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).
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Has reproduction · 84
AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.
PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups
An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures
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Has reproduction
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.
PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups
A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.
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Has reproduction · 91
Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.
PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 8 claims · 8 setups
CP and PDAC share a co-expression gene network identifiable via WGCNA on independent GEO datasets
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Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups
A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.
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Has reproduction · 40
On the holobiont 'predictome' of immunocompetence in pigs.
PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups
Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall
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Has reproduction · 71
Artificial intelligence-guided discovery of gastric cancer continuum.
PMID 36692601 · PMC9871434 · Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2023 · 8 claims · 8 setups
A Boolean implication network built from GSE66229 yields a GC-BoNE gene signature (Boolean paths C#11-2-4-14 and C#7-13-14) that classifies tumor vs normal/adjacent-normal gastric samples
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Has reproduction · 83
FAM3C/ILEI protein is elevated in psoriatic lesions and triggers psoriasiform hyperproliferation in mice.
PMID 37226685 · PMC10331587 · EMBO molecular medicine · 2023 · 8 claims · 8 setups
ILEI protein, but not mRNA, is elevated in psoriatic skin and correlates with disease severity
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Has reproduction · 63
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.
PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups
Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes
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Has reproduction · 50
The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.
PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.
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Has reproduction · 75
FEM: mining biological meaning from cell level in single-cell RNA sequencing data.
PMID 34909283 · PMC8641482 · PeerJ · 2021 · 8 claims · 5 setups
The FEM algorithm converts a single-cell gene expression matrix into a functional expression matrix using multi-module gene set enrichment analysis, utilizing information from all expressed genes rather than discarding filtered genes.
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Has reproduction · 75
Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.
PMID 41229397 · PMC12604667 · NAR genomics and bioinformatics · 2025 · 8 claims · 4 setups
scIGD is a Snakemake workflow that automates HLA allele-typing and allele-specific expression quantification from scRNA-seq data
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Has reproduction · 78
Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.
PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 8 setups
INVADE-seq (single-cell RNA-seq combined with 16S rRNA targeting) detects a sparse but widespread bacterial presence across diverse testicular cell types
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Has reproduction · 75
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.
PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups
The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival
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Has reproduction · 75
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.
PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 6 setups
geneshot identifies microbial genomic islands consistently associated with ICI response across independent cohorts
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Has reproduction · 76
A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.
PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups
58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date
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Has reproduction · 75
The formation of avian montane diversity across barriers and along elevational gradients.
PMID 35022441 · PMC8755808 · Nature communications · 2022 · 8 claims · 8 setups
Genetic differentiation is generally greater across the oceanic barrier separating Buru and Seram than across the lowland barrier separating New Guinea mountain ranges.
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Has reproduction · 88
Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo.
PMID 35707454 · PMC9178280 · F1000Research · 2021 · 8 claims · 6 setups
A.D.I.C.T. provides a robust, reproducible semi-automated imaging workflow for monitoring antibiotic stress response in bacteria in vivo
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Has reproduction · 93
Extensive transgressive gene expression in testis but not ovary in the homoploid hybrid Italian sparrow.
PMID 35726533 · PMC9542029 · Molecular ecology · 2022 · 7 claims · 8 setups
Italian sparrow testis exhibits extensive transgressive gene expression relative to both parental species
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Has reproduction · 68
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.
PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups
Chronic wound-edge tissue exhibits genome-wide DNA hypermethylation, with hypermethylation more prominent than hypomethylation across differentially methylated regions.
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Has reproduction · 63
Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution.
PMID 35977485 · PMC9644345 · Cell reports · 2022 · 8 claims · 8 setups
Bmp4 treatment instructs ESCs to downregulate pluripotency genes and upregulate genes associated with formative pluripotency and fate specification