Improved alignment of nucleosome DNA sequences using a mixture model (Q24810679)

5 July 2017

title

Improved alignment of nucleosome DNA sequences using a mixture model (English)

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5 July 2017

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Ji-Ping Z Wang

1

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5 July 2017

Jonathan Widom

series ordinal

2

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5 July 2017

language of work or name

English

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publication date

9 December 2005

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5 July 2017

published in

Nucleic Acids Research

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5 July 2017

volume

33

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5 July 2017

issue

21

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5 July 2017

page(s)

6743-6755

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

5 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

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

7 April 2017

1 reference

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Profile hidden Markov models

7 April 2017

1 reference

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Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome

7 April 2017

1 reference

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Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

The structure of DNA in the nucleosome core

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Role of DNA sequence in nucleosome stability and dynamics

28 September 2017

1 reference

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Remodeling of yeast CUP1 chromatin involves activator-dependent repositioning of nucleosomes over the entire gene and flanking sequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

28 September 2017

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Hidden Markov models of biological primary sequence information

28 September 2017

1 reference

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Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames

28 September 2017

1 reference

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UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

The bending of DNA in nucleosomes and its wider implications

28 September 2017

1 reference

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Toward a unified model of chromatin folding

28 September 2017

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A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells

28 September 2017

1 reference

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Neither Reb1p nor poly(dA*T) elements are responsible for the highly specific chromatin organization at the ILV1 promoter

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Structure, dynamics, and function of chromatin in vitro

30 May 2018

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Reconstitution experiments show that sequence-specific histone-DNA interactions are the basis for nucleosome phasing on mouse satellite DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Sequence periodicities in chicken nucleosome core DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

DNA engineering shows that nucleosome phasing on the African green monkey alpha-satellite is the result of multiple additive histone-DNA interactions

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Spontaneous sharp bending of double-stranded DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

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

28 November 2018

1 reference

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Modifying gene expression programs by altering core promoter chromatin architecture.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

DNA sequence plays a major role in determining nucleosome positions in yeast CUP1 chromatin.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Naturally occurring nucleosome positioning signals in human exons and introns

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Hybrid modeling, HMM/NN architectures, and protein applications

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

DNA Sequence Organization in Chromatosomes

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1310902

Short-range order in two eukaryotic genomes: relation to chromosome structure

28 November 2018

1 reference

12 December 2020

Positioning and stability of nucleosomes on MMTV 3'LTR sequences

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

Reconstitution of nucleosome positioning, remodeling, histone acetylation, and transcriptional activation on the PHO5 promoter

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKI977

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5 July 2017

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5 July 2017

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