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).

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia.

  PMID 41972591 · PMC13072394 · Biology · 2026 · 8 claims · 7 setups

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  GAFA integrates latent-space representation, pseudotime trajectory modeling, GRN inference, and machine learning-based gene panel discovery into a single coherent pipeline, unlike existing workflows that treat these steps independently.

  peripheral subset immune assigned scrna-seq latent-space automated

• Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

  PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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  Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

  peripheral ceph individuals cases strp genotyping fluorescent

• Single-cell atlas of the developing Down syndrome brain cortex.

  PMID 41545595 · PMC13004680 · Nature medicine · 2026 · 8 claims · 8 setups

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  RORB/FOXP1-expressing L4-like excitatory neurons are subtype-specifically and dramatically reduced in Down syndrome fetal cortex, especially at later stages (PCW16-20)

  fetal excitatory neural humanized single-nucleus immunostaining compositional

• A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

  PMID 41998142 · PMC13144478 · Experimental & molecular medicine · 2026 · 7 claims · 8 setups

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  Integrated scATAC/scRNA multi-omics analysis of developing mouse skin identifies gene network axes underlying skin lineage specification

  dorsal scrna-seq skin fibroblast scatac-seq scrna-seq spatial

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime

• Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

  PMID 41987329 · PMC13192178 · Genome biology · 2026 · 7 claims · 8 setups

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  Gene activity scores (GAS) show limited correlation with actual gene expression but effectively preserve cellular neighborhood structure and support clustering.

  e18 pbmc brain kidney scrna-seq share-seq gas

• Comparative single-cell landscape of immune cells in human livers affected HBV and non-viral cirrhosis.

  PMID 41815278 · PMC12971635 · Frontiers in medicine · 2025 · 8 claims · 7 setups

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  Macrophage-PLCG2 (anti-inflammatory) and CD8+ T-FABP5 subsets are expanded in HBV cirrhosis compared to non-viral cirrhosis

  liver myeloid scrna-seq spatial pathway