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. A. Ruiz, M. Deb, M. L. A. Lambers, A. Buckle, C. A. Brackley, D. Robertson, T. Hori, S. Webb, R. Kiewisz, T. Bepler, E. van Kwawegen, P. Risteski, K. Vukušić, I. M. Tolić, T. Müller-Reichert, T. Fukagawa, N. Gilbert, D. Marenduzzo, W. C. Earnshaw, G. J. P. L. Kops "Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin" Cell Accepted (2024) url  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