(Q36867676)

16 August 2017

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection (English)

1 reference

16 August 2017

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Takafumi N Yamaguchi

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Kyle Ellrott

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

J. Christopher Bare

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Michael Kellen

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Joshua M Stuart

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Paul C. Boutros

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

16

Gustavo Stolovitzky

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

15

Stephen H Friend

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

17

Adam A Margolin

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

2

Kathleen E Houlahan

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

5

Cristian Caloian

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

13

Thea C Norman

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

author name string

Yin Hu

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Christine P'ng

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Daryl Waggott

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Veronica Y Sabelnykova

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

David Haussler

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

publication date

18 May 2015

1 reference

16 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

volume

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

page(s)

623-630

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported

11 June 2020

copyright license

start time

18 May 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

crowdsourcing

0 references

cites work

RADIA: RNA and DNA integrated analysis for somatic mutation detection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Toward better benchmarking: challenge-based methods assessment in cancer genomics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Global optimization of somatic variant identification in cancer genomes with a global community challenge

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Discovery and saturation analysis of cancer genes across 21 tumour types

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Emerging landscape of oncogenic signatures across 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=4856034

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Signatures of mutational processes in 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=4856034

Comparing somatic mutation-callers: beyond Venn diagrams

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Discovering motifs that induce sequencing errors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Integrated genomic characterization of endometrial 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=4856034

Systematic analysis of challenge-driven improvements in molecular prognostic models for 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=4856034

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Wisdom of crowds for robust gene network inference

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Mutational processes molding the genomes of 21 breast 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=4856034

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Fast gapped-read alignment with Bowtie 2

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Cancer genomics: technology, discovery, and translation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

SomaticSniper: identification of somatic point mutations in whole genome sequencing 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=4856034

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=4856034

The variant call format and VCFtools

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

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=4856034

Integrative genomics viewer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing 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=4856034

Fast and SNP-tolerant detection of complex variants and splicing in short reads

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

BEDTools: a flexible suite of utilities for comparing genomic features

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Evaluation of CASP8 model quality predictions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

The Sequence Alignment/Map format and SAMtools

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Fast and accurate short read alignment with Burrows-Wheeler transform

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Conditional variable importance for random forests

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Bias in random forest variable importance measures: illustrations, sources and a 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=4856034

Statistical significance for genomewide studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

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=4856034

SeqControl: process control for DNA sequencing

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

pIRS: Profile-based Illumina pair-end reads simulator

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Random forest: a classification and regression tool for compound classification and QSAR modeling

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4856034

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

4 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.3407

Trial watch: Adaptive BATTLE trial uses biomarkers to guide lung cancer treatment

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25984700

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NMETH.3407

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

11 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

PubMed publication ID

25984700

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25984700%20AND%20SRC:MED&resulttype=core&format=json