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).

• Multimodal learning reveals plants' hidden sensory integration logic.

  PMID 41714925 · PMC13032346 · BMC genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  CoMM-BIP (Contrastive Multi-Modal learning with Biologically Informed Priors) integrates transcriptomic, metabolomic, and phenomic data using pathway-guided attention, information-theoretic disentanglement, and domain-aware augmentations

  tomato multimodal transcriptomics metabolomics

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.

  PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups

  Has reproduction · 40

  DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.

  simulated real-world simulation scrna-seq-based

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

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

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  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

• 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

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC

  colorectal same combined meturquoise microarray differential batch