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).

• Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.

  PMID 41714655 · PMC13039149 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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  scRNA-seq and spatial transcriptomics data provide a rich, underused source of information for calibrating tissue-scale PDE models of ligand dynamics.

  skin combined annotated scrna-seq single-cell spatial cell2location

• UBD: incorporating uncertainty in cell type proportion estimates from bulk samples to infer cell-type-specific profiles.

  PMID 41520227 · PMC12895075 · Briefings in bioinformatics · 2026 · 7 claims · 4 setups

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  Existing CTS deconvolution methods (e.g., CIBERSORTx, TCA, bMIND, CellDMC, HBI) require cell type proportions that are in practice only estimated, not known, introducing unaccounted uncertainty into CTS inference.

  simulated rosmap onek1k bulk simulation-based cell-type-specific type

• scGeno: a Hidden Markov Model approach to denoise chromosome-scale genotypes from single-cell data.

  PMID 41982479 · PMC13075984 · Bioinformatics advances · 2026 · 7 claims · 4 setups

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  scGeno, a categorical HMM, infers chromosome-level genotype states in mixed-genotype organisms by modeling sequential single-cell allelic expression ratios along chromosomes

  wild-type dnmt1 synthetic embryo single-cell posterior down-sampling

• Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

  PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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  Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

  archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence

• Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

  PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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  Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

  g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• Oncogenic mutations in GNAQ occur early in uveal melanoma.

  PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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  Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

  uveal peripheral normal well-characterized pcr sequencing array-based

• 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

• Integration of aged brain multi-omics reveals cross-system mechanisms underlying Alzheimer's disease heterogeneity.

  PMID 41950003 · PMC13244359 · Cell reports · 2026 · 8 claims · 7 setups

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  Multi-omics factor analysis (MOFA) integrating seven omics views from 1,358 ROS/MAP participants identifies cross-omics biological factors relating to AD phenotypes.

  dorsolateral brain postmortem cortex h3k9ac bulk proteomics

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

  PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

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  The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

  skin cloned mixed-type gene nested sequencing molecular

• Cross-ancestry genome-wide association studies of liver function biomarkers uncover pleiotropic variants, systemic disease links and therapeutic targets.

  PMID 41689074 · PMC13005531 · Genome medicine · 2026 · 8 claims · 8 setups

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  5,507 lead signals (P<5x10^-9) were identified for seven LFQBs across ancestries, including 210 novel loci

  hope biobank combined cross-ancestry gwas cross-ancestry functional-informed

• SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

  PMID 41726128 · PMC12917586 · Open medicine (Warsaw, Poland) · 2026 · 8 claims · 8 setups

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  SLC25A37 is causally associated with increased BPH risk, supported by MR, Bayesian colocalization, and reverse MR analyses

  prostate gwas eqtl bph single-cell mendelian bayesian

• 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

• Estimating in silico causal effects of DNA methylation on gene expression through genetic anchors in airway epithelium in asthma.

  PMID 42018614 · PMC13101850 · Science advances · 2026 · 8 claims · 8 setups

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  DNA methylation is a plausible causal driver of gene expression in the majority (73%) of tested eQTM pairs, more often than the reverse direction (28%)

  nasal genes snps types eqtm eqtl causal

• Genetic evidence supporting obesity as a risk factor for lung squamous cell carcinoma and the identification of MFAP1 as a shared genetic target.

  PMID 41820721 · PMC13096280 · Discover oncology · 2026 · 8 claims · 8 setups

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  BMI and LUSC show a significant positive genome-wide genetic correlation, robust to constrained-intercept sensitivity analysis and replicated by GNOVA.

  gwas gtex scrna-seq ldsc gnova ρ-hess

• Lineage specific recombination rates and microevolution in Listeria monocytogenes.

  PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Recombination is more prevalent in lineage II than in lineage I

  listeria allelic unique monocytogenes multilocus sawyer's genealogical

• Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.

  PMID 41852645 · PMC12993812 · PNAS nexus · 2026 · 8 claims · 8 setups

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  The Tokara Islands population is a cryptic species new to science, morphologically similar to but genetically distinct from Ijima's Leaf Warbler on the Izu Islands

  museum ijimae phylloscopidae genome-wide morphometric bioacoustic whole-genome

• 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

• A causal glycerophospholipid-IL-18R1-CD9 axis connects lipid metabolism and T-cell activation in atopic dermatitis.

  PMID 42061907 · PMC13132603 · Briefings in bioinformatics · 2026 · 7 claims · 8 setups

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  1-palmitoyl-2-arachidonoyl-GPC (PA-GPC) is a protective metabolite against AD that acts primarily by downregulating IL-18R1

  gwas skin training keratinocyte linkage two-sample bayesian