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 19

System / cell line: factor ✕ Assay: deconvolution ✕ Clear

Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

PMID 41950003 · PMC13244359 · Cell reports · 2026 · 8 claims · 7 setups

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Multi-omics factor analysis (MOFA) integrating seven omics views from 1,358 ROS/MAP participants identifies cross-omics biological factors relating to AD phenotypes.

dorsolateral brain postmortem cortex h3k9ac bulk proteomics
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
Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

PMID 41540084 · PMC12894745 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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The presence of immune cells in the environment significantly alters CLL cell activation

autologous monoculture non-adherent pbmc bulk flow deconvolution
Molecular subtype of recurrent implantation failure reveals distinct endometrial etiology of female infertility.

PMID 40660214 · PMC12257665 · Journal of translational medicine · 2025 · 8 claims · 8 setups

Has reproduction · 68

RIF endometrial samples segregate into two reproducible molecular subtypes: an immune-driven subtype (RIF-I) and a metabolic-driven subtype (RIF-M)

endometrial in-house bulk rif-degs meta-analysis sequencing immune
T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 78

Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

kidney scrna-seq microarray meblack microarray single-cell scissor
Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

Has reproduction · 66

At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

subcutaneous sat rhesus bulk gsea xcell
Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

Has reproduction · 50

Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

hnscc tcga-hnscc caf fibroblast single-cell bulk spatial
Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental
A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

PMID 42030938 · PMC13198283 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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A multiomic (snRNA-seq, snATAC-seq, WGS, CODEX) atlas defines a core set of pHGG neoplastic cell states shared across molecular subtypes

phgg neoplastic fetal single-nucleus whole-genome codex
Common pathogenic mechanisms in the hippocampus across neurodegenerative dementias: Alzheimer's disease, Down syndrome, and Parkinson's disease.

PMID 42078116 · PMC13128439 · NPJ dementia · 2026 · 8 claims · 6 setups

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Chronological age does not align with biological (transcriptional) age in hippocampal tissue from PDD, AD, and DSD dementia patients

post-mortem hippocampal bulk transcriptomic cell-type
Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

Has reproduction · 75

Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.

stage combined patients copy genome-wide targeted
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
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein
Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

PMID 40936936 · PMC12420628 · Frontiers in immunology · 2025 · 7 claims · 8 setups

Has reproduction · 71

A highly stem-like C0 MAFF+ tumor cell subtype dominates invasive LUAD, producing chemokines and activating lipid metabolism

luad tumor a549 single-cell infercnv pseudotime
Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

first-trimester decidual spots dnk 10x h&e type
Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

PMID 41498635 · PMC12948189 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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Five distinct malignant cell populations exist in SNSCC, with hypoxic (TC1) and proliferative (TC2) subtypes associated with adverse clinical outcomes.

snscc bulk single-nucleus bulk single-nucleus methylation
Single-cell and spatial transcriptomics analyses reveal tumor microenvironment-driven proliferation of NF2-associated vestibular schwannomas.

PMID 41957607 · PMC13200446 · Journal of neuroinflammation · 2026 · 8 claims · 7 setups

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NF2-VS tumors comprise 12 major cell lineages with distinct TME composition between Gardner and Wishart phenotypes

vestibular fresh nf2-vs fibroblast scrna-seq spatial multiplex
Dissecting tumor heterogeneity in colorectal cancer: uncovering the role of BCL2L1(+) cells through single-cell analysis.

PMID 41958675 · PMC13056825 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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scRNA-seq identifies five CRC tumor cell subtypes, with the C4 BCL2L1+ subtype predominantly enriched in liver metastases and showing enhanced proliferation, metabolic reprogramming, and anti-apoptotic activity

crc epcs malignant tcga scrna-seq infercnv cytotrace
DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

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Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

tcga-luad tcga luad dendritic-cell bulk survival pan-cancer

Experiments

Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

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

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.

Common pathogenic mechanisms in the hippocampus across neurodegenerative dementias: Alzheimer's disease, Down syndrome, and Parkinson's disease.

Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

Single-cell and spatial transcriptomics analyses reveal tumor microenvironment-driven proliferation of NF2-associated vestibular schwannomas.

Dissecting tumor heterogeneity in colorectal cancer: uncovering the role of BCL2L1(+) cells through single-cell analysis.

DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.