(Q35053798)

6 August 2017

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

1 reference

6 August 2017

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

Andrea Califano

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

5

Gustavo Stolovitzky

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

2

Adam A Margolin

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

3

Joshua M Stuart

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

language of work or name

English

0 references

publication date

17 September 2014

1 reference

6 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

volume

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

issue

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

page(s)

462

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

6 June 2020

copyright license

start time

1 September 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1186/s13059-014-0462-7

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

RNA design rules from a massive open laboratory

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Assessment of transcript reconstruction methods for RNA-seq

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

A Turing test for artificial expression data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

A comparative analysis of algorithms for somatic SNV detection in cancer.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Comparing somatic mutation-callers: beyond Venn diagrams

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

A large-scale evaluation of computational protein function prediction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Identifying personal genomes by surname inference

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Predicting outcomes in radiation oncology--multifactorial decision support systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Wisdom of crowds for robust gene network inference

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Games with a scientific purpose

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

A simple but highly effective approach to evaluate the prognostic performance of gene expression signatures

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Most random gene expression signatures are significantly associated with breast cancer outcome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Verification of systems biology research in the age of collaborative competition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Crowdsourcing network inference: the DREAM predictive signaling network challenge

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Genome structural variation discovery and genotyping

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

In silico research in the era of cloud computing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

AACR-FDA-NCI Cancer Biomarkers Collaborative consensus report: advancing the use of biomarkers in cancer drug development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Between a chicken and a grape: estimating the number of human genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Revealing strengths and weaknesses of methods for gene network inference

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Towards a rigorous assessment of systems biology models: the DREAM3 challenges

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Analysis of CASP8 targets, predictions and assessment methods.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Proteomics research to discover markers: what can we learn from Netflix?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Evaluation of CASP8 model quality predictions.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Prognostic gene signatures for non-small-cell lung cancer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Dynamic modularity in protein interaction networks predicts breast cancer outcome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Enabling personalized cancer medicine through analysis of gene-expression patterns

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Translating insights from the cancer genome into clinical practice

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Network modeling links breast cancer susceptibility and centrosome dysfunction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Assessment of homology-based predictions in CASP5.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

A large-scale experiment to assess protein structure prediction methods.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Seeking the wisdom of crowds through challenge-based competitions in biomedical research.

8 July 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

The self-assessment trap: can we all be better than average?

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

Lessons from the DREAM2 Challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

Crowd computing: using competitive dynamics to develop and refine highly predictive models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

Evaluation of DNA microarray results with quantitative gene expression platforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

New $10 million X Prize launched for tricorder-style medical device.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4318527

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

25 October 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

The value of feedback in forecasting competitions

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-014-0462-7

Taking pan-cancer analysis global

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25314947

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-014-0462-7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

6 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25314947%20AND%20SRC:MED&resulttype=core&format=json