano and M. Thiel "Slow Sites in an Exclusion Process with Limited Resources" Phys. Rev. E 82 051920 (2010) url

• C. A. Brackley, M. C. Romano, C. Grebogi and M. Thiel "Limited resources in a driven diffusion process" Phys. Rev. Lett. 105 078102 (2010) url

• C. A. Brackley and M. S. Turner "Two-point heterogeneous connections in a continuum neural field model" Biological Cybernetics 100 p371 (2009) url

• C. A. Brackley and M. S. Turner "Persistent fluctuations of activity in undriven continuum neural field models with power-law connections" Phys. Rev. E 79 011918 (2009) url

• C. A. Brackley and M. S. Turner "Random fluctuations of the firing rate function in a continuum neural field model" Phys. Rev. E 75 041913 (2007) url