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 283

Assay: immune ✕ Clear

Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

pancreatic kpc pdac tcga-paad rna-seq bulk proteomics
Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

PMID 41571662 · PMC12923738 · Nature communications · 2026 · 8 claims · 8 setups

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Fin and limb regeneration share conserved proximal and distal blastema territory markers, DNA damage repair activation, hif1a-mediated hypoxia response, and sequential pro-/anti-inflammatory gene programs.

polypterus axolotl zebrafish regenerating single-nucleus spatial single-cell
Epithelial-mesenchymal plasticity and immunosuppression in canine carcinomas reveals cross-species upregulation of CD109.

PMID 41571773 · PMC12929570 · Communications biology · 2026 · 8 claims · 4 setups

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EMP activation (increased vimentin, decreased E-cadherin) is associated with advanced histologic grade in canine mammary carcinomas

archived canine cmc same immunohistochemistry sequencing
Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.

PMID 41623476 · PMC12857400 · iScience · 2026 · 7 claims · 12 setups

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Splicing-modulatory drugs MS023 and indisulam act as inadvertent NMD inhibitors by downregulating SMG1 protein levels

4t1 tumor-draining arst panc02 mts tumor ifn-γ
The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

PMID 41625479 · PMC12857760 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

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Neutrophils in the lung metastatic niche comprise two functionally distinct subsets, Ly6g^high and Ly6g^low, based on Ly6g expression level

lung cramp cd8+ neutrophils single-cell flow genetic
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
POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

PMID 41645751 · PMC12891935 · Oncology reports · 2026 · 8 claims · 8 setups

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Integration of two HNSCC scRNA-seq datasets reveals two distinct fibroblast subtypes: POSTN- and POSTN+ fibroblasts

hnscc tcga-hnscc oscc oscc-derived single-cell bulk immunohistochemistry
Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

luad demtdmrgs gse131907 wgcna kegg univariate
Predictive modeling of molecular activity underlying physical cell-cell interactions.

PMID 41672069 · PMC12946745 · Cell reports methods · 2026 · 8 claims · 5 setups

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Gloss, an overlapping group lasso regression combining single-gene and curated pathway features, predicts LIPSTIC interaction intensity from scRNA-seq data

tumor intestine mediastinal organs lipsticv1 ulipstic cite-seq
Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

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A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

escc gse53625 gse160269 imvigor210 microarray univariate single-cell
Lactate metabolism-related interaction perturbation network enables robust stratification of hepatocellular carcinoma.

PMID 41689750 · PMC13009326 · Discover oncology · 2026 · 8 claims · 8 setups

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An LM-related gene interaction perturbation network can stratify HCC into four robust molecular subtypes (Cluster1-4)

tcga-hcc gse76427 gene consensus immune
Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

pca tcga-prad external scrna-seq bulk immune
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
The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

PMID 41730908 · PMC13039115 · Nature communications · 2026 · 8 claims · 8 setups

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EHF orchestrates an immunosuppressive maturation program in cDC1s and cDC2s downstream of TLR7/8/9 sensing of self-nucleic acids

ehf facs-sorted dss-induced lethal cd4+
Long-read sequencing and proteomics reveal blood transcriptome and protein expression profiles in multiple primary lung cancers.

PMID 41761147 · PMC13059216 · BMC cancer · 2026 · 6 claims · 7 setups

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MPC patients exhibit significantly increased blood transcript complexity, with higher numbers of DEGs, DETs, and DTU events than OPLC and HC groups

blood serum degs ont dia differential
IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

PMID 41766654 · PMC12948414 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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MPNST cells are more radioresistant than benign plexiform neurofibroma (pNF) cells in vitro

mpnst st88-14 nf9511.b jh-2-002 flow fractionated bulk
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
Precancerous niche remodelling dictates nascent tumour persistence.

PMID 41781610 · PMC13148994 · Nature · 2026 · 8 claims · 8 setups

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Newly emerging tumours actively remodel their surrounding stroma into a 'precancerous niche' that determines their long-term survival.

upper nascent oesophagus carcinogen-free immunofluorescence edu immune
Sensitizer-Induced Basophils Accelerate Skin Re-Epithelialization via IL-4/IL-13-Mediated Macrophage Polarization.

PMID 41787818 · PMC13139821 · Allergy · 2026 · 8 claims · 8 setups

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Basophils accumulate in wounded and oxazolone (OXA)-sensitized skin, peaking around day 3–6 post-injury

skin ear dorsal mcpt8-ct single-cell flow rt-qpcr
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

Experiments

Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

Comparative multi-omic analysis reveals conserved and derived mechanisms of fin and limb regeneration.

Epithelial-mesenchymal plasticity and immunosuppression in canine carcinomas reveals cross-species upregulation of CD109.

Pharmacological perturbation of splicing elicits SMG1 reduction: Implications for cancer therapy.

The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

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

POSTN(+) fibroblast‑secreted small extracellular vesicles drive macrophage M2 polarization through BMP4/BMPR2/Smad signaling.

Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

Predictive modeling of molecular activity underlying physical cell-cell interactions.

Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

Lactate metabolism-related interaction perturbation network enables robust stratification of hepatocellular carcinoma.

Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

GATA2 controls alveolar macrophage inflammatory gene expression and metabolic function.

The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

Long-read sequencing and proteomics reveal blood transcriptome and protein expression profiles in multiple primary lung cancers.

IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

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

Precancerous niche remodelling dictates nascent tumour persistence.

Sensitizer-Induced Basophils Accelerate Skin Re-Epithelialization via IL-4/IL-13-Mediated Macrophage Polarization.

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