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).

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• Fractional ridge regression: a fast, interpretable reparameterization of ridge regression.

  PMID 33252656 · PMC7702219 · GigaScience · 2020 · 7 claims · 2 setups

  Has reproduction · 84

  Ridge regression can be reparameterized in terms of the fraction γ between the L2-norms of the regularized and unregularized coefficient solutions (fractional ridge regression, FRR).

  synthetic brain benchmarking general

• Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition.

  PMID 15850495 · PMC1090572 · BMC genetics · 2005 · 8 claims · 6 setups

  Full-text index only

  Haplotype block definitions based on LD measures (Definitions 1, 2, 3, 5) produce fewer, shorter blocks with limited sequence coverage compared to the haplotype diversity-based method (Definition 4)

  unrelated same snps haplotype snp haplotype pairwise

• Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform.

  PMID 34927664 · PMC8754388 · Genetics and molecular biology · 2021 · 8 claims · 2 setups

  Has reproduction · 83

  GEAP is a GUI-based microarray analysis platform combining a C# front-end with an R (RTerm) back-end via the rgeap package, enabling analysis independent of manufacturer/platform.

  sqlite microarray software microarray

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray

• Population carrier frequency of hMSH2 and hMLH1 mutations.

  PMID 11104559 · PMC2363440 · British journal of cancer · 2000 · 6 claims · 6 setups

  Full-text index only

  Population carrier frequency of hMSH2/hMLH1 mutations in people aged 15-74 years is estimated at 1:3139 (95% CI 1:1247-1:7626)

  peripheral scottish finnish baltimore cdna pedigree systematic

• The proteogenomic path towards biomarker discovery.

  PMID 18764911 · PMC2574627 · Pediatric transplantation · 2008 · 8 claims · 8 setups

  Full-text index only

  Serum creatinine is a widely used but non-ideal biomarker for renal transplant monitoring because it lacks specificity and sensitivity for graft injury

  renal urine breast chronic microarray immunoassay gel

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative