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).

• Cell atlases and the developmental foundations of the phenotype.

  PMID 41662466 · PMC12904592 · PLoS computational biology · 2026 · 8 claims · 6 setups

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  There is a proportional relationship between average developmental similarity (⟨simD⟩) and average phenotypic similarity (⟨simP⟩) across genes, supporting the D–P rule on average

  caenorhabditis gene elegans single-cell phenotype non-negative

• Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists.

  PMID 16351744 · PMC1866390 · BMC bioinformatics · 2005 · 5 claims · 3 setups

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  OMIM Clinical Synopsis free-text phenotype and location names can be normalized and hierarchically structured into a controlled vocabulary suitable for computational analysis

  omim gene text statistical gene

• GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses.

  PMID 33758032 · PMC8547006 · mSystems · 2021 · 8 claims · 7 setups

  Has reproduction · 70

  GAUGE automatically annotates GEO microbial transcriptomic data sets (microarray and RNA-seq), increasing the proportion of annotatable studies from 4% to 33%

  microarray rna-seq aeruginosa mantel manual anova

• Gene-centric characteristics of genome-wide association studies.

  PMID 18060058 · PMC2092383 · PloS one · 2007 · 8 claims · 5 setups

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  High-density SNP chips using either direct or indirect selection approaches provide very high coverage in genic regions and capture most known common disease variants under the HapMap framework.

  phase omim snps snp disease genomic

• Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.

  PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups

  Has reproduction · 57

  t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes

  calanus same 11k degs bulk dimensionality differential

• Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.

  PMID 31346012 · PMC6658682 · Microbiology resource announcements · 2019 · 6 claims · 7 setups

  Has reproduction · 92

  Draft genome sequences of three multidrug-resistant Shigella clinical isolates from Pakistan (two S. flexneri, one S. sonnei) are reported as a resource for AMR surveillance.

  shigella bacterial antimicrobial whole-genome