ArticleGenome biology2014
Toward better benchmarking: challenge-based methods assessment in cancer genomics.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- ViLoN-a multi-layer network approach to data integration demonstrated for patient stratification.Nucleic acids research · 2023Article
- Training undergraduate research assistants with an outcome-oriented and skill-based mentoring strategy.Acta crystallographica. Section D, Structural biology · 2022Article
- Essential guidelines for computational method benchmarking.Genome biology · 2019Review
- Systematic benchmarking of omics computational tools.Nature communications · 2019Review
- Convolutional neural network scoring and minimization in the D3R 2017 community challenge.Journal of computer-aided molecular design · 2019Article
- Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables.Computational and structural biotechnology journal · 2019Review
- Why rankings of biomedical image analysis competitions should be interpreted with care.Nature communications · 2018Article
- Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.Genome biology · 2018Article
- geck: trio-based comparative benchmarking of variant calls.Bioinformatics (Oxford, England) · 2018Article
- Valection: design optimization for validation and verification studies.BMC bioinformatics · 2018Article
- Unearthing new genomic markers of drug response by improved measurement of discriminative power.BMC medical genomics · 2018Article
- A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.Cell systems · 2017Article
- Precision and recall oncology: combining multiple gene mutations for improved identification of drug-sensitive tumours.Oncotarget · 2017Article
- Crowdsourcing biomedical research: leveraging communities as innovation engines.Nature reviews. Genetics · 2016Review
- A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.PLoS computational biology · 2016Article
- Predicting protein function and other biomedical characteristics with heterogeneous ensembles.Methods (San Diego, Calif.) · 2016Article
- Systematic assessment of multi-gene predictors of pan-cancer cell line sensitivity to drugs exploiting gene expression data.F1000Research · 2016Article
- The path to routine use of genomic biomarkers in the cancer clinic.Genome research · 2015Review
- Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.Nature methods · 2015Article
- The Prostate Cancer DREAM Challenge: A Community-Wide Effort to Use Open Clinical Trial Data for the Quantitative Prediction of Outcomes in Metastatic Prostate Cancer.The oncologist · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Rapid technological development has created an urgent need for improved evaluation of algorithms for the analysis of cancer genomics data. We outline how challenge-based assessment may help fill this gap by leveraging crowd-sourcing to distribute effort and reduce bias.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.