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).

• iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

  PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups

  Has reproduction · 58

  iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.

  giab monocyte missense somatic germline rna-seq machine

• Combining evidence of preferential gene-tissue relationships from multiple sources.

  PMID 23950964 · PMC3741196 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 53

  A high-level integration approach combining three methods across four human microarray datasets, merged by consensus voting and a rule-based inner/total score, predicts preferentially expressed genes while reducing method- and study-specific bias.

  normal four microarray genes microarray computational bayes

• CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

  PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

  bulk previously round paired transfer-learning cross-species

• 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

• Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

  PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

  tissues genomic gtex hgmd long-read variant splice