(Q48240056)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

title

High-resolution TADs reveal DNA sequences underlying genome organization in flies (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

Kin Chung Lam

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

José Villaveces

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

Asifa Akhtar

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

language of work or name

English

0 references

publication date

15 January 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

published in

Nature Communications

1 reference

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9 April 2020

volume

1 reference

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9 April 2020

issue

1 reference

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9 April 2020

page(s)

189

1 reference

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Creative Commons Attribution 4.0 International

9 April 2020

start time

15 January 2018

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

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Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

22 May 2018

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Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

22 May 2018

1 reference

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DREF plays multiple roles during Drosophila development

22 May 2018

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Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

22 May 2018

1 reference

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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

22 May 2018

1 reference

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Chromatin Domains: The Unit of Chromosome Organization

22 May 2018

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Formation of Chromosomal Domains by Loop Extrusion.

22 May 2018

1 reference

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Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila

22 May 2018

1 reference

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deepTools2: a next generation web server for deep-sequencing data analysis

22 May 2018

1 reference

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TopDom: an efficient and deterministic method for identifying topological domains in genomes

22 May 2018

1 reference

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Standardizing chromatin research: a simple and universal method for ChIP-seq.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

UpSet: Visualization of Intersecting Sets.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

A CTCF Code for 3D Genome Architecture

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Insulator function and topological domain border strength scale with architectural protein occupancy

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Motif-based analysis of large nucleotide data sets using MEME-ChIP.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

CTCF: an architectural protein bridging genome topology and function

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Chromatin immunoprecipitation indirect peaks highlight long-range interactions of insulator proteins and Pol II pausing.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Self-organization of domain structures by DNA-loop-extruding enzymes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Identifying ChIP-seq enrichment using MACS.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Nature and function of insulator protein binding sites in the Drosophila genome.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

The NSL complex regulates housekeeping genes in Drosophila.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Topological domains in mammalian genomes identified by analysis of chromatin interactions

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Fast gapped-read alignment with Bowtie 2

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Regulation of chromatin organization and inducible gene expression by a Drosophila insulator

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

DREME: motif discovery in transcription factor ChIP-seq data

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

FIMO: scanning for occurrences of a given motif

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

The developmental transcriptome of Drosophila melanogaster

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Systematic protein location mapping reveals five principal chromatin types in Drosophila cells

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Regularization Paths for Generalized Linear Models via Coordinate Descent

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

BEDTools: a flexible suite of utilities for comparing genomic features

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Unlocking the secrets of the genome

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

BEAF regulates cell-cycle genes through the controlled deposition of H3K9 methylation marks into its conserved dual-core binding sites

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

The enhancer-blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor-binding sites.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Real-time detection of single-molecule DNA compaction by condensin I.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

The UCSC Table Browser data retrieval tool

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

A novel boundary element may facilitate independent gene regulation in the Antennapedia complex of Drosophila

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Computational analysis of core promoters in the Drosophila genome

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer-promoter interaction

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5768762

Greedy function approximation: A gradient boosting machine

14 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-017-02525-W

10.1038/S41467-017-02525-W

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

PubMed publication ID

29335486

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29335486%20AND%20SRC:MED&resulttype=core&format=json