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 multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.

  PMID 41640425 · PMC12864441 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  The TIs-ML multi-omics model predicts ICB response/survival in ccRCC with superior accuracy (AUC > 0.997) compared to single biomarkers like PD-L1 and TMB

  autoimmune igan scrna-seq bulk bulk scrna-seq scissor-based

• bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.

  PMID 41657247 · PMC12884093 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  bayesReact is a novel fully Bayesian generative model for inferring regulatory motif (e.g., miRNA) activity from bulk or single-cell expression data

  tcga gtex stem embryonic paired semi-synthetic single-cell

• The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

  PMID 41686183 · PMC12988592 · Cancer immunology research · 2026 · 7 claims · 7 setups

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  CD79A is a reliable transcriptomic/protein quantifier of B lymphocytes across differentiation stages, unlike CD19/CD20 whose expression changes upon activation

  healthy tcga luad til-b flow bulk single-cell

• ATRX loss couples genome instability at a G-rich repeat to dysregulation of human alpha-globin expression.

  PMID 41688464 · PMC13018553 · Nature communications · 2026 · 8 claims · 8 setups

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  ATRX deficiency downregulates α-globin (HBM/HBA) selectively in a subset of cells that exhibit DNA damage, rather than uniformly across the population

  cd34+ single day hudep-2 crispr-cas9 cfu single-cell

• α4 Integrin blockade impairs CD8+ T cell neuroimmune surveillance following SIV infection.

  PMID 41734020 · PMC13078879 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  α4 blockade preserves CD4+ Th1 cell access to brain parenchyma but impairs CD8 effector recruitment, disrupting antiviral control

  siv-infected live macaque cd4-δitga4 flow antibody single-cell

• Identification and validation of prognostic genes related to glycolysis and M2 macrophage in hepatocellular carcinoma: an integrated analysis of bulk RNA sequencing and single-cell RNA sequencing.

  PMID 41766871 · PMC12935947 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  52 candidate genes were identified at the intersection of glycolysis-related genes (GRGs), M2 macrophage-related genes (MRGs), and HCC-vs-control DEGs (DEGs2).

  tcga-lihc gse149614 key hcc bulk immune cox

• Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

  PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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  A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

  gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

• Identification and validation of prognostic genes associated with M2 macrophage and heme metabolism in lung adenocarcinoma through bulk and single-cell RNA sequencing analysis.

  PMID 41787185 · PMC13076703 · Discover oncology · 2026 · 8 claims · 8 setups

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  EPB41, ACP5, PPOX, RBM38, and TRIM58 were identified as prognostic genes for LUAD

  tcga-luad gse131907 clinical cibersort gsea spearman

• Dopamine enhances surface glial glycolysis via acetylcholine and insulin/insulin-like growth factor signaling in the honeybee.

  PMID 41797926 · PMC12964235 · iScience · 2026 · 8 claims · 5 setups

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  Bromocriptine (dopamine receptor agonist) increases glycolytic flux in forager bee brains

  forager targeted qpcr single-cell

• 3D-super-enhancers are condensate-associated cis-regulatory communities.

  PMID 41797539 · PMC12968393 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  BOUQUET integrates genome topology, chromatin occupancy, and graph theory (label propagation) to assign CREs and transcription protein machinery to target genes and identify protein-rich 'communities' associated with condensates.

  embryonic mesc thymocytes chip-seq hichip single-cell

• AJUBA: The Master Regulator Bridging EMT and Immune Evasion in Colorectal Cancer.

  PMID 41814682 · PMC13140425 · Mediators of inflammation · 2026 · 8 claims · 8 setups

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  AJUBA is markedly upregulated in CRC across multiple transcriptomic cohorts and is enriched in epithelial cells with activated EMT features

  tcga-crc crc paired hct116 bulk single-cell spatial

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral

• Lung scRNA-seq reveals chronic inflammation and emphysemous phenotype in mice with osteogenesis imperfecta.

  PMID 41822759 · PMC12978693 · Frontiers in genetics · 2026 · 8 claims · 3 setups

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  Aga2 mice show increased alveolar spacing (emphysematous phenotype) at postnatal day 28 (p28) but not at p5

  lung histology single-cell rnascope

• Patient-derived orthotopic xenograft models recapitulate the peritoneal dissemination of pancreatic cancer and delineate its transcriptional and regulatory programs.

  PMID 41673768 · PMC12998334 · Journal of experimental & clinical cancer research : CR · 2026 · 6 claims · 8 setups

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  Organoids derived from malignant effusions of PDAC patients reproducibly generate peritoneal metastases after orthotopic implantation into the pancreas of immunodeficient mice

  pdac organoids frozen pdox orthotopic single-nucleus single-cell

• Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

  PMID 39592593 · PMC11599844 · Nature communications · 2024 · 8 claims · 2 setups

  Has reproduction · 90

  Weak selection conferred by HSC variation created before birth can reliably yield clonal hematopoiesis later in life, demonstrated via shared prenatal circulation of monozygotic (MZ) twins.

  blood simulated fluctuating single-cell

• Visualizing stability: a sensitivity analysis framework for t-SNE embeddings.

  PMID 41552665 · PMC12808344 · Frontiers in bioinformatics · 2025 · 8 claims · 5 setups

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  The Implicit Function Theorem, combined with automatic differentiation, can be used to efficiently compute the complete sensitivity Jacobian of a converged t-SNE embedding with respect to the input data, avoiding differentiation through the full iterative optimizer.

  bulk proteomics single-cell biological t-sne gaussian

• CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

  PMID 41056017 · PMC12646653 · The Journal of clinical investigation · 2025 · 8 claims · 8 setups

  Has reproduction · 67

  Heterozygous CDKL1 missense variants (Cys143Arg, Ser206Leu, Thr135Met) were identified in 6 patients from 3 families with TAAD spectrum disorders

  patients cohort cdkl1 aortic exome gene structural

• Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.

  PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 5 setups

  Has reproduction · 94

  EiaD is a reproducible, versioned RNA-seq transcriptome dataset combining 916 healthy human eye samples and 1375 GTEx body samples across 19 eye and 54 body tissues, built with a Snakemake pipeline and served as a single SQLite database.

  gtex eye stem retinal bulk differential single-cell

• 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