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).

• RADAR: differential analysis of MeRIP-seq data with a random effect model.

  PMID 31870409 · PMC6927177 · Genome biology · 2019 · 8 claims · 6 setups

  Has reproduction · 10

  RADAR is a novel analytical tool for differential methylation analysis of MeRIP-seq data combining gene-level INPUT normalization with a Poisson random effect model.

  simulated fallopian pancreatic liver merip-seq m6a-merip-seq pca

• ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.

  PMID 41790830 · PMC12991369 · PLoS computational biology · 2026 · 8 claims · 3 setups

  Has reproduction · 83

  ConNIS provides an analytic solution for the probability of observing the longest insertion-free sequence within a gene given its length and number of insertion sites under non-essentiality.

  simulated four real simulation semi-synthetic real-world

• Hit selection with false discovery rate control in genome-scale RNAi screens.

  PMID 18628291 · PMC2504311 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  A Bayesian FDR-controlling methodology for hit selection in genome-scale RNAi HTS is proposed, using a direct posterior probability approach analogous to Newton et al.

  hela hepatitis simulated genome-scale simulation

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

  PMID 19028587 · PMC2686088 · Journal of structural biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Nucleotide-bound (ADP and ANP/AMP-PNP) Mer kinase domain adopts an autoinhibited DFG-Asp-in/αC-Glu-out conformation with an activation-loop residue inserted into the active site

  recombinant phosphorylated mer x-ray positional differential

• No evidence of a Neanderthal contribution to modern human diversity.

  PMID 18304371 · PMC2374707 · Genome biology · 2008 · 8 claims · 7 setups

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  There is no evidence of any Neanderthal contribution to modern human genetic diversity

  neanderthal culture modern genomic mitochondrial nuclear gene-specific

• POCUS: mining genomic sequence annotation to predict disease genes.

  PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

  Full-text index only

  Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

  omim genome disease comparative pocus expression-id