(Q42409736)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

title

A lattice model for transcription factor access to nucleosomal DNA (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

Vladimir B. Teif

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

Vladimir B. Teif

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

author name string

Ramona Ettig

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

language of work or name

English

0 references

publication date

1 October 2010

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

volume

99

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

issue

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

page(s)

2597-2607

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

Statistical-mechanical lattice models for protein-DNA binding in chromatin

15 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Condensed DNA: condensing the concepts.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Predicting gene-regulation functions: lessons from temperate bacteriophages

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

DNA methylation increases nucleosome compaction and rigidity

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Nucleosome positioning by genomic excluding-energy barriers

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

An ensemble model of competitive multi-factor binding of the genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Nucleosome disassembly intermediates characterized by single-molecule FRET.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Dynamics and function of compact nucleosome arrays

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Dynamics of nucleosomes revealed by time-lapse atomic force microscopy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

spFRET using alternating excitation and FCS reveals progressive DNA unwrapping in nucleosomes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Nucleosome positioning: how is it established, and why does it matter?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Using DNA mechanics to predict in vitro nucleosome positions and formation energies.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

From DNA sequence to transcriptional behaviour: a quantitative approach

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Incorporating nucleosomes into thermodynamic models of transcription regulation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

The nucleosome family: dynamic and growing

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Poly(dA:dT) tracts: major determinants of nucleosome organization

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

The DNA-encoded nucleosome organization of a eukaryotic genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Spontaneous access to DNA target sites in folded chromatin fibers

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Dynamic regulation of nucleosome positioning in the human genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Genome-wide approaches to studying chromatin modifications

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Interplay of ion binding and attraction in DNA condensed by multivalent cations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Physical methods used to study core histone tail structures and interactions in solution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

A genomic code for nucleosome positioning

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Rapid accessibility of nucleosomal DNA in yeast on a second time scale

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Histone H4-K16 acetylation controls chromatin structure and protein interactions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Scalable molecular dynamics with NAMD

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Ligand-induced DNA condensation: choosing the model.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Rapid spontaneous accessibility of nucleosomal DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Nucleosomes facilitate their own invasion

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

A biophysical approach to transcription factor binding site discovery

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

DNA looping in the RNA polymerase I enhancesome is the result of non-cooperative in-phase bending by two UBF molecules

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

VMD: visual molecular dynamics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Theory of single-dimensional absorption. II. Adsorption of small molecules on a heteropolymer.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Cooperative effects on binding of proteins to DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Nucleosome positioning by sequence, state of the art and apparent finale

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Predicting transcription factor affinities to DNA from a biophysical model.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Map analysis of ligand binding to a linear lattice

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Short-range interactions and size of ligands bound to DNA strongly influence adsorptive phase transition caused by long-range interactions

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2955348

Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes

16 August 2018

1 reference

12 December 2020

DNA spools under tension

1 reference

12 December 2020

Kinetic accessibility of buried DNA sites in nucleosomes

1 reference

12 December 2020

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites

1 reference

12 December 2020

[Effect of ligand interaction with the boundaries between different forms of DNA on intramolecular transitions]

1 reference

12 December 2020

Analytical model study of dendrimer/DNA complexes

1 reference

12 December 2020

A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites

1 reference

12 December 2020

Analysis of the nucleosome arrangement on satellite DNA

1 reference

12 December 2020

Calculation of binding isotherms for heterogeneous polymers

1 reference

12 December 2020

Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy

1 reference

12 December 2020

10.1016/J.BPJ.2010.08.019

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:20959101%20AND%20SRC:MED&resulttype=core&format=json

15 February 2020

PubMed publication ID

20959101

1 reference