(Q28533852)

Ming Yi

3

0 references

Albino Bacolla

Albino Bacolla

1

0 references

David N. Cooper

David N Cooper

14

0 references

Nuri A Temiz

2

Nuri A Temiz

0 references

Joseph Ivanic

4

Joseph Ivanic

0 references

Regina Z Cer

5

Regina Z Cer

0 references

Uma S Mudunuri

8

Uma S Mudunuri

0 references

Guliang Wang

9

Guliang Wang

0 references

Aklank Jain

10

Aklank Jain

0 references

Natalia Volfovsky

11

Natalia Volfovsky

0 references

Karen M Vasquez

16

Karen M Vasquez

0 references

author name string

Edward V Ball

7

0 references

Brian T Luke

12

0 references

Robert M Stephens

13

0 references

Jack R Collins

Creative Commons CC0 License

15

0 references

language of work or name

English

0 references

publication date

2013

0 references

published in

PLOS Genetics

0 references

volume

9

0 references

issue

9

0 references

page(s)

e1003816

0 references

copyright license

start time

26 September 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

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

19 March 2017

1 reference

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Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing

19 March 2017

1 reference

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Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

A landscape of driver mutations in melanoma

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Melanoma genome sequencing reveals frequent PREX2 mutations

19 March 2017

1 reference

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Mutational processes molding the genomes of 21 breast cancers

19 March 2017

1 reference

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Melanoma genetics: recent findings take us beyond well-traveled pathways

19 March 2017

1 reference

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Disease gene identification strategies for exome sequencing

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Integrated genomic analyses of ovarian carcinoma

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Initial genome sequencing and analysis of multiple myeloma

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

The genomic complexity of primary human prostate cancer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

A comprehensive catalogue of somatic mutations from a human cancer genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

An integrated genomic analysis of human glioblastoma multiforme

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

The genomic landscapes of human breast and colorectal cancers

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Initial sequencing and analysis of the human genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Patterns of somatic mutation in human cancer genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

The mutational landscape of head and neck squamous cell carcinoma

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Diverse somatic mutation patterns and pathway alterations in human cancers

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

APOBEC3B is an enzymatic source of mutation in breast cancer.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Genomic landscape of non-small cell lung cancer in smokers and never-smokers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Oxidative genome damage and its repair: implications in aging and neurodegenerative diseases.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Oxidatively induced DNA damage: mechanisms, repair and 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=3784513

Fast computation and applications of genome mappability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Whole genome sequencing of matched primary and metastatic acral melanomas

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Identification and correction of systematic error in high-throughput sequence 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=3784513

UCSF Chimera, MODELLER, and IMP: an integrated modeling system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited 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=3784513

UV wavelength-dependent DNA damage and human non-melanoma and melanoma skin 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=3784513

Sequence-specific error profile of Illumina sequencers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Pause locally, splice globally

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

High-resolution characterization of a hepatocellular carcinoma 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=3784513

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Non-B DNA-forming sequences and WRN deficiency independently increase the frequency of base substitution 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=3784513

Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Mutation patterns in cancer genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

The role of one-electron reduction of lipid hydroperoxides in causing DNA damage

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative 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=3784513

Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Mutational spectra of human 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=3784513

Large-scale inference of the point mutational spectrum in human segmental duplications

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Mutagenic potential of DNA-peptide crosslinks mediated by acrolein-derived DNA adducts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Origin of the heterogeneous distribution of the yield of guanyl radical in UV laser photolyzed DNA

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Long-distance electron transfer through DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

A free energy analysis of nucleic acid base stacking in aqueous solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Electronic structure and spectroscopy of nucleic acid bases: ionization energies, ionization-induced structural changes, and photoelectron spectra

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Theoretical and experimental study of valence-shell ionization spectra of guanine

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Solvent effects on ionization potentials of guanine runs and chemically modified guanine in duplex DNA: effect of electrostatic interaction and its reduction due to solvent

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Acceleration of 5-methylcytosine deamination in cyclobutane dimers by G and its implications for UV-induced C-to-T mutation hotspots

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3784513

Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes.

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

A nucleotide substitution model with nearest-neighbour interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Excited state, charge transfer, and spin dynamics in DNA hairpin conjugates with perylenediimide hairpin linkers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Mapping the Sites for Selective Oxidation of Guanines in DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Oxidative DNA damage through long-range electron transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Estimation of electronic coupling in pi-stacked donor-bridge-acceptor systems: correction of the two-state model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Dependence of DNA-protein cross-linking via guanine oxidation upon local DNA sequence as studied by restriction endonuclease inhibition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Guanine oxidation by electron transfer: one- versus two-electron oxidation mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

SNP-based prediction of the human germ cell methylation landscape.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Structure-dependent DNA damage and repair in a trinucleotide repeat sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Self‐consistent molecular orbital methods. XXIII. A polarization‐type basis set for second‐row elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

General atomic and molecular electronic structure system

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

MacMolPlt: a graphical user interface for GAMESS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Solving Non-Uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Base Pairing Enhances Fluorescence and Favors Cyclobutane Dimer Formation Induced upon Absorption of UVA Radiation by DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other fun

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Density Functionals with Broad Applicability in Chemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003816

Increased complexity of gene structure and base composition in vertebrates

21 January 2018

1 reference

12 December 2020

Oxidative Nucleobase Modifications Leading to Strand Scission

1 reference

12 December 2020

Electron donor-acceptor interactions with flanking purines influence the efficiency of thymine photodimerization

1 reference

12 December 2020

Estimation of DNA Sequence Context-dependent Mutation Rates Using Primate Genomic Sequences

1 reference

12 December 2020