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).

• Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

  PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

  synthetic eukaryotic simulated 16-species analytical comparative simulation

• treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.

  PMID 34001188 · PMC8127214 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 73

  treeclimbR proposes multiple candidate resolutions on a tree and selects the optimal one in a data-driven manner using three criteria (FDR-controlling range of t, number of rejected leaves, fewest internal nodes)

  synthetic semi-simulated microbiome mirna differential microbiome microrna

• 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

• WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.

  PMID 41911220 · PMC13048486 · PLoS computational biology · 2026 · 8 claims · 5 setups

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  WEPP is a pathogen-agnostic pipeline that uses phylogenetic placement of sequencing reads onto mutation-annotated trees (MATs) to identify candidate haplotypes and estimate their abundances

  sars-cov-2 mutation-annotated simulated synthetic real-world

• Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.

  PMID 41641705 · PMC12873609 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  Screening 202 cyanobacterial genomes identified 402 CRSs matching known RNA families (Rfam and Rho-independent terminators) and 409 novel CRSs.

  cyanobacterial peptide aligned local comparative genome sequence

• Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex.

  PMID 24883252 · PMC4034613 · PeerJ · 2014 · 8 claims · 8 setups

  Has reproduction · 54

  All three allopolyploid species are fixed hybrids combining the genomes of the two putative diploid parents hypothesized on the basis of previous crossing and molecular work.

  pooled perennial allopolyploid snp single-end read homoeologue

• Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics.

  PMID 41844632 · PMC13144610 · Nature communications · 2026 · 8 claims · 7 setups

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  BasCoD is a statistical testing framework using spectral subspace inclusion theory to evaluate whether a candidate background dataset is suitable for contrastive dimension reduction of a target dataset

  ts65dn ipscs k562 intestinal contrastive population-scale perturb-seq