Chris Brackley

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 othersEarnshaw, W. C. & Kops, G. J. P. L., 6 Jun 2024, In: Cell. 187, 12, p. 3006-3023.e26 45 p.

Research output: Contribution to journal › Article › peer-review

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File

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 othersRussell, L. J., 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

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File

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, 31

Research output: Contribution to journal › Article › peer-review

Open Access

File

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

Open Access

File

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

Open Access

File

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.e6

Research output: Contribution to journal › Article › peer-review

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File

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 othersMarenduzzo, D., Rippe, K. & Papantonis, A., 17 May 2018, In: Molecular Cell. 70, 4, p. 730-744.e6 21 p.

Research output: Contribution to journal › Article › peer-review

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

Open Access

File

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

Open Access

File

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, 6

Research 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. 891

Research output: Contribution to journal › Article › peer-review

Open Access

File

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

Open Access

File

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. 9458-9470

Research output: Contribution to journal › Article › peer-review

Open Access

File

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

Open Access

File

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

Open Access

File

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

Open Access

File