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).

• DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

  PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 84

  DeepProg is a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data

  cancer breast hepatocarcinoma tcga multi-omics gene rna-seq

• ProtoCloud: A prototypical self-explaining model for single-cell analysis.

  PMID 41997134 · PMC13261663 · Cell genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  ProtoCloud matches or outperforms existing annotation methods across 11 large-scale datasets, particularly for rare cell types

  diverse pbmc10k pbmc30k tsca scrna-seq latent gene

• Bayesian inference of RNA velocity incorporating timepoints, lineage bifurcations, and count data.

  PMID 41860983 · PMC13021174 · PLoS computational biology · 2026 · 8 claims · 8 setups

  Full-text index only

  VeloVAE significantly outperforms previous RNA velocity methods in data fit, accuracy of inferred differentiation directions, and transcription rate estimation.

  pancreas developing induced embryo scrna-seq

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk