Skip to main content
European Commission logo
polski polski
CORDIS - Wyniki badań wspieranych przez UE
CORDIS
CORDIS Web 30th anniversary CORDIS Web 30th anniversary

The physics of three dimensional chromosome and protein organisation within the cell

Publikacje

Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability

Autorzy: Marco Ancona, Davide Michieletto, Davide Marenduzzo
Opublikowane w: Physical Review E, Numer 101/4, 2020, ISSN 2470-0045
Wydawca: American Physical Society
DOI: 10.1103/physreve.101.042408

Mechanistic modeling of chromatin folding to understand function

Autorzy: Chris A. Brackey, Davide Marenduzzo, Nick Gilbert
Opublikowane w: Nature Methods, Numer 17/8, 2020, Strona(/y) 767-775, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/s41592-020-0852-6

Nonequilibrium Strategy for Fast Target Search on the Genome

Autorzy: F. Cagnetta, D. Michieletto, D. Marenduzzo
Opublikowane w: Physical Review Letters, Numer 124/19, 2020, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/physrevlett.124.198101

capC-MAP: software for analysis of Capture-C data

Autorzy: Adam Buckle, Nick Gilbert, Davide Marenduzzo, Chris A Brackley
Opublikowane w: Bioinformatics, Numer 35/22, 2019, Strona(/y) 4773-4775, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btz480

Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions

Autorzy: C A Brackley, D Marenduzzo
Opublikowane w: Briefings in Functional Genomics, Numer 19/2, 2020, Strona(/y) 111-118, ISSN 2041-2657
Wydawca: Oxford University Press
DOI: 10.1093/bfgp/elz032

Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting

Autorzy: Y. A. G. Fosado, D. Michieletto, D. Marenduzzo
Opublikowane w: Physical Review Letters, Numer 119/11, 2017, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/physrevlett.119.118002

Genome organization: experiments and modeling

Autorzy: Nick Gilbert, Davide Marenduzzo
Opublikowane w: Chromosome Research, Numer 25/1, 2017, Strona(/y) 1-4, ISSN 0967-3849
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10577-017-9551-2

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study

Autorzy: M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori, D. Marenduzzo, E. Orlandini
Opublikowane w: The Journal of Chemical Physics, Numer 147/4, 2017, Strona(/y) 044908, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.4995992

Nonequilibrium Chromosome Looping via Molecular Slip Links

Autorzy: C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Opublikowane w: Physical Review Letters, Numer 119/13, 2017, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/physrevlett.119.138101

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

Autorzy: Davide Michieletto, Davide Marenduzzo, Enzo Orlandini, Matthew Turner
Opublikowane w: Polymers, Numer 9/12, 2017, Strona(/y) 349, ISSN 2073-4360
Wydawca: MDPI AG
DOI: 10.3390/polym9080349

Simulating topological domains in human chromosomes with a fitting-free model

Autorzy: C. A. Brackley, D. Michieletto, F. Mouvet, J. Johnson, S. Kelly, P. R. Cook, D. Marenduzzo
Opublikowane w: Nucleus, Numer 7/5, 2016, Strona(/y) 453-461, ISSN 1949-1034
Wydawca: Landes Bioscience
DOI: 10.1080/19491034.2016.1239684

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

Autorzy: D. Michieletto, E. Orlandini, D. Marenduzzo
Opublikowane w: Scientific Reports, Numer 7/1, 2017, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-017-13916-w

Shaping epigenetic memory via genomic bookmarking

Autorzy: Michieletto, Davide; Chiang, Michael; Colì, Davide; Papantonis, Argyris; Orlandini, Enzo; Cook, Peter R; Marenduzzo, Davide
Opublikowane w: Nucleic Acids Research, Numer 6, 2018, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1101/184598

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains

Autorzy: Chris A. Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter R. Cook, Davide Marenduzzo
Opublikowane w: Biophysical Journal, Numer 112/6, 2017, Strona(/y) 1085-1093, ISSN 0006-3495
Wydawca: Biophysical Society
DOI: 10.1016/j.bpj.2017.01.025

Extrusion without a motor: a new take on the loop extrusion model of genome organization

Autorzy: C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, D. Marenduzzo
Opublikowane w: Nucleus, Numer 9/1, 2018, Strona(/y) 95-103, ISSN 1949-1034
Wydawca: Landes Bioscience
DOI: 10.1080/19491034.2017.1421825

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

Autorzy: Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook, Davide Marenduzzo
Opublikowane w: Nucleic Acids Research, Numer 44/8, 2016, Strona(/y) 3503-3512, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkw135

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

Autorzy: Chris A. Brackley, Jill M. Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R. Hughes, Veronica J. Buckle, Davide Marenduzzo
Opublikowane w: Genome Biology, Numer 17/1, 2016, Strona(/y) 59, ISSN 1474-760X
Wydawca: BioMed Central
DOI: 10.1186/s13059-016-0909-0

A single nucleotide resolution model for large-scale simulations of double stranded DNA

Autorzy: Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich, D. Marenduzzo
Opublikowane w: Soft Matter, Numer 12/47, 2016, Strona(/y) 9458-9470, ISSN 1744-683X
Wydawca: Royal Society of Chemistry
DOI: 10.1039/C6SM01859A

Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains

Autorzy: D. Michieletto, E. Orlandini, D. Marenduzzo
Opublikowane w: Physical Review X, Numer 6/4, 2016, ISSN 2160-3308
Wydawca: American Physical Society
DOI: 10.1103/PhysRevX.6.041047

Stochastic Model of Supercoiling-Dependent Transcription

Autorzy: C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella, D. Marenduzzo
Opublikowane w: Physical Review Letters, Numer 117/1, 2016, Strona(/y) 018101 (article number), ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/PhysRevLett.117.018101

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Autorzy: Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo, Argyris Papantonis
Opublikowane w: Molecular Systems Biology, Numer 12/12, 2016, Strona(/y) 891, ISSN 1744-4292
Wydawca: Nature Publishing Group
DOI: 10.15252/msb.20167311

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology

Autorzy: Enzo Orlandini, Davide Marenduzzo, Davide Michieletto
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 116/17, 2019, Strona(/y) 8149-8154, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1815394116

Physical principles of retroviral integration in the human genome

Autorzy: D. Michieletto, M. Lusic, D. Marenduzzo, E. Orlandini
Opublikowane w: Nature Communications, Numer 10/1, 2019, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-019-08333-8

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

Autorzy: Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert
Opublikowane w: Molecular Cell, Numer 72/4, 2018, Strona(/y) 786-797.e11, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2018.09.016

Dry active turbulence in a model for microtubule–motor mixtures

Autorzy: Ivan Maryshev, Andrew B. Goryachev, Davide Marenduzzo, Alexander Morozov
Opublikowane w: Soft Matter, Numer 15/30, 2019, Strona(/y) 6038-6043, ISSN 1744-683X
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sm00558g

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus

Autorzy: Davide Michieletto, Davide Colì, Davide Marenduzzo, Enzo Orlandini
Opublikowane w: Physical Review Letters, Numer 123/22, 2019, ISSN 0031-9007
Wydawca: American Physical Society
DOI: 10.1103/physrevlett.123.228101

Magnetic polymer models for epigenetics-driven chromosome folding

Autorzy: Davide Colì, Enzo Orlandini, Davide Michieletto, Davide Marenduzzo
Opublikowane w: Physical Review E, Numer 100/5, 2019, ISSN 2470-0045
Wydawca: American Physical Society
DOI: 10.1103/physreve.100.052410

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling

Autorzy: Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley, Giuseppe Gonnella, Davide Marenduzzo
Opublikowane w: Biophysical Journal, Numer 117/2, 2019, Strona(/y) 369-376, ISSN 0006-3495
Wydawca: Biophysical Society
DOI: 10.1016/j.bpj.2019.04.023

Polymer Modeling Predicts Chromosome Reorganization in Senescence

Autorzy: Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo, Tamir Chandra
Opublikowane w: Cell Reports, Numer 28/12, 2019, Strona(/y) 3212-3223.e6, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2019.08.045

Nucleosome positions alone can be used to predict domains in yeast chromosomes

Autorzy: Oliver Wiese, Davide Marenduzzo, Chris A. Brackley
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 116/35, 2019, Strona(/y) 17307-17315, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.1817829116

Non-equilibrium effects of molecular motors on polymers

Autorzy: M. Foglino, E. Locatelli, C. A. Brackley, D. Michieletto, C. N. Likos, D. Marenduzzo
Opublikowane w: Soft Matter, Numer 15/29, 2019, Strona(/y) 5995-6005, ISSN 1744-683X
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sm00273a

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

Autorzy: Peter R Cook, Davide Marenduzzo
Opublikowane w: Nucleic Acids Research, Numer 46/19, 2018, Strona(/y) 9895-9906, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gky763

Plectoneme dynamics and statistics in braided polymers

Autorzy: Giada Forte, Michele Caraglio, Davide Marenduzzo, Enzo Orlandini
Opublikowane w: Physical Review E, Numer 99/5, 2019, ISSN 2470-0045
Wydawca: American Physical Society
DOI: 10.1103/physreve.99.052503

Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins

Autorzy: A. Bonato, C. A. Brackley, J. Johnson, D. Michieletto, D. Marenduzzo
Opublikowane w: Soft Matter, Numer 16/9, 2020, Strona(/y) 2406-2414, ISSN 1744-683X
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sm01875a

Wyszukiwanie danych OpenAIRE...

Podczas wyszukiwania danych OpenAIRE wystąpił błąd

Brak wyników