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 258

System / cell line: protein-protein ✕ Clear

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

PMID 19917080 · PMC2784802 · BMC genomics · 2009 · 8 claims · 4 setups

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Genome-wide deletion screening identified 149 genes whose deletion causes NiSO4 sensitivity and 119 genes whose deletion confers NiSO4 resistance.

cerevisiae lists yeast genome-wide functional protein-protein
Structural genomics and drug discovery for infectious diseases.

PMID 19860716 · PMC2789569 · Infectious disorders drug targets · 2009 · 7 claims · 4 setups

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CSGID applies high-throughput X-ray crystallography structural genomics to NIAID category A-C pathogen proteins to enable structure-aided drug discovery, with a goal of 400 protein/protein-ligand structures

selenomethionine-substituted recombinant genes x-ray high-throughput purification
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

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A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

platelets platelet anti-coagulated lc-ms phospho-proteomic membrane
Research Spotlight: New multiparameter bioanalytical technologies for applications in personalized medicine, drug discovery and fundamental biology.

PMID 21083072 · PMC3106349 · Bioanalysis · 2009 · 8 claims · 8 setups

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High-density arrays of silicon photonic microring resonators enable label-free, multiplexed detection of DNA, miRNA, and protein biomarkers from a single small-volume sample

silicon undiluted model label-free multiplexed cytokine
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

hela candidate screen genome-wide propidium sirna
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

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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
Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

PMID 38987624 · PMC11236978 · Scientific reports · 2024 · 6 claims · 8 setups

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Four hub genes (E2F1, GATA3, HDAC5, MSH2) serve as diagnostic biomarkers for VTE in BD with high accuracy (AUC 0.816)

peripheral degs candidate microarray weighted protein–protein
Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups

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MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways

left mus combined heart microarray weighted bulk
Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups

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90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

abdominal gingival overlapping interacting microarray weighted kegg
Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

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Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

bimaculatus prothoracic differentially gbig rna-seq genome differential
ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

PMID 41592570 · PMC13069865 · Cell genomics · 2026 · 8 claims · 7 setups

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ChromBERT is pre-trained via masked reconstruction on the Cistrome-Human-6K dataset (6,391 cistromes, 991 transcription regulators) to learn genome-wide interaction syntax of transcription regulators

lines chromosome embryonic transcription chip-seq chromhmm hi-c
ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

PMID 41639695 · PMC12958617 · BMC medicine · 2026 · 8 claims · 8 setups

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CSC proportion is elevated in lymph node metastatic tumor tissue (BRCA_LNMT) compared to primary tumor (BRCA_PT)

4t1 brca tcga-brca top single-cell spatial bulk
An NSP2-MYB module orchestrates flavonoid biosynthesis and nodule symbiosis.

PMID 41643674 · PMC7619063 · Current biology : CB · 2026 · 8 claims · 8 setups

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NSP1 and NSP2 promote expression of flavonoid biosynthesis genes during nutrient starvation and rhizobial symbiosis in Medicago truncatula

medicago nicotiana recombinant yeast rna-seq qpcr targeted
Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

PMID 41699006 · PMC13002898 · Scientific reports · 2026 · 8 claims · 8 setups

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CDC20, PLK1, BUB1, CDC45, and CDCA5 are concordantly identified as hub genes across seven NCBI-GEO datasets and the Pakistani RNA-seq dataset

pakistani pdac overlapping tcga-paad bulk functional protein-protein
Unravelling Synaptic and Metabolic Mechanisms of Cognitive Resilience in Asymptomatic Alzheimer's Disease Across Two Alzheimer's Disease Cohorts.

PMID 41723778 · PMC12996523 · Cellular and molecular neurobiology · 2026 · 6 claims · 6 setups

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Integrating DEG, DET, and DUT analyses (rather than DEGs alone) provides a more comprehensive view of the molecular mechanisms of AsymAD, since some genes/transcripts are only detected by transcript-level methods.

postmortem combined ppi hippocampus bulk functional protein-protein
Rare variant analyses provide insights into the genetic architecture of endometriosis.

PMID 41736152 · PMC13001359 · Human genomics · 2026 · 7 claims · 8 setups

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Gene-based burden testing of rare LoF and deleterious missense variants identifies SOGA1 as significantly associated with endometriosis after Bonferroni correction

unrelated finngen biobank soga1 exome gene-based protein-protein
Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

PMID 41808025 · PMC13085422 · BMC genomics · 2026 · 8 claims · 7 setups

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E2 exposure induces male-to-female gonadal sex reversal in CGS, confirmed by histological evidence across developmental stages.

gonadal tail-tip deg candidate rna-seq histology rt-qpcr
OptiSyn: an interpretable, multi-omics-driven graph convolutional network framework for synergy-oriented drug combination design in disease treatment.

PMID 41877167 · PMC13011277 · Chinese medicine · 2026 · 8 claims · 8 setups

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Eight AS-associated hub genes were identified through integration of multi-omics datasets (DEG analysis, WGCNA, scRNA-seq, Mendelian randomization, PPI module analysis)

gtex as-associated tcm representative differential weighted single-cell
GRNFormer: accurate gene regulatory network inference using graph transformer.

PMID 41883144 · PMC13069479 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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GRNFormer is a generalizable graph transformer framework for GRN inference from single-cell or bulk transcriptomics data across species, cell types, and platforms without cell-type annotations or prior regulatory information

hematopoietic embryonic dendritic hepatocytes scrna-seq chip-seq string
Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.

PMID 41942785 · PMC13053443 · Journal of molecular medicine (Berlin, Germany) · 2026 · 8 claims · 8 setups

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A PDAC-enriched myoCAF-c1 fibroblast cluster is closely associated with epithelial-mesenchymal transition (EMT) and angiogenesis

pdac myocaf-c1-derived tcga-paad scrna-seq spatial bulk

Experiments

A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

Structural genomics and drug discovery for infectious diseases.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

Research Spotlight: New multiparameter bioanalytical technologies for applications in personalized medicine, drug discovery and fundamental biology.

A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

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

Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

ChromBERT: A foundation model for learning interpretable representations for context-specific transcriptional regulatory networks.

ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

An NSP2-MYB module orchestrates flavonoid biosynthesis and nodule symbiosis.

Dysregulated expression of cell cycle regulators CDC20, PLK1, BUB1, CDC45, CDCA5 in pancreatic ductal adenocarcinoma.

Unravelling Synaptic and Metabolic Mechanisms of Cognitive Resilience in Asymptomatic Alzheimer's Disease Across Two Alzheimer's Disease Cohorts.

Rare variant analyses provide insights into the genetic architecture of endometriosis.

Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

OptiSyn: an interpretable, multi-omics-driven graph convolutional network framework for synergy-oriented drug combination design in disease treatment.

GRNFormer: accurate gene regulatory network inference using graph transformer.

Integrative multimodal transcriptomics identifies a cancer-associated fibroblast membrane signature for predicting prognosis and therapeutic response in pancreatic ductal adenocarcinoma.