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).

• Bcipep: a database of B-cell epitopes.

  PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups

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  Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases

  synthetic antigenic anti-peptide sequence

• DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization.

  PMID 14519203 · PMC328457 · Genome biology · 2003 · 7 claims · 5 setups

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  DiagHunter identifies large-scale synteny blocks within or between genomes efficiently despite background noise and genomic discontinuities, without performing sequence alignment

  arabidopsis synthetic blastp-based blastn-based simulation

• Peptide bioinformatics: peptide classification using peptide machines.

  PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups

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  The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.

  illustrative query generic synthetic bio-basis orthogonal hyperplane

• Stability analysis of mixtures of mutagenetic trees.

  PMID 18366778 · PMC2335279 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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  Mutagenetic trees mixture models capture multiple alternative pathways of ordered accumulation of genetic events (e.g., HIV resistance mutations, cancer chromosomal aberrations).

  simulated hiv-1 hiv timed simulation genotypic mutagenetic

• A comparative study on recombination activity in cattle.

  PMID 41942849 · PMC13067647 · Genetics, selection, evolution : GSE · 2026 · 8 claims · 8 setups

  Has reproduction · 93

  Genotype data with high systematic missingness across breeds and arrays can be streamlined and analysed with three complementary recombination-estimation approaches (HMM-based LINKPHASE3, deterministic hsphase, likelihood-based hsrecombi)

  six paternal alphasimr-simulated brown snp recombination simulation