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 692

Assay: single-cell ✕ Clear

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.

PMID 41688638 · PMC12987725 · Nature genetics · 2026 · 8 claims · 8 setups

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Variants in the OR51E1–OR51E2 locus, encoding microbiome-derived fatty acid chemosensors expressed in enteroendocrine cells, are associated with gut microbial richness

adults subset intestinal enteroendocrine genome-wide sanger single-cell
Blood-based epigenetic instability linked to human aging and disease.

PMID 41690920 · PMC13018287 · Nature communications · 2026 · 7 claims · 8 setups

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31,744 unmethylated (and 6143 methylated) CpG loci in blood show highly consistent, stable methylation in young healthy individuals and are defined as Epigenetically Stable Loci (ESLs)

blood normal paired aml illumina whole-genome methylation
Müller glial and microglial responses coupled to recovery of cone photoreceptors following limited cone ablation in zebrafish retina.

PMID 41691075 · PMC12992573 · Scientific reports · 2026 · 7 claims · 6 setups

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24-hour 10mM Mtz immersion of adult gnat2:nfsb-mCherry zebrafish causes death of only a limited number of cone photoreceptors rather than widespread ablation

retinal retina dissociated live tunel immunofluorescence rt-qpcr
Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses.

PMID 41736867 · PMC12927306 · iScience · 2026 · 8 claims · 8 setups

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NARVI, a deep neural network trained on expression-velocity relationships of passed genes, can impute RNA velocity for dropped genes that conventional tools (e.g., scVelo, UniTVelo) fail to calculate

hematopoietic lung erythroid bone scrna-seq cross-validation
Nuclear Myosin 1 links genomic architecture to adipose tissue remodeling, metabolic inflammation and obesity in mice.

PMID 41748556 · PMC13004839 · Cell death & disease · 2026 · 8 claims · 8 setups

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NM1 is required for metabolic homeostasis during adipocyte differentiation

nm1 epididymal mefs het atac-seq bulk rna-seq
Multi-omics analyses related to mitochondria and ageing in triple-negative breast cancer implicate PYCR1 potentiates tumor progression.

PMID 41749247 · PMC13041056 · Cancer cell international · 2026 · 8 claims · 8 setups

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A 4-gene mitochondrial ageing-related risk score (MARS) model (PYCR1, MAPT, CEBPA, BCL2A1) predicts TNBC prognosis

tcga-brca gse58812 gse18728 metabric bulk single-cell immunohistochemistry
ASCL1 promotes nuclear shrinkage in transdifferentiation by suppressing NUP37.

PMID 41759523 · PMC12985393 · Stem cell reports · 2026 · 7 claims · 8 setups

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ASCL1-mediated transdifferentiation (AMp) of human fibroblasts to induced neurons causes marked nuclear shrinkage while cell size remains unchanged

mrc5 ag22056 ipsc-derived embryonic immunofluorescence single-cell rt-qpcr
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
VISTA drives pancreatic tumor progression through modulation of the tumor-associated macrophage polarity.

PMID 41776161 · PMC13194722 · Nature communications · 2026 · 8 claims · 8 setups

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VISTA deficiency significantly impairs PDAC tumor growth and prolongs survival in murine orthotopic models

pan02 cd45+ tumor mice orthotopic pharmacological flow
Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

PMID 41779856 · PMC12959402 · Science advances · 2026 · 7 claims · 6 setups

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Lung tumors drive expansion of both CD27+ and CD27- pulmonary γδ T cells, which acquire distinct spatial and phenotypic changes in the tumor microenvironment

spc-cre+ microdissected sorted merged flow confocal single-cell
Cis-regulatory evolution reveals sensory trade-offs as a genetic basis for temporal niche evolution in tapirs.

PMID 41779860 · PMC12959415 · Science advances · 2026 · 8 claims · 8 setups

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Tapirs reverted from a cathemeral ancestor to a nocturnal/crepuscular niche, accompanied by coordinated sensory reallocation: regressive vision (corneal opacity, reduced acuity) with enhanced auditory and chemosensory systems.

terrestris single-copy mammalian tapir whole-genome comparative ancestral
The complement system contributes to the immunosuppressive microenvironment of uveal melanoma.

PMID 41803879 · PMC13130498 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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Primary UM (pUM) preferentially expresses early complement pathway components over terminal membrane attack complex elements, with early factors showing prognostic significance.

short-term metastatic normal pum bulk label-free single-cell
Loss of fungal sensing exacerbates liver injury in a murine model of MASLD.

PMID 41805789 · PMC13135407 · JCI insight · 2026 · 8 claims · 8 setups

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Patients with advanced liver fibrosis exhibit distinct gut mycobiota profiles, with the genus Penicillium notably reduced in severe fibrosis

fecal wild-type gut card9 16s random diet-induced
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

PMID 41807385 · PMC12979833 · Nature communications · 2026 · 8 claims · 8 setups

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Integration of CAD GWAS summary statistics with epigenetic data from 45 cell types identifies 1580 candidate CAD genes

cad-associated disease-relevant types cad variant epigenetic tf-snv
Smoking promotes colorectal cancer via the CKAP2L/AREG axis.

PMID 41823522 · PMC13038336 · International journal of oncology · 2026 · 8 claims · 8 setups

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Smoking is positively associated with CRC risk, confirmed by both cross-sectional (NHANES) and Mendelian randomization analyses

participants european crc hct116 cross-sectional two-sample single-cell
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
Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.

PMID 41837870 · PMC13248853 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 6 setups

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Micropatterned cardioids generated from hiPSCs co-develop mesoderm-heart and endoderm-foregut/liver lineages, including a previously unreported non-neural ectoderm population.

hipsc-derived crispr-engineered micropatterned scrna-seq whole-mount clearing single-cell
FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

PMID 41839892 · PMC13201544 · Nature communications · 2026 · 8 claims · 6 setups

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FineST, a bimodal contrastive learning model integrating histology (Virchow2 ViT features) and spatial gene expression, enables nuclei-resolved high-resolution RNA imputation.

colorectal crc breast he-stained spatial type ccc
Smoking-induced dysregulation of transposable elements in the small airway epithelium.

PMID 41845375 · PMC13107634 · Respiratory research · 2026 · 8 claims · 6 setups

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Cigarette smoking dysregulates TE expression in the SAE, with 191 upregulated and 111 downregulated TE compared to nonsmokers

sae hsabci-ns1.1 bulk single-cell te-gene
MetaScreener: a robust dual-mode framework for directional prioritization of actionable signatures through multi-dataset and multi-approach integration.

PMID 41845481 · PMC13107662 · Journal of translational medicine · 2026 · 8 claims · 7 setups

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MetaScreener is a dual-mode framework (DiffMetaScreener for discrete labels, CorMetaScreener for continuous variables) integrating over 4,000 analysis pipelines to compute activation/inhibition directionality indices (ADI/IDI/DI) for gene signatures

crc independent ctrp rko differential robustness single-cell

Experiments

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.

Blood-based epigenetic instability linked to human aging and disease.

Müller glial and microglial responses coupled to recovery of cone photoreceptors following limited cone ablation in zebrafish retina.

Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses.

Nuclear Myosin 1 links genomic architecture to adipose tissue remodeling, metabolic inflammation and obesity in mice.

Multi-omics analyses related to mitochondria and ageing in triple-negative breast cancer implicate PYCR1 potentiates tumor progression.

ASCL1 promotes nuclear shrinkage in transdifferentiation by suppressing NUP37.

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

VISTA drives pancreatic tumor progression through modulation of the tumor-associated macrophage polarity.

Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

Cis-regulatory evolution reveals sensory trade-offs as a genetic basis for temporal niche evolution in tapirs.

The complement system contributes to the immunosuppressive microenvironment of uveal melanoma.

Loss of fungal sensing exacerbates liver injury in a murine model of MASLD.

Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci.

Smoking promotes colorectal cancer via the CKAP2L/AREG axis.

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

Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.

FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis.

Smoking-induced dysregulation of transposable elements in the small airway epithelium.

MetaScreener: a robust dual-mode framework for directional prioritization of actionable signatures through multi-dataset and multi-approach integration.