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 25

System / cell line: single-cell ✕ Assay: selection ✕ Clear

Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset.

PMID 41807428 · PMC13103403 · Scientific data · 2026 · 8 claims · 4 setups

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A paired scRNA-seq and scATAC-seq dataset was generated from NPCs differentiated over Days 0, 7, 13, and 20 under baseline and Aβ 1-42 exposure conditions

hipsc-derived hippocampal scrna-seq scatac-seq flow
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups

Has reproduction · 45

Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data

tumor-infiltrating peripheral cd4+ tumor single-cell unsupervised pearson
Inferring a spatial code of cell-cell interactions across a whole animal body.

PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups

Has reproduction · 90

cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells

elegans computational single-cell random genetic
Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

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MSI gastric cancer samples show significantly greater T cell infiltration and a lower proportion of epithelial cells compared to GS samples

gastric epithelial stomach nod-scid single-cell cnv differential
Monocytes Defined by Platelet Interactions and Oxidative Stress Signaling Underlie HIV-Associated Atherosclerosis.

PMID 41823228 · PMC13055746 · Journal of the American Heart Association · 2026 · 8 claims · 8 setups

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Two monocyte clusters (platelet-monocyte complex [PMC] and CD14+ monocytes) contribute independently to vascular immune dysregulation in PLWH

circulating plasma platelet-monocyte cd14+ single-cell plasma bulk
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

Has reproduction · 49

ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

ptc degs key bulk kegg weighted
Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna
Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

PMID 41815567 · PMC12973086 · Cardiovascular diagnosis and therapy · 2026 · 8 claims · 8 setups

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SMU1 is identified as a novel macrophage-related gene associated with AAA development, serving as a potential diagnostic biomarker and therapeutic target

aaa macrophage-related merged gwas single-cell bulk rt-qpcr
Machine learning-driven transcriptomic and single-cell profiling of programed cell death patterns in colon cancer.

PMID 41854308 · PMC13009810 · Science progress · 2026 · 8 claims · 8 setups

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Disulfidptosis and anoikis are consistently identified as the most robust prognostic PCD patterns in colon cancer across six independent machine learning algorithms

colon coad ssgsea-based machine differential
Benchmarking LLM-based agents for single-cell omics analysis.

PMID 41742311 · PMC13064268 · Genome biology · 2026 · 8 claims · 8 setups

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Introduces a comprehensive benchmarking evaluation system comprising an open-source agent platform, 18 evaluation metrics across four dimensions, and 50 real-world single-cell omics tasks

agent single-cell spatial scatac-seq llm-agent scrna-seq spatial
A stem and progenitor cell-derived gene expression signature is prognostic for survival in myelofibrosis.

PMID 41481381 · PMC13155955 · Blood · 2026 · 8 claims · 4 setups

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A 24-gene HSPC-derived weighted-sum expression score (MPN24) is prognostic for overall survival in myelofibrosis

peripheral lin-cd34+ pb-mncs pm-c1 bulk single-cell nanostring
Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups

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MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework

bulk single-cell tcga glioma gsva aucell machine
Cross-species prediction reveals chromatin regions with increased accessibility in humans.

PMID 41984952 · PMC13082337 · Science advances · 2026 · 8 claims · 8 setups

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CNNs trained exclusively on human ATAC-seq data achieve cross-species prediction performance in chimpanzees and macaques comparable to species-specific models

lymphoblastoid prefrontal six chimpanzee bulk single-cell cnn
Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups

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New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach

hela automated stepwise training-set-size
Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

PMID 41620539 · PMC12916760 · Scientific reports · 2026 · 8 claims · 9 setups

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76 overlapping genes were identified between COPD-associated DEGs and oxidative stress-related genes.

lung genecards differentially bronchial bulk database functional
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
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
Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

PMID 41939867 · PMC13043422 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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CXCL13, IL33, TLR4, and IGF1 are core IPF genes consistently linked to immune infiltration and fibrotic remodeling across bulk, single-cell, spatial, and blood multi-omics data

lung candidate bulk normalized bulk ppi machine
Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.

PMID 42112332 · PMC13149443 · Frontiers in immunology · 2026 · 7 claims · 8 setups

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A 6-gene (RGS20, ADA, AICDA, SLC12A5, RUFY4, CDK5RAP3) prognostic risk model was constructed for ccRCC from ammonia death-related genes

tcga-kirc gse159115 clinical bulk univariate gsea

Experiments

Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset.

Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

Inferring a spatial code of cell-cell interactions across a whole animal body.

Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

Monocytes Defined by Platelet Interactions and Oxidative Stress Signaling Underlie HIV-Associated Atherosclerosis.

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

Comprehensive analysis for the role of macrophage-driven genes in abdominal aortic aneurysm.

Machine learning-driven transcriptomic and single-cell profiling of programed cell death patterns in colon cancer.

Benchmarking LLM-based agents for single-cell omics analysis.

A stem and progenitor cell-derived gene expression signature is prognostic for survival in myelofibrosis.

Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.

Cross-species prediction reveals chromatin regions with increased accessibility in humans.

Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.

Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

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.

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

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

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation.

Identification of a prognostic signature based on ammonia metabolism-related genes in clear cell renal cell carcinoma: an integrated analysis of bulk and single-cell transcriptomics.