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Single particle trajectory statistic to reconstruct chromatin organization and dynamics

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/j.1460-2075.1990.tb08144.xopenalex-snapshot

The size of chromatin loops in HeLa cells.

inferredcites →https://doi.org/10.1006/jcph.1995.1039openalex-snapshot

Fast Parallel Algorithms for Short-Range Molecular Dynamics

inferredcites →https://doi.org/10.1016/b978-0-12-800046-5.00009-6openalex-snapshot

Computational Models of Large-Scale Genome Architecture

inferredcites →https://doi.org/10.1016/j.bpj.2014.10.018openalex-snapshot

Residence Times of Receptors in Dendritic Spines Analyzed by Stochastic Simulations in Empirical Domains

inferredcites →https://doi.org/10.1016/j.bpj.2015.09.003openalex-snapshot

Analysis and Interpretation of Superresolution Single-Particle Trajectories

inferredcites →https://doi.org/10.1016/j.bpj.2015.11.3520openalex-snapshot

Physical Modeling of Dynamic Coupling between Chromosomal Loci

inferredcites →https://doi.org/10.1016/j.bpj.2016.02.003openalex-snapshot

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains

inferredcites →https://doi.org/10.1016/j.bpj.2017.04.018openalex-snapshot

Direct Observation of Cell-Cycle-Dependent Interactions between CTCF and Chromatin

inferredcites →https://doi.org/10.1016/j.bpj.2017.11.3265openalex-snapshot

De Novo Prediction of Human Chromosome Structures: Epigenetic Marking Patterns Encode Genome Architecture

inferredcites →https://doi.org/10.1016/j.ceb.2011.03.010openalex-snapshot

Physical nuclear organization: loops and entropy

inferredcites →https://doi.org/10.1016/j.cell.2006.12.048openalex-snapshot

Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

inferredcites →https://doi.org/10.1016/j.cell.2013.02.010openalex-snapshot

Chromatin Movement in the Maintenance of Genome Stability

inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

inferredcites →https://doi.org/10.1016/j.cell.2017.04.013openalex-snapshot

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension

inferredcites →https://doi.org/10.1016/j.celrep.2016.04.003openalex-snapshot

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

inferredcites →https://doi.org/10.1016/j.celrep.2017.01.018openalex-snapshot

Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories

inferredcites →https://doi.org/10.1016/j.molcel.2013.10.021openalex-snapshot

Centromere Tethering Confines Chromosome Domains

inferredcites →https://doi.org/10.1016/j.molcel.2015.02.033openalex-snapshot

Imaging Live-Cell Dynamics and Structure at the Single-Molecule Level

inferredcites →https://doi.org/10.1016/j.neuron.2010.05.026openalex-snapshot

Single-Molecule Discrimination of Discrete Perisynaptic and Distributed Sites of Actin Filament Assembly within Dendritic Spines

inferredcites →https://doi.org/10.1016/j.physleta.2012.01.014openalex-snapshot

Coagulation–fragmentation for a finite number of particles and application to telomere clustering in the yeast nucleus

inferredcites →https://doi.org/10.1016/j.physrep.2017.02.002openalex-snapshot

Polymer physics of nuclear organization and function

inferredcites →https://doi.org/10.1016/s0079-6107(00)00018-3openalex-snapshot

Twisting and stretching single DNA molecules

inferredcites →https://doi.org/10.1038/embor.2013.142openalex-snapshot

Cohesin and the nucleolus constrain the mobility of spontaneous repair foci

inferredcites →https://doi.org/10.1038/nature21429openalex-snapshot

3D structures of individual mammalian genomes studied by single-cell Hi-C

inferredcites →https://doi.org/10.1038/nmeth.1176openalex-snapshot

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

inferredcites →https://doi.org/10.1038/nmeth.2411openalex-snapshot

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

inferredcites →https://doi.org/10.1038/nsmb.3347openalex-snapshot

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

inferredcites →https://doi.org/10.1038/s41467-018-05009-7openalex-snapshot

Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair

inferredcites →https://doi.org/10.1038/s41467-018-05606-6openalex-snapshot

Interphase human chromosome exhibits out of equilibrium glassy dynamics

inferredcites →https://doi.org/10.1038/s41556-018-0192-2openalex-snapshot

Single particle trajectories reveal active endoplasmic reticulum luminal flow

inferredcites →https://doi.org/10.1038/s41588-018-0175-zopenalex-snapshot

Dynamic interplay between enhancer–promoter topology and gene activity

inferredcites →https://doi.org/10.1038/s41594-017-0015-3openalex-snapshot

Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING)

inferredcites →https://doi.org/10.1038/s41598-017-10842-9openalex-snapshot

Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration

inferredcites →https://doi.org/10.1063/1.472208openalex-snapshot

Diffusion limited first contact of the ends of a polymer: Comparison of theory with simulation

inferredcites →https://doi.org/10.1073/pnas.1102255108openalex-snapshot

Single-molecule investigations of the stringent response machinery in living bacterial cells

inferredcites →https://doi.org/10.1073/pnas.1204799109openalex-snapshot

Complexity of chromatin folding is captured by the strings and binders switch model

inferredcites →https://doi.org/10.1073/pnas.1220313110openalex-snapshot

Micron-scale coherence in interphase chromatin dynamics

inferredcites →https://doi.org/10.1073/pnas.1319473110openalex-snapshot

Distribution of directional change as a signature of complex dynamics

inferredcites →https://doi.org/10.1073/pnas.1506257112openalex-snapshot

Topology, structures, and energy landscapes of human chromosomes

inferredcites →https://doi.org/10.1073/pnas.1714980114openalex-snapshot

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

inferredcites →https://doi.org/10.1088/0034-4885/66/1/201openalex-snapshot

Stretching of macromolecules and proteins

inferredcites →https://doi.org/10.1088/0305-4470/37/31/r01openalex-snapshot

The restaurant at the end of the random walk: recent developments in the description of anomalous transport by fractional dynamics

inferredcites →https://doi.org/10.1088/1478-3975/13/2/026001openalex-snapshot

The folding landscape of the epigenome

inferredcites →https://doi.org/10.1093/nar/gkv100openalex-snapshot

Inferential modeling of 3D chromatin structure

inferredcites →https://doi.org/10.1101/gad.176156.111openalex-snapshot

Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination

inferredcites →https://doi.org/10.1101/gad.277863.116openalex-snapshot

CTCF: making the right connections

inferredcites →https://doi.org/10.1101/gad.608210openalex-snapshot

Cohesin organizes chromatin loops at DNA replication factories

inferredcites →https://doi.org/10.1103/physreve.76.051805openalex-snapshot

Random loop model for long polymers

inferredcites →https://doi.org/10.1103/physreve.84.021906openalex-snapshot

Narrow escape through a funnel and effective diffusion on a crowded membrane

inferredcites →https://doi.org/10.1103/physreve.87.052713openalex-snapshot

Improved estimation of anomalous diffusion exponents in single-particle tracking experiments

inferredcites →https://doi.org/10.1103/physreve.88.052604openalex-snapshot

Polymer model with long-range interactions: Analysis and applications to the chromatin structure

inferredcites →https://doi.org/10.1103/physreve.92.052109openalex-snapshot

Recovering a stochastic process from super-resolution noisy ensembles of single-particle trajectories

inferredcites →https://doi.org/10.1103/physreve.96.012503openalex-snapshot

Statistics of randomly cross-linked polymer models to interpret chromatin conformation capture data

inferredcites →https://doi.org/10.1103/physrevlett.109.108302openalex-snapshot

Computation of the Mean First-Encounter Time Between the Ends of a Polymer Chain

inferredcites →https://doi.org/10.1126/science.1065366openalex-snapshot

Chromosome Dynamics in the Yeast Interphase Nucleus

inferredcites →https://doi.org/10.1146/annurev-biophys-062215-010830openalex-snapshot

Imaging Specific Genomic DNA in Living Cells

inferredcites →https://doi.org/10.1146/annurev-genet-120417-031334openalex-snapshot

Chromosome Dynamics in Response to DNA Damage

inferredcites →https://doi.org/10.1146/annurev-statistics-060116-054204openalex-snapshot

Statistical Methods for Large Ensembles of Super-Resolution Stochastic Single Particle Trajectories in Cell Biology

inferredcites →https://doi.org/10.1186/s12860-016-0111-yopenalex-snapshot

High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division

inferredcites →https://doi.org/10.1186/s13059-015-0745-7openalex-snapshot

Analysis methods for studying the 3D architecture of the genome

inferredcites →https://doi.org/10.1371/journal.pcbi.1003867openalex-snapshot

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

inferredcites →https://doi.org/10.1371/journal.pcbi.1004433openalex-snapshot

Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions

inferredcites →https://doi.org/10.1371/journal.pcbi.1005469openalex-snapshot

Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data

inferredcites →https://doi.org/10.1371/journal.pcbi.1005659openalex-snapshot

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

inferredcites →https://doi.org/10.1371/journal.pone.0117722openalex-snapshot

Guidelines for the Fitting of Anomalous Diffusion Mean Square Displacement Graphs from Single Particle Tracking Experiments

inferredcites →https://doi.org/10.1534/genetics.112.140608openalex-snapshot

Structure and Function in the Budding Yeast Nucleus

inferredcites →https://doi.org/10.7554/elife.02230openalex-snapshot

Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

inferredcites →https://doi.org/10.7554/elife.25776openalex-snapshot

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/405969openalex-snapshot

Hi-D: Nanoscale mapping of nuclear dynamics in single living cells

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