Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair (Q33976821)

30 July 2017

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair (English)

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30 July 2017

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30 July 2017

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Gad Getz

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John Stamatoyannopoulos

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object named as

John A Stamatoyannopoulos

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Levi A Garraway

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30 July 2017

Paz Polak

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30 July 2017

Michael S Lawrence

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30 July 2017

Nina Stoletzki

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Petar Stojanov

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30 July 2017

Robert E Thurman

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30 July 2017

Sergei Mirkin

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Shamil R Sunyaev

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language of work or name

English

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publication date

15 December 2013

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30 July 2017

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32

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71-75

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https://scigraph.springernature.com/pub.10.1038/nbt.2778

30 July 2017

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cites work

Mutational heterogeneity in cancer and the search for new cancer-associated genes

1 reference

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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

5 July 2018

1 reference

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APOBEC3B is an enzymatic source of mutation in breast cancer.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Highly recurrent TERT promoter mutations in human melanoma

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

An expansive human regulatory lexicon encoded in transcription factor footprints

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

The accessible chromatin landscape of the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Chronic low-dose ultraviolet-induced mutagenesis in nucleotide excision repair-deficient cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Melanoma genome sequencing reveals frequent PREX2 mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Mutational processes molding the genomes of 21 breast cancers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

KEGG for integration and interpretation of large-scale molecular data sets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Regulation of nucleotide excision repair by UV-DDB: prioritization of damage recognition to internucleosomal DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

A high-resolution map of human evolutionary constraint using 29 mammals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Determinants and dynamics of genome accessibility

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Initial genome sequencing and analysis of multiple myeloma

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

DNA polymerases and cancer.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Open, repair and close again: chromatin dynamics and the response to UV-induced DNA damage

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Advances in understanding cancer genomes through second-generation sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Oxidative stress triggers the preferential assembly of base excision repair complexes on open chromatin regions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

A small-cell lung cancer genome with complex signatures of tobacco exposure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

A comprehensive catalogue of somatic mutations from a human cancer genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Human mutation rate associated with DNA replication timing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Transcription-coupled DNA repair: two decades of progress and surprises

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Xeroderma pigmentosum genes: functions inside and outside DNA repair

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Eukaryotic nucleotide excision repair: from understanding mechanisms to influencing biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Oxidative and nitrative DNA damage in animals and patients with inflammatory diseases in relation to inflammation-related carcinogenesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Initiation of DNA repair mediated by a stalled RNA polymerase IIO.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Repair of UV lesions in nucleosomes--intrinsic properties and remodeling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Functional characterization of global genomic DNA repair and its implications for cancer.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Repair of oxidized DNA bases in the yeast Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Clusters of S1 nuclease-hypersensitive sites induced in vivo by DNA damage

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Mammalian DNA nucleotide excision repair reconstituted with purified protein components.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Nuclease hypersensitive sites in chromatin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

Evolution at two levels in humans and chimpanzees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4116484

The large-scale distribution of somatic mutations in cancer genomes.

5 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNBT.2778

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNBT.2778

BEDOPS: high-performance genomic feature operations

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNBT.2778

Nucleosomal structure of undamaged DNA regions suppresses the non-specific DNA binding of the XPC complex

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24336318

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24336318

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NBT.2778

1 reference

Dimensions Publication ID

30 July 2017

0 references

1 reference

30 July 2017

1 reference