(Q34764038)

4 August 2017

Drosophila functional elements are embedded in structurally constrained sequences (English)

1 reference

4 August 2017

0 references

2

Amos Tanay

1 reference

4 August 2017

1

Ephraim Kenigsberg

1 reference

4 August 2017

30 May 2013

1 reference

4 August 2017

1 reference

4 August 2017

9

1 reference

4 August 2017

e1003512

1 reference

4 August 2017

5

1 reference

Creative Commons Attribution 4.0 International

4 August 2017

start time

30 May 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Controls 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=3671938

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

An expansive human regulatory lexicon encoded in transcription factor footprints

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The accessible chromatin landscape of the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Fast gapped-read alignment with Bowtie 2

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Joint genotyping on the fly: identifying variation among a sequenced panel of inbred lines

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The Drosophila melanogaster Genetic Reference Panel

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Three-dimensional folding and functional organization principles of the Drosophila genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Mouse genomic variation and its effect on phenotypes and gene regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Widespread signatures of recent selection linked to nucleosome positioning in the human lineage.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Determinants of nucleosome organization in primary human cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

A cis-regulatory map of the Drosophila genome.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Identification of functional elements and regulatory circuits by Drosophila modENCODE

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

H2A.Z nucleosomes enriched over active genes are homotypic

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Transcriptional enhancers in animal development and evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

High nucleosome occupancy is encoded at human regulatory sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

G+C content dominates intrinsic nucleosome occupancy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The UCSC Genome Browser database: update 2010

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Structural and functional constraints in the evolution of protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Widespread genomic signatures of natural selection in hominid evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Hotspots of biased nucleotide substitutions in human genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Pervasive hitchhiking at coding and regulatory sites in humans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The DNA-encoded nucleosome organization of a eukaryotic genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Evolution acts on enhancer organization to fine-tune gradient threshold readouts

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Positive and negative selection on noncoding DNA in Drosophila simulans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The impact of recombination on nucleotide substitutions in the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Nucleosome organization in the Drosophila genome.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Dynamic regulation of nucleosome positioning in the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Analysis of sequence conservation at nucleotide resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Frequent gain and loss of functional transcription factor binding sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Discovering motifs in ranked lists of DNA sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

GC-biased segregation of noncoding polymorphisms in Drosophila

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Discovery of functional noncoding elements by digital analysis of chromatin structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Comprehensive analysis of the base composition around the transcription start site in Metazoa

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Coordinate enhancers share common organizational features in the Drosophila genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The International HapMap Project

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Looping and interaction between hypersensitive sites in the active beta-globin locus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

The genome sequence of Drosophila melanogaster

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3671938

Chromatin organization is a major influence on regional mutation rates in human cancer cells.

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Adaptive evolution of non-coding DNA in Drosophila

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Inferring divergence of context-dependent substitution rates in Drosophila genomes with applications to comparative genomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Overview of the yeast genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Evolutionary footprints of nucleosome positions in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003512

Local Rates of Recombination Are Positively Correlated with GC Content in the Human Genome

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23750124

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1003512

1 reference

release_yzl2yg2ji5gh5nrcckoheu5hjy

4 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/yzl2yg2ji5gh5nrcckoheu5hjy

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

3671938

1 reference

4 August 2017

1 reference

PubMed ID

23750124