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 324

System / cell line: enriched ✕ Clear

Methods for the proteomic identification of protease substrates.

PMID 19729334 · PMC2787889 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

Full-text index only

Gel-based methods (2D-DiGE, diagonal electrophoresis, PROTOMAP) identify protease substrates by comparing proteolyzed versus control samples via electrophoretic migration differences followed by MS identification

lysate jurkat apoptotic yeast 2d-dige protomap cofradic
Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

Full-text index only

The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

pbmcs blood apoe genes microarray rt-qpcr elisa
Comparative transcriptome analysis of two pomelo accessions with different parthenocarpic ability provides insight into the molecular mechanisms of parthenocarpy in pomelo (Citrus grandis).

PMID 39135650 · PMC11317442 · Frontiers in plant science · 2024 · 6 claims · 6 setups

Full-text index only

G pomelo exhibits significantly higher parthenocarpic ability (ovary growth, cell division, fruit setting) than S pomelo following emasculation

pomelo ripe degs morphological phytohormone fruit
Identification of Molecular Subtypes of Clear-Cell Renal Cell Carcinoma in Patient-Derived Xenografts Using Multi-Omics.

PMID 40282537 · PMC12026142 · Cancers · 2025 · 8 claims · 7 setups

Full-text index only

Each ccRCC PDX resembles one of the human molecular subtypes closely at both the transcript and protein levels.

ccrcc differentially bulk lc-ms targeted
Cycloheximide-resistant ribosomes reveal adaptive translation dynamics in C. elegans.

PMID 40929375 · PMC12477835 · Genetics · 2026 · 8 claims · 8 setups

Full-text index only

A P55Q substitution in ribosomal protein RPL-36A confers strong resistance to cycloheximide in C. elegans

elegans crispr-cas9 larval rna-seq
RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

PMID 41222189 · PMC12857227 · GigaScience · 2026 · 8 claims · 8 setups

Full-text index only

RNA-SeqEZPZ is the first open-source tool offering a point-and-click interface with interactive plots, spanning raw FASTQ reads through differential gene and pathway analysis.

generic paired-end aligned gene bulk adapter read
Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

PMID 41563441 · PMC13007207 · Diabetes · 2026 · 8 claims · 7 setups

Full-text index only

5′ single-cell library preparation protocols outperform 3′ protocols for transcript identification and read length

lines pancreatic spleen dtc single-cell bulk ngs
Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

PMID 41832957 · PMC13137218 · Cell reports · 2026 · 8 claims · 8 setups

Full-text index only

Generated a single-nucleus multiome (snATAC + gene expression) dataset from 357 human dorsolateral prefrontal cortex samples (ages 15-100, European and African admixed ancestry), yielding over 1.5 million cells as a public resource.

postmortem million+ pfc each single-nucleus umap pseudobulk
DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

Full-text index only

Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

validation cns healthy genes methylation copy-number gene-set
Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code.

PMID 42206359 · PMC13216745 · Nucleic acids research · 2026 · 8 claims · 8 setups

Full-text index only

High GAF occupancy is required for chromatin looping and gene regulation at PREs

drosophila third gaf dac_tss cut&run micro-c hi-c
TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

Full-text index only

TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated
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

Full-text index only

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
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

Full-text index only

A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime
Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

PMID 41507195 · PMC12881518 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

A multi-omics strategy combined with TWAS reveals brain-region-specific molecular signatures and striking gene dysregulation concentrated in inhibitory neurons in an FXTAS mouse model.

brain prefrontal pfc gabaergic bulk single-nuclei immunofluorescent
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

Full-text index only

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
Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

PMID 41528819 · PMC12958807 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

Full-text index only

Differential gene expression caused by disruption of daf-2/InsR during L1 starvation is daf-16-dependent.

elegans bulk principal hierarchical
Integrating human plasma proteomes with genome-wide association data implicates novel proteins and drug targets for rheumatoid arthritis.

PMID 41540382 · PMC12892679 · Clinical proteomics · 2026 · 8 claims · 8 setups

Full-text index only

PWAS integrating RA GWAS with ARIC and INTERVAL plasma pQTL data identified 35 genetically regulated proteins (42 associations) significantly associated with RA risk.

plasma shared gtex blood proteome-wide two-sample bayesian
Temporal multiomics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation.

PMID 41545424 · PMC12920657 · Scientific data · 2026 · 8 claims · 8 setups

Full-text index only

Generated a high-resolution, time-resolved multi-omics dataset (RNA-seq, ribosome profiling, and quantitative proteomics) tracking mRNA, translation, and protein dynamics across hESC differentiation into definitive endoderm and polyhormonal pancreatic cells

hesc-derived rues2 extracted star-aligned rna-seq ribosome quantitative
pmid-41619802

PMID 41619802 · PMC12908066 · 8 claims · 7 setups

Full-text index only

Heat shock, HSP90 inhibition, and polyQ aggregation launch fundamentally distinct RNA expression programs rather than a shared stress response.

muscle q175 striatum gene bulk enrichr principal
Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

Has reproduction · 64

Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

Experiments

Methods for the proteomic identification of protease substrates.

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

Comparative transcriptome analysis of two pomelo accessions with different parthenocarpic ability provides insight into the molecular mechanisms of parthenocarpy in pomelo (Citrus grandis).

Identification of Molecular Subtypes of Clear-Cell Renal Cell Carcinoma in Patient-Derived Xenografts Using Multi-Omics.

Cycloheximide-resistant ribosomes reveal adaptive translation dynamics in C. elegans.

RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.

DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code.

TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

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

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

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

Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

Integrating human plasma proteomes with genome-wide association data implicates novel proteins and drug targets for rheumatoid arthritis.

Temporal multiomics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation.

pmid-41619802

Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.