Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Screening large-scale association study data: exploiting interactions using random forests.

  PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups

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  Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.

  simulated same simulation random fisher

• Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection.

  PMID 31533612 · PMC6751684 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 69

  An ensemble feature selection method based on classifier consensus identifies a robust 100-miRNA signature from TCGA data.

  tcga geo 100-mirna mirna feature bibliographic

• Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.

  PMID 18276640 · PMC2346606 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Illumina HumanHap300 arrays are substantially more efficient than Affymetrix Genechip HindIII arrays for DNA-pooling based GWAS

  pools same publicly simulated pooling individual simulation

• Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.

  PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups

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  OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.

  real tailored blood algorithm snp

• Accuracy of predicting the genetic risk of disease using a genome-wide approach.

  PMID 18852893 · PMC2561058 · PloS one · 2008 · 8 claims · 4 setups

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  Deterministic equations can predict the accuracy (r_gĝ) of genome-wide genetic risk/value prediction for continuous, dichotomous, and case-control study designs.

  simulated stochastic

• Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.

  PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups

  Has reproduction · 96

  Data-driven, high-dimensional ML approaches that learn multivariate signatures directly from genome-wide transcriptomic data (no prior gene selection) yield accurate and robust AML classifiers.

  peripheral pbmc datasets hg-u133 gene bulk machine

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine