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 reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.

  PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups

  Has reproduction · 91

  DeClust is a reference-profile-free deconvolution method that incorporates molecular subtyping directly into the deconvolution process, outputting cohort-level cancer subtype and stromal reference profiles rather than per-individual profiles

  tcga simulated muscle-invasive ccrcc computational simulation-based deconvolution

• Current status of use of high throughput nucleotide sequencing in rheumatology.

  PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 8 setups

  Has reproduction · 83

  RNA-Seq is the most represented HTS assay used in rheumatology research, primarily for biomarker identification in blood or synovial tissue.

  pubmed sequence blood patients systematic sra rna-seq

• treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.

  PMID 34001188 · PMC8127214 · Genome biology · 2021 · 7 claims · 6 setups

  Has reproduction · 73

  treeclimbR proposes multiple candidate resolutions on a tree and selects the optimal one in a data-driven manner using three criteria (FDR-controlling range of t, number of rejected leaves, fewest internal nodes)

  synthetic semi-simulated microbiome mirna differential microbiome microrna

• Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.

  PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups

  Has reproduction · 61

  Omics Playground is a user-friendly, interactive self-service platform for in-depth analysis, visualization, and interpretation of transcriptomics and proteomics data, including single-cell RNA-seq.

  l1000 bulk lc-ms single-cell

• Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 7 claims · 6 setups

  Has reproduction · 75

  XCR during iPSC reprogramming is hierarchical, with distinct subsets of X-linked genes reactivating early, intermediate, late, and very late

  mus mefs bulk independent allele-specific fluorescence-activated live

• Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

  PMID 35269470 · PMC8909161 · Cells · 2022 · 8 claims · 7 setups

  Has reproduction · 88

  COVID-19 and HLH share a transcriptional overlap of 239 unique common differentially expressed genes (DEGs), 237 of which are up-regulated

  patients pbmcs plasma derived bulk single-cell quantitative

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

  PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

  Has reproduction · 83

  Vascular macrophages form a spatiotemporal niche in direct contact with mural cells across microvascular and macrovascular beds

  cx3cr1-mφ rfp-rep coronary peritoneal intravital confocal single-cell

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 7 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer

  e9.5 xenopus bulk rt-qpcr whole-mount

• Community assessment of methods to deconvolve cellular composition from bulk gene expression.

  PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups

  Has reproduction · 63

  Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.

  admixtures cancer tumor bulk bulk admixture crowdsourced

• De novo identification of CD4(+) T cell epitopes.

  PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

  nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

• Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.

  PMID 35053177 · PMC8773604 · Biomolecules · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  The 76GS, KS, and MLR EMT scoring metrics show concordant trends in quantifying EMP across bulk RNA-seq datasets spanning multiple cancer types

  bulk py2t mcf10a airway transcriptomic rna-seq single-cell

• Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis.

  PMID 36323713 · PMC9630272 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  Loss of AR in stromal Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development in vivo

  ugm hi-myc prostate hmyctg+ genetically single-cell immunohistochemistry

• A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

  PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

  Has reproduction · 85

  Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

  tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry

• Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

  PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus

• Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

  PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

  Has reproduction · 87

  NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

  lines bulk single-cell housekeeping bulk pca single-sample

• An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

  PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 63

  Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

  hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune

• Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

  PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups

  Has reproduction · 75

  Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.

  aortic gene computational normalized bulk ppi connectivity

• Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.

  PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 7 claims · 7 setups

  Has reproduction · 100

  A distinct gene co-expression module with a prominent T cell signature is associated with unstable plaques.

  carotid calcified atherosclerotic cell-specific microarray single-cell immunohistochemistry

• Charting and probing the activity of ADARs in human development and cell-fate specification.

  PMID 39537590 · PMC11561244 · Nature communications · 2024 · 8 claims · 6 setups

  Has reproduction · 100

  RNA editing (AEI) and ADAR/ADARB1/ADARB2 expression show organ-specific dynamic shifts across fetal-to-adult developmental stages in human forebrain, hindbrain, heart, liver, kidney, and testis

  organ same 8-week-old week alu site-specific gene