(Q33784572)

29 July 2017

title

Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast (English)

1 reference

29 July 2017

3

1 reference

29 July 2017

4

Amos Tanay

1 reference

29 July 2017

1

Ephraim Kenigsberg

1 reference

29 July 2017

Amir Bar

2

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29 July 2017

publication date

23 December 2010

1 reference

PLOS Computational Biology

29 July 2017

published in

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29 July 2017

volume

6

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29 July 2017

issue

12

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29 July 2017

page(s)

e1001039

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Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

23 December 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

The role of nucleosome positioning in the evolution of gene regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

G+C content dominates intrinsic nucleosome occupancy

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

The UCSC Genome Browser database: update 2010

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

What controls nucleosome positions?

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Histone modifications at human enhancers reflect global cell-type-specific gene expression

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

ChIP-seq accurately predicts tissue-specific activity of enhancers

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Population genomics of domestic and wild yeasts

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

The DNA-encoded nucleosome organization of a eukaryotic genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

The impact of the nucleosome code on protein-coding sequence evolution in yeast

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Distinct modes of regulation by chromatin encoded through nucleosome positioning signals

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Nucleosome organization in the Drosophila genome.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Dynamic regulation of nucleosome positioning in the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

A high-resolution atlas of nucleosome occupancy in yeast

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Frequent gain and loss of functional transcription factor binding sites

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Genome-wide transcription and the implications for genomic organization

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Empirical fitness landscapes reveal accessible evolutionary paths

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Compensatory vs. pseudocompensatory evolution in molecular and developmental interactions

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

A genomic code for nucleosome positioning

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Extensive low-affinity transcriptional interactions in the yeast genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Genome-scale identification of nucleosome positions in S. cerevisiae

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Transcriptional regulatory code of a eukaryotic genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

On the probability of fixation of mutant genes in a population

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Sequencing and comparison of yeast species to identify genes and regulatory elements

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

RNA secondary structure and compensatory evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

SGD: Saccharomyces Genome Database

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

RNA folding in Drosophila shows a distance effect for compensatory fitness interactions

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Maintenance of pre-mRNA secondary structure by epistatic selection.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Sequence periodicities in chicken nucleosome core DNA.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3009600

Evolution of alternative transcriptional circuits with identical logic

4 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001039

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001039

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001039

Factor graphs and the sum-product algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001039

Evolutionary footprints of nucleosome positions in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001039

A Population Genetics Model for Multiple Quantitative Traits Exhibiting Pleiotropy and Epistasis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1001039

Inferring natural selection on fine-scale chromatin organization in yeast

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21203484

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1001039

1 reference

journals/ploscb/KenigsbergBST10

29 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

29 July 2017

1 reference