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).

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

  PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

  nsclc coad brca tcga scrna-seq bulk rna-seq

• 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

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• The transcription factor HHEX maintains glucocorticoid levels and protects adrenals from androgen-induced lipid depletion.

  PMID 41519914 · PMC12891536 · Nature communications · 2026 · 8 claims · 8 setups

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  HHEX is the most enriched transcription factor in glucocorticoid-producing zona fasciculata (zF) cells, conserved across mouse, rat, and human adrenal

  sf1-cre-high adrenocortical scrna-seq rnascope immunohistochemistry

• Single-immunocyte transcriptomics reveal the role of natural killer cell-dependent exogenous antigen presentation in ankylosing spondylitis severity.

  PMID 41593306 · PMC12868835 · Experimental & molecular medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Innate antibacterial defense functions are generally enhanced in most cell types at AS onset and are negatively associated with AS severity

  pbmcs gwas pbmc-derived cd4+ single-cell bulk mendelian

• HIV-seq reveals gene expression differences between HIV-transcribing cells from viremic and suppressed people with HIV.

  PMID 41776157 · PMC12957429 · Nature communications · 2026 · 7 claims · 8 setups

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  HIV-seq (10x 5' scRNA-seq spiked with HIV-specific capture primers targeting R-U5-pre-gag, pol, tat-rev exon2, Psi, and RRE) increases detection of HIV RNA+ cells and HIV transcripts per cell compared to conventional 5' scRNA-seq

  cd4+ cd8+ pbmcs scrna-seq cite-seq differential

• Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

  PMID 41986506 · PMC13226668 · The EMBO journal · 2026 · 8 claims · 6 setups

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  Single-cell transcriptome profiling of 245,878 islet cells from 48 donors (ND/PD/T2D) identifies 14 distinct, robust islet cell types detected in every donor

  pancreatic aggregated endoc-βh3 subset droplet-based pseudobulk unsupervised

• 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

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• 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