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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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
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
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Glioblastoma stem cells show transcriptionally correlated spatial organization.
PMID 41577992 · PMC12894897 · Communications biology · 2026 · 8 claims · 5 setups
GSCs from different patient samples exhibit diverse, characteristic multicellular spatial patterns in culture (e.g., anisotropic vs isotropic packing, overlapping vs non-overlapping space utilization)
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Leveraging the germ layer development patterns to predict prognosis and identify MEST as a novel therapeutic target in glioma.
PMID 41501725 · PMC12870398 · Cancer cell international · 2026 · 7 claims · 8 setups
MEST is a key oncogenic GLD-related gene and a novel therapeutic target in glioma, identified via a machine learning feature selection framework
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Gene expression profiling identifies potential biomarkers for vaso-occlusive episodes in sickle cell disease.
PMID 41797711 · PMC13041688 · JCI insight · 2026 · 8 claims · 5 setups
Pathways linked to complement activation, coagulation, and IL-6/JAK/STAT3 signaling are enriched during VOEs in CD45+ leukocytes
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Has reproduction · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.
PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups
Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups
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Has reproduction · 73
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.
PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups
Mitophagy affects tumour development, immune cell infiltration, and prognosis in HPV-associated HNSCC
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Identification and validation of prognostic genes associated with M2 macrophage and heme metabolism in lung adenocarcinoma through bulk and single-cell RNA sequencing analysis.
PMID 41787185 · PMC13076703 · Discover oncology · 2026 · 8 claims · 8 setups
EPB41, ACP5, PPOX, RBM38, and TRIM58 were identified as prognostic genes for LUAD
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 71
Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.
PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups
Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments
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Has reproduction · 88
Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.
PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups
CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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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
HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts
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An integrated single-cell lung cancer atlas reveals distinct fibroblast phenotypes between adenocarcinoma and squamous cell carcinomas.
PMID 41577803 · PMC12920623 · NPJ precision oncology · 2026 · 8 claims · 8 setups
Inflammatory CAFs (iCAFs) predominate in LUAD, whereas myofibroblastic CAFs (mCAFs) predominate in LUSC
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Humoral IgG1 responses to tumor antigens underpin clinical outcomes in immune checkpoint blockade.
PMID 41593194 · PMC13004670 · Nature medicine · 2026 · 8 claims · 5 setups
PD-1 blockade induces tumor-specific IgG1+ plasma cell responses that complement cellular immunity and contribute to clinical benefit
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Transcriptome-based high-frequency recurrence index predicts frequent recurrence in non-muscle-invasive bladder cancer after Bacillus Calmette-Guérin therapy.
PMID 41749284 · PMC13040970 · BMC medicine · 2026 · 8 claims · 7 setups
A 75-gene HfRI signature predicts high-frequency recurrence (≥2 recurrences) in NMIBC patients
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Identification of Poor Prognosis-Associated Fibroblast Subpopulation Signature Genes Utilizing the Scissor Algorithm to Classify Colorectal Cancer Subtypes and Evaluate the Immune Landscape.
PMID 41787974 · PMC13180509 · Gut and liver · 2026 · 8 claims · 8 setups
Scissor+ fibroblast subpopulations significantly correlated with prognosis were identified in CRC using the Scissor algorithm integrating scRNA-seq, bulk RNA-seq, and clinical data
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Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.
PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups
SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival
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Single-cell dissection of regulated cell death dynamics in ovarian aging.
PMID 41689119 · PMC13005338 · Journal of ovarian research · 2026 · 8 claims · 8 setups
The RCD landscape of ovarian aging had not previously been characterized at single-cell resolution
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Has reproduction · 61
Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data.
PMID 33575569 · PMC7671354 · NAR genomics and bioinformatics · 2020 · 8 claims · 5 setups
Omics Playground is a user-friendly, interactive self-service platform for in-depth analysis, visualization, and interpretation of transcriptomics and proteomics data, including single-cell RNA-seq.