(Q36959187)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

title

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Joanna Achinger-Kawecka

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Aaron Lun

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Denis C Bauer

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Clare Stirzaker

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Sean O'Donoghue

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

author name string

Fabian A Buske

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Kenneth Sabir

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Cathryn M Gould

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Elena Zotenko

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Saul A Bert

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Katherine A Giles

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Susan J Clark

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Gordon K Smyth

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

publication date

6 April 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

volume

26

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

page(s)

719-731

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

The Molecular Taxonomy of Primary Prostate Cancer

31 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Predicting chromatin organization using histone marks.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Functional organization of the human 4D Nucleome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Spatial genomic heterogeneity within localized, multifocal prostate cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Multiple functional variants in long-range enhancer elements contribute to the risk of SNP rs965513 in thyroid cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Chromatin architecture reorganization during stem cell differentiation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Recurrent copy number alterations in prostate cancer: an in silico meta-analysis of publicly available genomic data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Deletions of chromosomal regulatory boundaries are associated with congenital disease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Identification of alternative topological domains in chromatin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Organization of the mitotic chromosome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Divergence of mammalian higher order chromatin structure is associated with developmental loci

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Regional activation of the cancer genome by long-range epigenetic remodeling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Oncogenic transcription factors as master regulators of chromatin topology: a new role for ERG in prostate cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Oncogene-mediated alterations in chromatin conformation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Epigenomic enhancer profiling defines a signature of colon cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Spatial partitioning of the regulatory landscape of the X-inactivation centre

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Topological domains in mammalian genomes identified by analysis of chromatin interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

ChromHMM: automating chromatin-state discovery and characterization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Polycomb-repressed genes have permissive enhancers that initiate reprogramming

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Discovery and characterization of chromatin states for systematic annotation of the human genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Integrative genomic profiling of human prostate cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

29 September 2017

Chromosome territories

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

A genome-wide screen for microdeletions reveals disruption of polarity complex genes in diverse human cancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Agglomerative epigenetic aberrations are a common event in human breast cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

DLEC1 and MLH1 promoter methylation are associated with poor prognosis in non-small cell lung carcinoma

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Epigenetic inactivation of a cluster of genes flanking MLH1 in microsatellite-unstable colorectal cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Regional copy number-independent deregulation of transcription in cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Capturing chromosome conformation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Functional and topological characteristics of mammalian regulatory domains.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

VEGFR1 and NRP1 endothelial expressions predict distant relapse after radical prostatectomy in clinically localized prostate cancer

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Estimation and assessment of raw copy numbers at the single locus level

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Clinical significance of different types of p53 gene alteration in surgically treated prostate cancer

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

GAT: a simulation framework for testing the association of genomic intervals

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4889976

4 September 2018

Identifiers

DOI

10.1101/GR.201517.115

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27053337%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

1 reference