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).

• 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

• A network model for the correlation between epistasis and genomic complexity.

  PMID 18648534 · PMC2481279 · PloS one · 2008 · 8 claims · 5 setups

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  In small networks with multifunctional nodes, lack of redundancy, and absence of alternative pathways, epistasis is antagonistic on average.

  two-pathway network

• 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

• CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

  PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

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  CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

  neftel kim scrna-seq same scrna-seq ground-truth robustness

• STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.

  PMID 42044152 · PMC13160441 · PLoS computational biology · 2026 · 8 claims · 8 setups

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  STARCall combines image stitching and cross-cycle alignment into a single joint optimization step (via ConStitch) that minimizes both inter-cycle and intra-cycle alignment error.

  stem slice a549 u2os image situ simulated