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).

• ERG phase separation attenuates cellular senescence.

  PMID 41704762 · PMC12907116 · iScience · 2026 · 8 claims · 6 setups

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  Centenarian PBMCs exhibit a distinct, more functionally engaged chromatin accessibility landscape compared to controls and typical elderly individuals

  pbmcs atac-seq rna-seq cibersortx

• Epigenetic regulation of serine biosynthesis by PHF8 during neurogenesis.

  PMID 41714361 · PMC13022353 · EMBO reports · 2026 · 8 claims · 8 setups

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  PHF8 is required for neural stem cell (NSC) proliferation in vitro

  developing nscs embryonic single-cell shrna growth

• Multimodal learning reveals plants' hidden sensory integration logic.

  PMID 41714925 · PMC13032346 · BMC genomics · 2026 · 8 claims · 8 setups

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  CoMM-BIP (Contrastive Multi-Modal learning with Biologically Informed Priors) integrates transcriptomic, metabolomic, and phenomic data using pathway-guided attention, information-theoretic disentanglement, and domain-aware augmentations

  tomato multimodal transcriptomics metabolomics

• Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

  PMID 41715179 · PMC13020291 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Glutamine secretion from M2 macrophages to tumor cells via SLC38A5 is the core mCCC pathway upregulated in metastatic OSCC lesions compared to primary lesions.

  oscc epithelial tcga-oscc hsc-3 scrna-seq hdwgcna bulk

• Bromodomain protein IBD1 bridges histone acetylation and H2A.Z deposition to fine-tune transcription.

  PMID 41728948 · PMC12926916 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  IBD1's bromodomain recognizes H3K9/K14 di-acetylation to recruit the SWR complex subunit ARP6, ensuring precise H2A.Z incorporation into chromatin

  tetrahymena recombinant native cut&tag sequencing

• Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

  PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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  The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

  tcga-brca senescent normal single-cell machine univariate gene

• 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

• CD38 expression by neonatal human naive CD4+ T cells shapes their distinct metabolic and tolerogenic properties.

  PMID 41746743 · PMC13078883 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  CD38 is markedly more highly expressed on cord blood (CB) naive CD4+ T cells than adult blood (AB) naive CD4+ T cells, with an age-dependent gradient from fetal to pediatric life.

  pbmcs sorted scrna-seq naive flow bulk compass

• Annotation-free prediction of immunotherapy response in melanoma using single-cell transcriptomic data.

  PMID 41758825 · PMC12948085 · PloS one · 2026 · 8 claims · 6 setups

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  AI-based predictive models built on unannotated scRNA-seq data (cell-by-gene expression matrices) can classify melanoma patients as ICI responders vs. non-responders

  cd45+ scrna-seq independent scrna-seq single-gene-level pathway-level

• Regulatory-like FOXP3+Helios+CD4+ T conventional cells correlate with T-cell activation after Orca-T immunotherapy.

  PMID 41758930 · PMC13197979 · Blood · 2026 · 8 claims · 6 setups

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  Orca-T immunotherapy leads to increased phenotypic T-cell activation compared with unmanipulated PBSC grafts, persisting for months after treatment.

  peripheral sorted fresh cryopreserved flow single-cell tcr

• Role of CTGF-LRP1 in impaired healing of cesarean section incisions.

  PMID 41764198 · PMC13066582 · Nature communications · 2026 · 8 claims · 8 setups

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  A specific fibroblast subgroup (FB3) in niche tissue shows LRP1 deficiency associated with reduced extracellular matrix (ECM) synthesis capacity

  myometrium adjacent sections fibroblasts single-cell hematoxylin masson's

• IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

  PMID 41766654 · PMC12948414 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  MPNST cells are more radioresistant than benign plexiform neurofibroma (pNF) cells in vitro

  mpnst st88-14 nf9511.b jh-2-002 flow fractionated bulk

• scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

  PMID 41769845 · PMC12996892 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  scDock is an integrated pipeline connecting scRNA-seq processing, cell-cell communication inference, and molecular docking-based drug discovery through a single configuration file

  diabetic kidney ppia glimepiride-ppia scrna-seq cell-cell type

• 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

• 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

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  Scissor+ fibroblast subpopulations significantly correlated with prognosis were identified in CRC using the Scissor algorithm integrating scRNA-seq, bulk RNA-seq, and clinical data

  tcga gse39582 gse166555 scrna-seq bulk single-cell cell-cell

• PVT1 lincRNA signals an androgen-dependent transcriptional activation program of oncogenes in prostate cancer cells.

  PMID 41792045 · PMC13139993 · International journal of cancer · 2026 · 8 claims · 7 setups

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  PVT1 knockdown significantly reduces LNCaP cell proliferation and increases sensitivity to apoptosis

  lncap tcga-prad rt-qpcr trypan transwell

• Integrative CSF profiling identifies disease-specific immune responses in leptomeningeal disease.

  PMID 41794040 · PMC13006398 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  CSF exhibits distinct, disease-specific immune landscapes across CNSL, BrMs, and GB-associated LMD

  csf peripheral brain cell-free single-cell deep spatial

• A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

  PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups

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  Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families

  pad phylogenetic est est-based

• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease-specific signatures.

  PMID 36527260 · PMC10952672 · Glia · 2023 · 6 claims · 3 setups

  Has reproduction · 26

  The bulk microglial and monocyte transcriptomic program is highly contingent on the disease environment, challenging the notion of a universal microglial disease signature

  acutely microglia c57bl meta-analysis integration spectral

• IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 7 claims · 3 setups

  Has reproduction · 78

  IsomiR Window is a novel integrated pipeline plus browser GUI that combines over ten third-party tools with a new algorithm capable of detecting all types of isomiRs (5' end, 3' end, tailings, SNP/editing, and fuzzy combinations)

  simulated basal isomir small-rna-seq mirna