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).

• Aligned cross-modal integration and regulatory heterogeneity characterization of single-cell multiomic data with deep contrastive learning.

  PMID 41588477 · PMC12833949 · Genome medicine · 2026 · 8 claims · 4 setups

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  scMDCF outperforms existing state-of-the-art scMulti-omics integration and clustering models across various types of scMulti-omics datasets, including robustness against batch effects

  single immune dorsolateral cite-seq scrna-atac-seq snmulti-omics

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein

• 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

• omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

  PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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  omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

  blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk

• CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

  PMID 41481570 · PMC12758788 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  CellPredX is a unified semi-supervised framework integrating domain adaptation and deep metric learning to align heterogeneous embeddings for cross-modality cell type annotation.

  pbmc fetal pancreas gse149683 matched unmatched cross-protocol