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 17

System / cell line: real ✕ Assay: cell-type ✕ Clear

Spider: a flexible and unified framework for simulating spatial transcriptomics data.

PMID 41237053 · PMC12790819 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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Spider simulates ST data without requiring real ST data as a reference

simulated hypothalamus dorsolateral spatial clustering cell-cell
DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

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DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

heart cortex visual brain spatial cell-type
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups

Has reproduction · 90

pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics

bulk hek293 single-cell bone prioritized single-cell spike-in
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

mda-mb231 epithelial breast early-stage cdna quantitative facs
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
omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk
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
OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

PMID 41335419 · PMC12766913 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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OTMODE, using an unbalanced Sinkhorn algorithm and Wald test, improves differential feature identification in single-cell multi-omics data

simulated classical degs naive simulated bulk real
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
EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

dbps tfs common ctcf deep comparative feature-ablation
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr
Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

PMID 41503159 · PMC12770975 · NAR genomics and bioinformatics · 2026 · 8 claims · 6 setups

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Eight prominent imputation methods (MAGIC, SAVER, scVI, DCA, scBiG, kNN-smoothing, scImpute, ALRA) were systematically evaluated for their ability to recover the true non-zero expression fraction using simulated and real-world scRNA-seq data

basal tracheal airway k562 simulated scrna-seq imputation
Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

PMID 16895434 · PMC1534073 · PLoS computational biology · 2006 · 8 claims · 7 setups

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The density of transmembrane gene duplicates positively correlates with the estimated maximum number of cell types of common ancestors

transmembrane simulated age duplicate maximum kernel monte
CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

bulk previously round paired transfer-learning cross-species
TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

PMID 40124621 · PMC11929507 · PeerJ · 2025 · 8 claims · 8 setups

Has reproduction · 79

TGF-β signaling pathway activity is significantly increased in fibroblasts from cervical cancer samples compared to normal samples and correlates with tumor proliferation and differentiation.

cervical tcga-cesc hela scrna-seq scrna-seq wgcna cox
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
Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.

PMID 41507908 · PMC12879358 · Lipids in health and disease · 2026 · 8 claims · 8 setups

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Early hepatocyte-specific APA remodeling, characterized by 3' UTR lengthening of metabolism-related genes (especially LPGAT1), occurs in MASLD and is established before fibrosis progression

liver hepg2 293t serum bulk single-cell oil

Experiments

Spider: a flexible and unified framework for simulating spatial transcriptomics data.

DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

Targeted and personalized immunotherapy in lung adenocarcinoma: single-cell RNA sequencing of MAFF+ tumor cells and the therapeutic potential of FOS.

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

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

OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

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

EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

Evaluating imputation methods for accurate estimation of cell population fractions in single-cell RNA sequencing.

Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families.

CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

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

Alternative polyadenylation mediated the downregulation of lysophosphatidylglycerol acyltransferase 1 in metabolic dysfunction-associated steatotic liver disease.