Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations. (Q38806570)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28468672%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

title

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations (English)

1 reference

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19 March 2020

2

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19 March 2020

Christophe Zimmer

series ordinal

4

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19 March 2020

author name string

Jean-Michel Arbona

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28468672%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Emmanuelle Fabre

series ordinal

3

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19 March 2020

publication date

3 May 2017

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19 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28468672%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

volume

18

1 reference

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19 March 2020

issue

1

1 reference

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19 March 2020

page(s)

81

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28468672%20AND%20SRC:MED&resulttype=core&format=json

Polymer physics of chromosome large-scale 3D organisation

19 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

DNA damage signalling targets the kinetochore to promote chromatin mobility

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromosome position determines the success of double-strand break repair

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Insulator dysfunction and oncogene activation in IDH mutant gliomas

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Modeling chromosomes: Beyond pretty pictures.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

High-quality genome (re)assembly using chromosomal contact data

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Filling annotation gaps in yeast genomes using genome-wide contact maps

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Relevance and limitations of crowding, fractal, and polymer models to describe nuclear architecture.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Computational models of large-scale genome architecture.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Systematic characterization of the conformation and dynamics of budding yeast chromosome XII.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Effect of nuclear architecture on the efficiency of double-strand break repair

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Functional implications of genome topology.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Through thick and thin: the conundrum of chromatin fibre folding in vivo

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Open and closed domains in the mouse genome are configured as 10-nm chromatin fibres

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

From microbes to numbers: extracting meaningful quantities from images

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Normalization of a chromosomal contact map.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromosomes without a 30-nm chromatin fiber

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Mating-type genes and MAT switching in Saccharomyces cerevisiae

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Spatial partitioning of the regulatory landscape of the X-inactivation centre

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Topological domains in mammalian genomes identified by analysis of chromatin interactions

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromatin organization - the 30 nm fiber

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Principles of chromosomal organization: lessons from yeast

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Gene positioning and expression

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Living without 30nm chromatin fibers

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

The budding yeast nucleus.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Looping probabilities in model interphase chromosomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Structure and dynamics of interphase chromosomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Higher-order structures of chromatin: the elusive 30 nm fiber

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

The budding yeast spindle pole body: structure, duplication, and function

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Localization accuracy in single-molecule microscopy

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Capturing chromosome conformation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

High-voltage electron tomography of spindle pole bodies and early mitotic spindles in the yeast Saccharomyces cerevisiae

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Dynamical modeling of three-dimensional genome organization in interphase budding yeast.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

A three-dimensional model of the yeast genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

How to build a yeast nucleus.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

The genome folding mechanism in yeast

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

High-resolution statistical mapping reveals gene territories in live yeast

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Polymer chain models of DNA and chromatin.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

Inferential structure determination.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5414205

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

31 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13059-017-1199-X

21 January 2018

emcee: The MCMC Hammer

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS13059-017-1199-X

Unravelled nucleosomes, nucleosome beads and higher order structures of chromatin: Influence of non-histone components and histone H1

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28468672

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Functional compartmentalization of the nucleus in the budding yeast Saccharomyces cerevisiae

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28468672

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Live imaging of telomeres: yKu and Sir proteins define redundant telomere-anchoring pathways in yeast

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28468672

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-017-1199-X

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28468672%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

19 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28468672%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

PubMed publication ID

28468672

1 reference