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).

• Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

  PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.

  hepg2 computational same bead-based integer comparative

• IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

  PMID 25406361 · PMC4274634 · RNA (New York, N.Y.) · 2015 · 8 claims · 6 setups

  Has reproduction · 30

  Existing ab initio assemblers (Cufflinks, Scripture) annotate at most one 3' boundary per terminal exon and therefore cannot assemble coexpressed tandem 3' UTR isoforms.

  mapped simulated rna-seq ict1 computational benchmarking 3'-seq

• Protocol for single-cell optimization objective and trade-off inference.

  PMID 41790544 · PMC12992945 · STAR protocols · 2026 · 6 claims · 6 setups

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  SCOOTI is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs

  mcf10a serum-starved contact-inhibited zygote bulk scrna-seq genome-scale

• Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.

  PMID 35624178 · PMC9142503 · Nature communications · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  pcSecYeast, a proteome-constrained genome-scale model integrating metabolism, translation, and detailed secretory pathway processing (translocation, PTMs, folding, misfolding, degradation), was constructed for S. cerevisiae

  cerevisiae genome-scale unit expression

• Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

  PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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  The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

  recombinant selenomethionine-substituted ge-gi models surface x-ray computational

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Single-cell and spatial transcriptomics define 20E-driven developmental reprogramming in silkworm wing disc.

  PMID 41730863 · PMC13039787 · Nature communications · 2026 · 8 claims · 7 setups

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  Wing morphogenesis (Wm) cells act as central progenitors/differentiation hub, giving rise to epithelial and cuticle lineages under lineage-specific transcription factors

  mori spodoptera scrna-seq stereo-seq snrna-seq