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).

• 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

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  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

• PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells.

  PMID 41565684 · PMC12881479 · Nature communications · 2026 · 8 claims · 8 setups

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  PURE-seq integrates FACS sorting directly into PIP-seq barcoding reaction tubes, minimizing manual handling and cell loss for rare-cell single-cell sequencing.

  hek293t pbmcs melanoma bone single-cell infercnv gene

• Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

  PMID 41587266 · PMC13011956 · The Journal of bone and joint surgery. American volume · 2026 · 8 claims · 5 setups

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  ACL tissue is heterogeneous, containing 5 major cell types: fibroblasts, pericytes, endothelial cells, macrophages, and T cells.

  acl differentially study flow single-cell immunofluorescence

• BayesRare: Bayesian mixture model for population-level rare cell type detection in multi-subject single-cell RNA sequencing data.

  PMID 41632592 · PMC12867491 · Briefings in bioinformatics · 2026 · 8 claims · 4 setups

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  BayesRare is a hierarchical Bayesian mixture model framework for population-level rare cell type detection in multi-subject scRNA-seq data

  synthetic breast kidney parkinson's scrna-seq

• A multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.

  PMID 41640425 · PMC12864441 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  The TIs-ML multi-omics model predicts ICB response/survival in ccRCC with superior accuracy (AUC > 0.997) compared to single biomarkers like PD-L1 and TMB

  autoimmune igan scrna-seq bulk bulk scrna-seq scissor-based

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

  PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

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  OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

  tcga-luad geo lung single-cell bulk ssgsea cibersort

• Predictive modeling of molecular activity underlying physical cell-cell interactions.

  PMID 41672069 · PMC12946745 · Cell reports methods · 2026 · 8 claims · 5 setups

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  Gloss, an overlapping group lasso regression combining single-gene and curated pathway features, predicts LIPSTIC interaction intensity from scRNA-seq data

  tumor intestine mediastinal organs lipsticv1 ulipstic cite-seq

• RMzyme: regulations of RNA-modifying enzymes in humans.

  PMID 41672979 · PMC12895048 · Signal transduction and targeted therapy · 2026 · 8 claims · 7 setups

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  RMzyme is a comprehensive multiomics knowledgebase covering 179 human RNA-modifying proteins across 18 major RNA modification types and 63 human tissues

  nomo1 molm13 tissues cptac merip-seq bulk single-cell

• Increased IL4I1 expression predicts poor survival and modulates the immune microenvironment in acute myeloid leukemia.

  PMID 41680858 · PMC12910993 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  IL4I1 mRNA expression is significantly elevated in AML compared to normal controls

  tcga-laml bone thp-1-derived thp-1 bulk kaplan-meier deg

• Context-specific regulatory genetic variation in MTOR dampens neutrophil-T cell crosstalk in pneumonia-associated sepsis.

  PMID 41741465 · PMC13057173 · Nature communications · 2026 · 8 claims · 7 setups

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  The MTOR eQTL variant rs4845987 has context-specific, opposite effects on MTOR expression: decreasing it in activated T cells and increasing it in neutrophils.

  blood bulk eqtl sepsis bulk cell-type colocalisation

• Colonic Engyodontium fungus triggers neutrophil antimicrobial activity to suppress Lactobacillus johnsonii-derived glutamic acid-maintained Tregs.

  PMID 41770903 · PMC13078882 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  A commensal Ascomycota fungus, Engyodontium sp., was isolated live from mouse feces using a Dectin-2-Fc fusion protein

  feces colonic colon ncm460 its flow qpcr

• Integrative omics and experimental validation reveal METTL17 and SLC27A1 as biomarkers and potential therapeutic targets in chronic kidney disease.

  PMID 41766913 · PMC12946038 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  METTL17 and SLC27A1 are identified as consistently dysregulated key genes bridging mitochondrial dysfunction and macrophage polarization in CKD

  kidney peripheral uuo bulk single-cell cibersort

• Targeting the Lipid Metabolism Proteins FASN and GPAM in Alveolar Type II Cells Decreases Lung Metastasis.

  PMID 41778850 · PMC7619144 · Cancer discovery · 2026 · 7 claims · 8 setups

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  AT2 cells and surfactant lipids (e.g., PC, PE, PI, PG) are enriched in the vicinity of breast cancer lung metastases in both patients and mice

  postmortem lungs lung at2 immunohistochemistry maldi-msi longitudinal

• The complement system contributes to the immunosuppressive microenvironment of uveal melanoma.

  PMID 41803879 · PMC13130498 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Primary UM (pUM) preferentially expresses early complement pathway components over terminal membrane attack complex elements, with early factors showing prognostic significance.

  short-term metastatic normal pum bulk label-free single-cell

• CDK4/6 inhibition mitigates chemotherapy-induced expansion of TP53-mutant clonal hematopoiesis.

  PMID 41814002 · PMC12987733 · Nature genetics · 2026 · 7 claims · 6 setups

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  Trilaciclib reduces chemotherapy-induced expansion of DDR-gene (TP53, PPM1D, CHEK2) clonal hematopoiesis across four randomized clinical trials and diverse chemotherapy regimens

  peripheral c57bl bone deep competitive flow

• How bacterial communities expand functional repertoires.

  PMID 17238278 · PMC1750926 · PLoS biology · 2006 · 8 claims · 7 setups

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  The human microbiome contains roughly 100 times as many genes as does the human genome

  bacteroides distal interleukin-10-deficient macrophages transcriptional metagenomic microbiota

• Nitric oxide and redox regulation in the liver: part II. Redox biology in pathologic hepatocytes and implications for intervention.

  PMID 20400112 · PMC2907433 · The Journal of surgical research · 2011 · 8 claims · 8 setups

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  ROS/RNS generated during hepatic ischemia/reperfusion cause cellular damage via mitochondrial dysfunction, ATP depletion, ion disturbances, and membrane/lysosomal disruption

  inos enos enos-overexpressing orthotopic genetic transgenic clinical

• Infrequent involvement of p53 gene mutations in the tumourigenesis of Japanese prostate cancer.

  PMID 7691145 · PMC1968625 · British journal of cancer · 1993 · 6 claims · 3 setups

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  p53 gene mutations are infrequent in the tumorigenesis of primary Japanese prostate cancer

  prostate pcr-sscp sequencing

• [Research progress in SELDI-TOF MS and its clinical applications].

  PMID 17168305 · PMC7148935 · Sheng wu gong cheng xue bao = Chinese journal of biotechnology · 2006 · 4 claims · 4 setups

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  Proteinchip profiling based on SELDI-TOF MS is a powerful and innovative proteomic technology for biomarker discovery and diagnostic/prognostic assay development.

  malignancies infectious neurological diabetic seldi-tof