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References from Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1039/d0cp01877e
10.1039/d0cp01877e · External reference
Defining functionally relevant spatial chromatin domains: it is a tad complicated
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10.1007/s10577-016-9545-5
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Comparative study on chromatin loop callers using hi-c data reveals their effectiveness
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10.1080/19491034.2020.1782024 · External reference
Compaction and segregation of sister chromatids via active loop extrusion
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The dynamic role of cohesin in maintaining human genome architecture
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Lamina-associated domains: peripheral matters and internal affairs
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From reads to insight: a hitchhiker's guide to atac-seq data analysis
2020 · External reference
Detect accessible chromatin using atac-sequencing, from principle to applications
2019 · External reference
Quantitative mnase-seq accurately maps nucleosome occupancy levels
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Unresolved reference
2014 · External reference
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Loopsage: an energy-based Monte Carlo approach for the loop extrusion modelling of chromatin
10.1016/j.ymeth.2024.01.015 · 2024 · External reference
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10.1016/j.ceb.2020.04.011 · External reference
The interplay between asymmetric and symmetric dna loop extrusion
10.7554/elife.63528 · 2020 · External reference
Spring model–chromatin modeling tool based on openmm
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Principles of 3d compartmentalization of the human genome
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10.1101/gr.205062.116
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cudammc: Gpu-enhanced multiscale Monte Carlo chromatin 3d modelling
10.1093/bioinformatics/btad588 · 2023 · External reference
10.1038/nprot.2018.009
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10.1007/978-3-031-37404-3 · 2023 · External reference
Fundamental concepts of classical chaos. Part ii: fractals and chaotic dynamics
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Lamin b1 mapping reveals the existence of dynamic and functional euchromatin lamin b1 domains
10.1038/s41467-018-05912-z · 2018 · External reference
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10.1080/19491034.2019.1570810 · External reference
Openmm: a hardware-independent framework for molecular simulations
10.1109/mcse.2010.27 · 2010 · External reference
Pyvista: 3d plotting and mesh analysis through a streamlined interface for the visualization toolkit (vtk)
10.21105/joss.01450 · 2019 · External reference
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10.1007/s10577-016-9548-2 · External reference
10.1016/j.ceb.2014.01.003
10.1016/j.ceb.2014.01.003 · External reference
10.1101/cshperspect.a000638
10.1101/cshperspect.a000638 · External reference
Lamina-associated domains: peripheral matters and internal affairs
10.1186/s13059-020-02003-5 · 2020 · External reference
Unresolved reference
2023 · External reference
Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale
10.1080/19491034.2020.1868105 · 2021 · External reference
10.1101/cshperspect.a003889
10.1101/cshperspect.a003889 · External reference
Chromosome territories and the global regulation of the genome
10.1002/gcc.22732 · 2019 · External reference
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A brief review of nucleosome structure
10.1016/j.febslet.2015.05.016 · 2015 · External reference
Kilobase pair chromatin fiber contacts promoted by living-system- like dna linker length distributions and nucleosome depletion
10.1021/acs.jpcb.7b00998 · 2017 · External reference
Mesoscale simulations of two nucleosome-repeat length oligonucleosomes
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