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).

• 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

  Full-text index only

  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

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn