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).

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders.

  PMID 41653922 · PMC13034722 · Molecular cell · 2026 · 8 claims · 8 setups

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  Heterozygous de novo missense mutations in RING1 and RNF2 are found in individuals with neurodevelopmental/intellectual disability phenotypes

  cohorts prc1 ring1a elegans variant structural western

• Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.

  PMID 41637188 · PMC12932927 · Cell reports · 2026 · 8 claims · 8 setups

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  Combined MPRA enhancer assays, RNA-seq (DE/ATU) analysis, and CRISPR-Cas9 engineering to dissect the function of 94 rare non-coding variants (RNVs) associated with blood traits

  k-562 chrf-288-11 hl-60 thp-1 massively bulk crispr-cas9

• Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

  PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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  TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

  pbmcs pbmc cd8+ single-cell cell-type expression

• Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

  PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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  Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

  tissues genomic gtex hgmd long-read variant splice

• S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

  PMID 41556263 · PMC13042551 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  S3RL is a separable representation learning framework that denoises sparse spatial transcriptomic data and enhances biologically relevant signals by integrating gene expression, spatial coordinates, and histological image features.

  dorsolateral dlpfc nanostring spatial cell-type multi-platform

• Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex.

  PMID 41803120 · PMC12982666 · Nature communications · 2026 · 7 claims · 4 setups

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  Mainly excitatory cortical neurons are affected by TDP-43 pathology in the ALS/ALS-FTD motor cortex

  post-mortem publicly als single-nucleus single-nucleus spatial genotyping

• Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.

  PMID 42100854 · PMC13229940 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  SCEG-HiC, a weighted graphical lasso (wglasso) method, predicts enhancer-gene links from single-cell multi-omics data by integrating bulk average Hi-C as a prior penalty matrix

  specified covid-19 scatac scatac-seq bulk

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 7 claims · 8 setups

  Has reproduction

  208 novel common blood pressure SNPs and 53 rare variants were discovered in GWASs of SBP, DBP and pulse pressure in up to 776,078 participants from MVP and collaborating studies.

  multi-ethnic mvp tissues kidney genome-wide exome transcriptome-wide

• Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

  PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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  R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

  bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation

• Rare variant analyses provide insights into the genetic architecture of endometriosis.

  PMID 41736152 · PMC13001359 · Human genomics · 2026 · 7 claims · 8 setups

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  Gene-based burden testing of rare LoF and deleterious missense variants identifies SOGA1 as significantly associated with endometriosis after Bonferroni correction

  unrelated finngen biobank soga1 exome gene-based protein-protein

• Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

  PMID 41618434 · PMC12930932 · Genome biology · 2026 · 8 claims · 7 setups

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  PEFT enables accurate transfer of Borzoi to new datasets while significantly reducing GPU memory and runtime compared to joint training or full fine-tuning

  gtex encode wi-38 thp-1 bulk eqtl variant-flowfish

• 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

• 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

• Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.

  PMID 41691315 · PMC12927254 · Genome medicine · 2026 · 8 claims · 8 setups

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  Tumor purity-adjusted DNA methylation profiling of 95 primary LUAD samples identifies four distinct epigenetic subtypes (epitypes M1-M4)

  luad methylation sequencing targeted

• Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB.

  PMID 41505470 · PMC12810902 · PLoS genetics · 2026 · 8 claims · 6 setups

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  1,25D treatment induces widespread transcriptional and chromatin accessibility changes in colonic organoids

  colonic bulk atac-seq gene

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

  ectopic geo gse5108 training microarray wgcna machine

• RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

  PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

  airway asm most single rna-seq quantitative qrt-pcr

• OptiSyn: an interpretable, multi-omics-driven graph convolutional network framework for synergy-oriented drug combination design in disease treatment.

  PMID 41877167 · PMC13011277 · Chinese medicine · 2026 · 8 claims · 8 setups

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  Eight AS-associated hub genes were identified through integration of multi-omics datasets (DEG analysis, WGCNA, scRNA-seq, Mendelian randomization, PPI module analysis)

  gtex as-associated tcm representative differential weighted single-cell

• SMART: spatial multi-omic aggregation using graph neural networks and metric learning.

  PMID 41896208 · PMC13031631 · Nature communications · 2026 · 8 claims · 5 setups

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  SMART accurately identifies spatial regions of anatomical structures and is compatible with spatial datasets of any type and number of omics layers

  simulated lymph brain spleen simulated spatial multi-section