(Q33349451)

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Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens

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scholarly article

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Europe PubMed Central

PubMed publication ID

26 July 2017

Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens (English)

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

Saccharomyces cerevisiae

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William S. Noble

3

object named as

William Stafford Noble

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

author name string

Sheila M Reynolds

1

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

Jeff A Bilmes

2

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

publication date

8 July 2010

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

PLOS Computational Biology

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

6

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

7

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

e1000834

1 reference

Europe PubMed Central

PubMed publication ID

26 July 2017

copyright license

Creative Commons Attribution 4.0 International

8 July 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

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H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

The DNA-encoded nucleosome organization of a eukaryotic genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Predicting human nucleosome occupancy from primary sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Nucleosome positioning in human HOX gene clusters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Geometry of the nucleosomal DNA superhelix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Dynamic regulation of nucleosome positioning in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Hydrodynamic studies on defined heterochromatin fragments support a 30-nm fiber having six nucleosomes per turn

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Genomic sequence is highly predictive of local nucleosome depletion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

A high-resolution atlas of nucleosome occupancy in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Nucleosome positioning signals in genomic DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

High-resolution profiling of histone methylations in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

A genomic code for nucleosome positioning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Improved alignment of nucleosome DNA sequences using a mixture model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Repbase Update, a database of eukaryotic repetitive elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

X-ray structure of a tetranucleosome and its implications for the chromatin fibre

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Molecular recognition of the nucleosomal "supergroove".

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Announcing the worldwide Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

DNA helix: the importance of being GC-rich

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Role of DNA sequence in nucleosome stability and dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

The pitch of chromatin DNA is reflected in its nucleotide sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Sequence periodicities in chicken nucleosome core DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2900294

21 June 2018

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000834

21 January 2018

Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000834

21 January 2018

DBTSS: database of transcription start sites, progress report 2008.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000834

21 January 2018

ALU-ring elements in the primate genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/20628623

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome positions predicted through comparative genomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/20628623

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Labile H3.3+H2A.Z nucleosomes mark 'nucleosome-free regions'

1 reference

https://pubmed.ncbi.nlm.nih.gov/20628623

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome positioning by human Alu elements in chromatin

1 reference

https://pubmed.ncbi.nlm.nih.gov/20628623

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/20628623

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PCBI.1000834

1 reference

https://api.fatcat.wiki/v0/release/3t4vp5ip3ffldmmyg2ztrih4sy

30 July 2022

based on heuristic

mapped directly with Wikidata item

DBLP publication ID

journals/ploscb/ReynoldsBN10

1 reference

DBLP Dataset 2021-01-02

28 January 2021

release_3t4vp5ip3ffldmmyg2ztrih4sy

1 reference

https://api.fatcat.wiki/v0/release/3t4vp5ip3ffldmmyg2ztrih4sy

30 July 2022

based on heuristic

mapped directly with Wikidata item

PMC publication ID

1 reference

https://api.fatcat.wiki/v0/release/3t4vp5ip3ffldmmyg2ztrih4sy

30 July 2022

based on heuristic

mapped directly with Wikidata item

PubMed publication ID

1 reference

https://api.fatcat.wiki/v0/release/3t4vp5ip3ffldmmyg2ztrih4sy

30 July 2022

based on heuristic

mapped directly with Wikidata item

ResearchGate publication ID

0 references

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