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).

• A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

  PMID 41975483 · PMC13185235 · Genome biology · 2026 · 7 claims · 7 setups

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  scProTrans, a deep learning framework combining sequence knowledge (dna2vec gene embeddings, ProtT5 protein embeddings) with a cross-omics attention mechanism, translates single-cell transcriptome data into proteome profiles

  multi-omics pbmcs datasets fully cite-seq cross-technology tri-omics

• Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.

  PMID 42100854 · PMC13229940 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  SCEG-HiC, a weighted graphical lasso (wglasso) method, predicts enhancer-gene links from single-cell multi-omics data by integrating bulk average Hi-C as a prior penalty matrix

  specified covid-19 scatac scatac-seq bulk

• MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.

  PMID 41811907 · PMC12998955 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  MultiPert reliably predicts both perturbed gene expression and protein abundance profiles from single-cell multi-omics data

  thp-1 kidney gse156478 computational zinb-vae autoencoder eccite-seq

• Benchmarking LLM-based agents for single-cell omics analysis.

  PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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  Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

  agent single-cell spatial scatac-seq llm-agent scrna-seq spatial