(Q37298599)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

title

Using DNA mechanics to predict in vitro nucleosome positions and formation energies (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

author name string

Karissa Fortney

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Daria A Gaykalova

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Vasily M Studitsky

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

Jonathan Widom

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

language of work or name

English

0 references

publication date

9 June 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

volume

37

1 reference

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30 January 2020

issue

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

page(s)

4707-4722

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

The DNA-encoded nucleosome organization of a eukaryotic genome

30 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

DNA physical properties determine nucleosome occupancy from yeast to fly.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Genomic sequence is highly predictive of local nucleosome depletion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

A high-resolution atlas of nucleosome occupancy in yeast

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Nucleosome positioning signals in genomic DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

A genomic code for nucleosome positioning

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Gene expression from random libraries of yeast promoters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Protein-DNA binding specificity predictions with structural models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Measurement of histone-DNA interaction free energy in nucleosomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Reconstitution of nucleosome core particles from recombinant histones and DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

The nucleosome: from genomic organization to genomic regulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

The structure of DNA in the nucleosome core

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Role of DNA sequence in nucleosome stability and dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Zero background yeast reporter plasmids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Estimating the persistence length of a worm-like chain molecule from force-extension measurements

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Crystal structure of the nucleosome core particle at 2.8 A resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Binding of TFIID to the CYC1 TATA boxes in yeast occurs independently of upstream activating sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Artificial nucleosome positioning sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

A determining influence for CpG dinucleotides on nucleosome positioning in vitro

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Structure and conformation of helical nucleic acids: analysis program (SCHNAaP).

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Construction, analysis, and transcription of model nucleosomal templates

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Identification and distinct regulation of yeast TATA box-containing genes

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Nucleosomes unfold completely at a transcriptionally active promoter.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

TGGA repeats impair nucleosome formation.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2724288

Identification and characterization of genomic nucleosome-positioning sequences

2 September 2018

1 reference

12 December 2020

Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP)

1 reference

12 December 2020

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

Effects of DNA sequence and histone-histone interactions on nucleosome placement

1 reference

12 December 2020

Nucleosome positions predicted through comparative genomics

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKP475

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19509309%20AND%20SRC:MED&resulttype=core&format=json

30 January 2020

PubMed publication ID

19509309

1 reference