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).

• Prediction of myeloid malignant cells in Fanconi anemia using machine learning.

  PMID 41557613 · PMC12818649 · PloS one · 2026 · 6 claims · 7 setups

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  A DNN classifier trained on AML scRNA-seq data accurately predicts AML-like transcriptional profiles at single-cell resolution

  bone predicted-aml healthy scrna-seq reference-based stemnet

• AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PM(2.5) exposure.

  PMID 41912520 · PMC13194984 · Nature communications · 2026 · 8 claims · 6 setups

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  A fine-tuned Geneformer (single-cell transcriptomics transformer) model classifies PM2.5 exposure status and generalizes better than BERT models trained from scratch, especially with limited data.

  lung fine-tuned biobank single-cell bulk gene

• scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.

  PMID 41907409 · PMC13019583 · iScience · 2026 · 8 claims · 8 setups

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  scMILD identifies condition-associated cells using only sample-level labels via a dual-branch MIL architecture with a shared encoder

  simulated lupus covid-19 ulcerative simulated mixture scrna-seq

• A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.

  PMID 41663439 · PMC12996591 · Nature communications · 2026 · 7 claims · 7 setups

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  Aggregating peaks from 624 high-quality bulk ATAC-seq datasets defines ~1.4 million observed consensus peaks (cPeaks) covering ~30% of the genome.

  bulk scatac-seq cnn gm12878 bulk scatac-seq deep

• CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

  PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

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  CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

  species gm12878 types chromatin cross-protein cross-cell-type