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).

• A pan-cancer single-cell transcriptomic atlas of human bone metastases.

  PMID 41619722 · PMC12923970 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Constructed a pan-cancer single-cell transcriptomic atlas of 62 human bone metastases (predominantly spinal) across 13 primary cancer types, with paired primary tumor and normal bone marrow samples.

  bone paired plasmacytoma malignant scrna-seq ihc infercnv

• Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models.

  PMID 34858485 · PMC8631472 · Frontiers in genetics · 2021 · 8 claims · 5 setups

  Has reproduction · 62

  A DNN model built on 34 top-ranked hub genes achieves the highest prediction accuracy (AUC 92.11%) for distinguishing primary from bone-metastasized tumors

  breast degs geo tcga microarray protein-protein machine

• Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

  PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

  Full-text index only

  A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

  gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

• A genome wide linkage scan of metacarpal size and geometry in the Framingham Study.

  PMID 18449921 · PMC2574919 · American journal of human biology : the official journal of the Human Biology Council · 2008 · 8 claims · 4 setups

  Full-text index only

  Metacarpal geometric indices (length, midshaft width, MCT, MCI, MZ) show significant heritability, ranging from 0.51 (MCT) to 0.82 (length)

  hand individuals same radiogrammetry genome-wide variance

• Aged murine bone marrow myeloid and mesenchymal cells develop unique senescence phenotypes.

  PMID 41592025 · PMC13038201 · The Journal of clinical investigation · 2026 · 7 claims · 8 setups

  Full-text index only

  Myeloid-lineage cells (monocytes, macrophages, myeloid progenitors) show the highest expression of p16 and SASP markers among bone marrow immune cell types in aged mice

  bone femur skeletal single-cell mass cytof

• Multiomics combined drugs to explore the potential mechanism and treatment of ankylosing spondylitis.

  PMID 41673882 · PMC13047816 · Journal of orthopaedic surgery and research · 2026 · 8 claims · 8 setups

  Full-text index only

  Effector CD8+ memory T (Tem) cells are significantly elevated in AS patients compared to healthy controls

  bone peripheral effector interspinous single-cell cibersortx cell-cell

• Spatially resolved osteoblast-traced transcriptomics uncovers TGF-β as a combination target with sclerostin in osteoporosis.

  PMID 41927532 · PMC13046724 · Bone research · 2026 · 8 claims · 8 setups

  Full-text index only

  Spatially resolved osteoblast-traced transcriptomics (lineage tracing + SLACS) identifies TGF-β signaling as a regulator of osteoblast activation state on quiescent bone surfaces

  dmp1-creert2 gfp+ spatial mc3t3-e1 spatially cell-type gsea

• 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

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• Systematic background selection with BasCoD enhances contrastive dimension reduction in single cell genomics.

  PMID 41844632 · PMC13144610 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  BasCoD is a statistical testing framework using spectral subspace inclusion theory to evaluate whether a candidate background dataset is suitable for contrastive dimension reduction of a target dataset

  ts65dn ipscs k562 intestinal contrastive population-scale perturb-seq

• Non-linear mapping for exploratory data analysis in functional genomics.

  PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.

  leukaemia small srbct brain relaxation self-organising sammon's

• ChemR23 prevents phenotypic switching of vascular smooth muscle cells into macrophage-like foam cells in atherosclerosis.

  PMID 41264461 · PMC13017563 · Cardiovascular research · 2026 · 8 claims · 7 setups

  Full-text index only

  Non-haematopoietic (vascular) ChemR23 deficiency increases atherosclerotic lesion size and enhances VSMC proliferation and VSMC-derived foam cell formation

  apoe adventitia-stripped advanced aortic atherosclerotic bulk single-cell

• Immuno-metabolic dysregulation in type 2 diabetes is associated with altered neutrophil functional plasticity, mitochondrial dysfunction, and compromised responses in sepsis.

  PMID 41520116 · PMC12882159 · Journal of translational medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  Proportions of functionally restricted neutrophil subpopulations (phagocytosis-only vs NETosis-only) are significantly altered in T2D and fail to elicit an immune response upon sepsis induction

  peripheral bone plasma neutrophils flow bulk global

• The functional landscape of alternative splicing in hematopoietic lineage commitment.

  PMID 41593078 · PMC12946277 · Nature communications · 2026 · 7 claims · 8 setups

  Full-text index only

  FAScore, a Random Forest model integrating 19 dynamic, structural, and conservation features, predicts functional exon-skipping AS events with high accuracy in a species- and lineage-specific manner.

  umbilical bone fetal zebrafish bulk machine exon

• A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

  PMID 30833571 · PMC6399342 · Nature communications · 2019 · 6 claims · 8 setups

  Has reproduction · 90

  A GWAS of 12,312 CTS cases and 389,344 controls in UK Biobank identifies 16 novel genome-wide significant susceptibility loci for CTS

  biobank surgically gwas transformed genome-wide sequencing gene-based

• Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.

  PMID 41253754 · PMC12627582 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 10

  Gli1+ fetal cells are the precursors of postnatal long-lived chondroprogenitors (LLCPs) in the growth plate

  fetal left-cart-p21 gli1-creer cartilage single-nuclei scenic bulk

• Understanding sex differences in environmental health: a thought leaders' roundtable.

  PMID 15064168 · PMC1241928 · Environmental health perspectives · 2004 · 8 claims · 8 setups

  Full-text index only

  Dioxin and corticosteroids both cause thymic atrophy but via distinct mechanisms; dioxin's atrophy kinetics resemble those induced by estrogen despite acting through a different receptor.

  laboratory mice nzb c57bl thymus radiation autoimmune

• MafB is a conserved transcriptional regulator of macrophage development and functional identity across tissues and species.

  PMID 41759510 · PMC7618887 · Immunity · 2026 · 8 claims · 8 setups

  Full-text index only

  MafB is required for full differentiation of bone-marrow-derived macrophages (BMDMs) in vitro and for development of most RTMs in vivo

  bmdms peritoneal rtms irradiated bulk hashtag-barcoded intracellular

• Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.

  PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 7 setups

  Has reproduction

  CD4+ T cells and B cells independently and significantly contribute to MS GWAS heritability enrichment, distinct from a merely shared immune regulatory landscape.

  flow-sorted cd4+ hematopoietic gwas bulk atac-seq stratified

• Malarial hemozoin activates the NLRP3 inflammasome through Lyn and Syk kinases.

  PMID 19696895 · PMC2722371 · PLoS pathogens · 2009 · 7 claims · 8 setups

  Full-text index only

  Hemozoin induces IL-1β maturation and secretion in an NLRP3-, ASC- and caspase-1-dependent, but NLRC4-independent, manner

  pma-differentiated bone-marrow-derived asc nlrp3 elisa western peritoneal

• The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

  PMID 41625479 · PMC12857760 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  Neutrophils in the lung metastatic niche comprise two functionally distinct subsets, Ly6g^high and Ly6g^low, based on Ly6g expression level

  lung cramp cd8+ neutrophils single-cell flow genetic