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).

Publications 1.3k Datasets 392.5k Experiments 74

System / cell line: immune ✕ Assay: abundance ✕ Clear

Single-cell spatial transcriptomics reveals tumor microenvironment heterogeneity in primary and lymph node-metastatic small cell lung cancer.

PMID 41916294 · PMC13130650 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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Three malignant subclusters (C5, C6, C9) are enriched in LNM tumors and display distinct metabolic and angiogenic programs alongside spatial immune exclusion

pt-lnm spatial single-cell multi-organ single-cell multiplex h&e
Paneth cell SIRT1 deficiency increases intestinal stress resistance by modulating the gut microbiota.

PMID 41826553 · PMC13076647 · EMBO reports · 2026 · 8 claims · 8 setups

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Generated a novel Paneth-cell-specific SIRT1 knockout mouse model (SIRT1 PKO, Sirt1 f/f;Defa6-Cre+)

small immune facs-sorted ileum single-cell facs qpcr
Aged murine bone marrow myeloid and mesenchymal cells develop unique senescence phenotypes.

PMID 41592025 · PMC13038201 · The Journal of clinical investigation · 2026 · 7 claims · 8 setups

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Myeloid-lineage cells (monocytes, macrophages, myeloid progenitors) show the highest expression of p16 and SASP markers among bone marrow immune cell types in aged mice

bone femur skeletal single-cell mass cytof
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 71

IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration

luad normal bulk wgcna tumor
Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

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RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic
A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

Has reproduction · 51

An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

bladder tcga bulk univariate integrative
Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups

Has reproduction · 40

An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts

bladder skin bulk integrative immune
A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

PMID 41559646 · PMC12910786 · BMC cancer · 2026 · 6 claims · 8 setups

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A tumor cell metaprogram (MP7) identified from scRNA-seq of CSCC shows elevated hypoxia, invasion, metastasis, proliferation, and angiogenesis scores compared to other metaprograms.

cscc tcga-cscc mp7 siha single-cell bulk gene
GATA2 controls alveolar macrophage inflammatory gene expression and metabolic function.

PMID 41712459 · PMC13134736 · JCI insight · 2026 · 8 claims · 8 setups

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GATA2 deficiency promotes enhanced inflammatory gene expression and metabolic dysfunction in alveolar macrophages in response to type 2 stimuli

bal cd11c+ ams lung flow immunostaining bodipy
Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

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A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

tcga-blca blca paired wgcna differential machine
Fibroblast-associated CTHRC1 as a key indicator of recurrence risk in prostate cancer.

PMID 41832493 · PMC13101373 · World journal of surgical oncology · 2026 · 7 claims · 8 setups

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Pathological T stage, N stage, Gleason score, and TP53 mutation are associated with higher PRAD recurrence risk

tcga geo prad scrna-seq bulk single-cell cell-cell
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine
Mapping Genetic Regulation of Transcription to Identify Functional Variants and Genes Associated with Pancreatic Cancer Risk.

PMID 41824785 · PMC13205582 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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A genome-wide cis-eQTL meta-analysis of 482 pancreatic tissues (177 TCGA tumor + 305 GTEx normal) identified 1,123,483 significant SNP-gene pairs, 709,720 unique eQTLs, and 13,758 eGenes (FDR<0.05)

tcga chinese significant egenes cis-eqtl gwas variant
Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events.

PMID 41254329 · PMC12627558 · Communications medicine · 2025 · 7 claims · 6 setups

Has reproduction · 71

Blood of steroid non-responders shows elevated Tc1/Tc17 CD8+ T cells and Th1/Th17-associated interleukins before steroid initiation

pbmcs pbmc serum snap-frozen spectral pd-1 ici-bound
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups

Has reproduction

A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.

tcga-blca gse32894 deep transfer machine
Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.

PMID 42047819 · PMC13125642 · Cancer immunology, immunotherapy : CII · 2026 · 7 claims · 8 setups

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A novel ecDNA-related Gene Prognostic Score Model (EGPSM) was constructed using an integrated framework of 101 machine learning algorithm combinations and validated in training, testing, and external cohorts.

osteosarcoma treatment-naive bulk 143b bulk single-cell cibersort
Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

PMID 42050900 · PMC13137916 · Medical science monitor : international medical journal of experimental and clinical research · 2026 · 8 claims · 8 setups

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TAGs are linked to HGSOC progression and yield a candidate prognostic model

hgsoc tcga-ov scrna-seq-derived single-cell bulk cellchat
Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

PMID 41674979 · PMC12885896 · Translational cancer research · 2026 · 8 claims · 8 setups

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A FAM-related gene prognostic model (FAMGM) built using CoxBoost and random survival forest was identified as the optimal model among 101 machine learning combinations, based on highest average C-index across TCGA-BRCA and GSE96058 cohorts

tcga-brca gse96058 brca breast bulk single-cell spatial
Peripheral Immune and Metabolic Dysregulation in Migraine, Ménière's Disease, and Vestibular Migraine: A Single-Cell Atlas Study.

PMID 41953397 · PMC13054517 · Human mutation · 2026 · 8 claims · 8 setups

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T cell abundance is significantly increased in MI compared to HC, while monocyte abundance is reduced, identifying T cells as a key pathogenic cell type

pbmcs pbmc-derived degs pbmc single-cell differential kegg
Multi-Omic Profiling of T Cell-Mediated Rejection After Kidney Transplantation Reveals B Cell Receptor Repertoire Expansion and Its Prognostic Relevance.

PMID 41467897 · PMC12752722 · FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026 · 8 claims · 8 setups

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The BCR repertoire, particularly the IgG isotype, is significantly expanded in TCMR compared to stable renal function (STA) across independent renal transplant cohorts

kidney healthy lp-1 bcr bulk triple

Experiments

Single-cell spatial transcriptomics reveals tumor microenvironment heterogeneity in primary and lymph node-metastatic small cell lung cancer.

Paneth cell SIRT1 deficiency increases intestinal stress resistance by modulating the gut microbiota.

Aged murine bone marrow myeloid and mesenchymal cells develop unique senescence phenotypes.

Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

GATA2 controls alveolar macrophage inflammatory gene expression and metabolic function.

Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

Fibroblast-associated CTHRC1 as a key indicator of recurrence risk in prostate cancer.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

Mapping Genetic Regulation of Transcription to Identify Functional Variants and Genes Associated with Pancreatic Cancer Risk.

Blood and tissue correlates of steroid non-response in checkpoint inhibition-induced immune-related adverse events.

Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.

Telomerase-Associated Genes as Prognostic Markers in High-Grade Serous Ovarian Cancer.

Novel fatty acid metabolism-related molecular subtyping and prognostic signature for breast cancer.

Peripheral Immune and Metabolic Dysregulation in Migraine, Ménière's Disease, and Vestibular Migraine: A Single-Cell Atlas Study.

Multi-Omic Profiling of T Cell-Mediated Rejection After Kidney Transplantation Reveals B Cell Receptor Repertoire Expansion and Its Prognostic Relevance.