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).

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).

  PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 5 setups

  Has reproduction · 67

  HASCAD, a DNN-based cell composition deconvolution model, predicts the fractions of up to 15 immune cell types from bulk RNA-seq.

  pbmc bulk tcga-lihc harmony-symphony scrna-seq simulated bulk

• 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

• 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

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

  PMID 41229397 · PMC12604667 · NAR genomics and bioinformatics · 2025 · 8 claims · 4 setups

  Has reproduction · 75

  scIGD is a Snakemake workflow that automates HLA allele-typing and allele-specific expression quantification from scRNA-seq data

  aida merkel-cell 20k myeloma scrna-seq

• Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy.

  PMID 33723257 · PMC7961017 · Nature communications · 2021 · 7 claims · 7 setups

  Has reproduction · 70

  Mucosal-associated invariant T (MAIT) cells are more abundant in the circulation of metastatic melanoma patients who respond to anti-PD-1 therapy than in non-responders, before and during therapy.

  peripheral cd3+cd8+ pbmc-derived pbmc high-dimensional single-cell flow

• Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

  PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 85

  Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs

  left eqtl degs merged bulk two-sample functional

• Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

  PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 7 claims · 7 setups

  Has reproduction · 71

  HIV-1 and PAH share 109 co-expressed genes primarily enriched in type I interferon (IFN) pathways.

  pbmc shared gene microarray kegg

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 7 setups

  Has reproduction · 63

  Independent human liver immune scRNA-seq datasets can be combined into an integrated meta-atlas in which all datasets co-cluster, despite differing cell-type proportions between studies.

  liver combined normal differential scrna-seq integrated reference

• Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.

  PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups

  Has reproduction · 48

  277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways

  synovial rosacea co-expressed serum microarray weighted protein-protein

• COVID-19 vaccination atlas using an integrative systems vaccinology approach.

  PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups

  Has reproduction · 69

  mRNA vaccines induce transient but strong immune responses after booster doses

  pbmcs immune pbmc bulk gene principal

• Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers.

  PMID 34721945 · PMC8555559 · Oncoimmunology · 2021 · 8 claims · 6 setups

  Has reproduction · 44

  In tumors, infiltrating γδ T cells (predominantly TCRVγnon9) are quantitatively correlated with and aligned to CD8 T cells for differentiation, exhaustion, gene expression, and response to immune checkpoint therapy.

  splenic healthy tumor syngeneic single-cell scrnaseq citeseq