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 13

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

Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

PMID 41566530 · PMC12906006 · Genome biology · 2026 · 7 claims · 6 setups

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Pseudobulk and real bulk RNA-seq deconvolution performance differ significantly, and method ranking consistency is lower between pseudobulk and real bulk than within either data type alone

breast real colon tcga paired pseudobulk bulk
Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

PMID 41807578 · PMC13230996 · Molecular systems biology · 2026 · 7 claims · 8 setups

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CSI-TME is a computational pipeline that deconvolves bulk tumor RNA-seq into cell-type-specific expression (via CODEFACS), infers transcriptional states per cell type via ICA, and identifies IC pairs from two cell types whose joint activity is associated with survival via Cox regression

idh-mutant tcga cgga deconvolved scrna-seq bulk independent
A cellular epigenetic classification system for glioblastoma.

PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

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ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

gbm healthy pseudo-bulk tcga illumina single-cell deconvolution
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

PMID 39682743 · PMC11640164 · Cells · 2024 · 8 claims · 5 setups

Has reproduction

Estimated T-cell infiltration differs significantly across melanoma, bladder, ovarian, and pancreatic cancers, tracking known immunogenic potential.

tumor melanoma orien bulk gene kaplan-meier
Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

Has reproduction · 84

A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

tcga-brca triple-negative ffpe bulk univariate kaplan-meier
Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.

PMID 41701761 · PMC12928580 · PLoS computational biology · 2026 · 8 claims · 5 setups

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Driver2Comm is a computational framework that identifies intrinsic-extrinsic (IE) pathways functionally connecting cancer cell driver genes with their associated CCC signatures in the TME using single-cell transcriptomics data.

pdac genes tcga single-cell copy fisher's
scSurv: a deep generative model for single-cell survival analysis.

PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

simulated tcga melanoma renal scrna-seq bulk single-cell
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 8 setups

Has reproduction · 89

SARS-CoV-2 infection induces a strong interferon-driven antiviral response in the nasopharynx, with up-regulation of viral sensors, T cell/NK chemokines, and antiviral effectors

nasopharyngeal airway patient-matched swab shotgun gsea biological
Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

Has reproduction · 70

Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups

Has reproduction · 85

Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs

left eqtl degs merged bulk two-sample functional
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups

Has reproduction · 92

Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.

skeletal merged myogenic muscle scrnaseq batch-correction differential
Digital sorting of complex tissues for cell type-specific gene expression profiles.

PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 85

The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

liver im-9 immune deconvolved microarray simulation roc
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson

Experiments

Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

A cellular epigenetic classification system for glioblastoma.

Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.

scSurv: a deep generative model for single-cell survival analysis.

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.

Digital sorting of complex tissues for cell type-specific gene expression profiles.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.