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).

• SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

  PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

  Full-text index only

  SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

  melanocortin same paired test chromatogram tracediff weak

• The use of edge-betweenness clustering to investigate biological function in protein interaction networks.

  PMID 15740614 · PMC555937 · BMC bioinformatics · 2005 · 8 claims · 7 setups

  Full-text index only

  Edge-Betweenness clustering separates protein interaction graphs into subgraphs whose GO term distributions show significant correlations, revealing biologically meaningful functional modules.

  interaction yeast edge-betweenness chi-squared robustness

• Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).

  PMID 15339345 · PMC517707 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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  A Bayesian mixture model is proposed to account for within-class biological variability in SAGE/Digital-Northern/MPSS tag counting data.

  astrocytoma same sage classical beta-binomial

• Adaptations to climate in candidate genes for common metabolic disorders.

  PMID 18282109 · PMC2242814 · PLoS genetics · 2008 · 8 claims · 7 setups

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  A network-based bioinformatics approach (Molecular Triangulation) was used to select 82 candidate genes belonging to the core subnetwork of metabolic syndrome phenotypes.

  individuals population genic compiled snp spearman bayesian

• Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome.

  PMID 34561431 · PMC8463674 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 100

  revTWMR, a reverse transcriptome-wide Mendelian Randomization approach integrating GWAS and whole-blood trans-eQTL summary statistics, is proposed to estimate the causal effect of a phenotype on gene expression.

  blood ra-associated genome-wide revtwmr transcriptome-wide reverse functional

• CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

  PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 8 setups

  Has reproduction · 42

  CanCellCap, a multi-domain learning framework integrating domain adversarial learning and Mixture of Experts, identifies cancer cells across all tissues, cancers, and sequencing platforms by extracting tissue-common and tissue-specific gene expression patterns.

  testing datasets tisch2 prostate scrna-seq simulated spatial

• Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments.

  PMID 36988509 · PMC10128000 · mBio · 2023 · 7 claims · 7 setups

  Has reproduction · 100

  SRB modify niches (e.g., pH) to affect species coexistence during organic matter degradation

  coastal marine marinilabiliales srb-inhibited 16s molecular physicochemical

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc