(Q37574108)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

title

Computational approaches to identify functional genetic variants in cancer genomes (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Paul Flicek

21

1 reference

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6 March 2020

Núria López-Bigas

28

1 reference

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6 March 2020

Abel Gonzalez-Perez

1

1 reference

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6 March 2020

Ville Mustonen

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Boris Reva

3

1 reference

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6 March 2020

Graham R. S. Ritchie

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Miguel Vazquez

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Lynn Fink

8

1 reference

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6 March 2020

Gary D. Bader

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Paul C. Boutros

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

B. F. Francis Ouellette

14

1 reference

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6 March 2020

Jüri Reimand

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Rune Linding

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

25

Chris Sander

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

27

Lincoln D Stein

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

5

Pau Creixell

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

17

Tatsuhiro Shibata

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

6

Rachel Karchin

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

author name string

Karin S Kassahn

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

John V Pearson

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Lakshmi Muthuswamy

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Adam Butler

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Serge Dronov

20

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Nick B Shannon

22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Hannah Carter

23

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Li Ding

24

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

Josh M Stuart

26

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group

29

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

publication date

1 August 2013

1 reference

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6 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

volume

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

page(s)

723-729

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

issue

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1038/nmeth.2562

6 March 2020

exact match

0 references

cites work

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1 reference

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23 August 2017

1 reference

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

23 August 2017

1 reference

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Highly recurrent TERT promoter mutations in human melanoma

23 August 2017

1 reference

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TERT promoter mutations in familial and sporadic melanoma

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

23 August 2017

1 reference

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CRAVAT: cancer-related analysis of variants toolkit

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

23 August 2017

1 reference

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An integrated map of genetic variation from 1,092 human genomes

23 August 2017

1 reference

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Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Annotation of functional variation in personal genomes using RegulomeDB

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

GENCODE: the reference human genome annotation for The ENCODE Project

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

An integrated encyclopedia of DNA elements in the human genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Genome sequencing identifies a basis for everolimus sensitivity

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Functional impact bias reveals cancer drivers

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

A landscape of driver mutations in melanoma

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

MuSiC: identifying mutational significance in cancer genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Predicting the functional impact of protein mutations: application to cancer genomics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

23 August 2017

1 reference

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Hallmarks of Cancer: The Next Generation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

23 August 2017

1 reference

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International network of cancer genome projects

23 August 2017

1 reference

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A method and server for predicting damaging missense mutations

23 August 2017

1 reference

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An effective model for natural selection in promoters

23 August 2017

1 reference

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

A comprehensive catalogue of somatic mutations from a human cancer genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Bi-directional SIFT predicts a subset of activating mutations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

The ontology of biological sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

MEME SUITE: tools for motif discovery and searching

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Diversity and complexity in DNA recognition by transcription factors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Human Splicing Finder: an online bioinformatics tool to predict splicing signals

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Determinants of protein function revealed by combinatorial entropy optimization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

CanPredict: a computational tool for predicting cancer-associated missense mutations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Patterns of somatic mutation in human cancer genomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

The consensus coding sequences of human breast and colorectal cancers

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

A census of human cancer genes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

SIFT: Predicting amino acid changes that affect protein function

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Mutations of the BRAF gene in human cancer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

dbSNP: the NCBI database of genetic variation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

23 August 2017

The Hallmarks of Cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

A systems approach to measuring the binding energy landscapes of transcription factors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Human mutation rate associated with DNA replication timing

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

Navigating cancer network attractors for tumor-specific therapy

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

The Human Gene Mutation Database: 2008 update

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

RAS oncogenes: the first 30 years.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3919555

1 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2562

McKusick's Online Mendelian Inheritance in Man (OMIM)

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2562

IntOGen: integration and data mining of multidimensional oncogenomic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2562

Performance of mutation pathogenicity prediction methods on missense variants

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2562

Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23900255

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The UCSC Genome Browser

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.2562

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.2562

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23900255%20AND%20SRC:MED&resulttype=core&format=json