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).

• 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

• 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

• TRAP5 Inhibition Targeting Scar-Associated Macrophages Ameliorates Acute Kidney Injury to Chronic Kidney Disease Transition.

  PMID 41773735 · PMC13159109 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  A distinct scar-associated macrophage (SM) subset marked by high Acp5/TRAP5, Ctsk, Mmp9, and Spp1 emerges and predominates during the renal remodeling/CKD phase after AAI-induced AKI

  kidney ckd aai unilateral single-cell velocity pseudotime

• Dextrorotatory kynurenine suppresses acute rejection through inhibiting M1 macrophage-mediated inflammation.

  PMID 41644740 · PMC12988155 · EMBO molecular medicine · 2026 · 8 claims · 7 setups

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  Elevated serum D-Kyn levels correlate with stable graft function, while lower D-Kyn is associated with acute rejection

  serum kidney allogeneic ion scrna-seq pseudotime

• CAR-M2 immunotherapy resolves renal fibrosis via revascularization and apoptosis of profibrotic Cxcr2(+) endothelial cells.

  PMID 41887221 · PMC13130657 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  CAR-M2 macrophages (anti-FAP CAR + IL-4-secreting, 4-1BB/CD3ζ costimulatory domains) specifically target and phagocytose FAP+ fibroblasts

  kidney car-m2 macrophages uuo scrna-seq histology live-cell

• Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

  PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.

  PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups

  Has reproduction · 50

  huSA is a comprehensive, publicly accessible database integrating bulk RNA-seq, scRNA-seq, and spatial transcriptomics data across 17 skin diseases and 63 independent datasets

  skin scrna-seq scrna-seq transcription cell-cell

• Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

  PMID 41821037 · PMC12983708 · Genome biology · 2026 · 8 claims · 8 setups

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  Horizontal integration of scRNA-seq and snRNA-seq improves cell-type identification

  renal kidney pbmc heart scrna-seq snrna-seq snatac-seq

• PBRM1 Deficiency Reshapes an Immune Suppressive Microenvironment Through Epigenetic Tuning of PBRM1-KDM5C-IL6 Axis in ccRCC.

  PMID 41514194 · PMC13042695 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  PBRM1 deficiency increases infiltration of immunosuppressive M2 tumor-associated macrophages (TAMs) and creates an immune-excluded tumor microenvironment

  vhl kidney pbrm1 immunodeficient scrna-seq multiplex crispr-cas9

• MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.

  PMID 41811907 · PMC12998955 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  MultiPert reliably predicts both perturbed gene expression and protein abundance profiles from single-cell multi-omics data

  thp-1 kidney gse156478 computational zinb-vae autoencoder eccite-seq

• Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

  PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

  peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell

• Patient-derived kidney organoids recapitulate ADPKD and facilitate the identification of Rho pathway inhibitors as candidate therapeutics.

  PMID 41946363 · PMC13130689 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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  Multi-lineage adult renal organoids (MAROs) can be established directly from adult human kidney tissue and expanded long-term while retaining proximal tubule and collecting duct lineages

  maros patient-derived pkd_orgs bulk single-cell immunofluorescence

• Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets.

  PMID 41971949 · PMC13068006 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

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  spVIPES decomposes unpaired scRNA-seq datasets with nonmatching features into shared and private latent representations using a Product of Experts framework

  simulated zebrafish kidney peripheral simulated cross-species scrna-seq

• A copula-infused graph neural network for cell type classification in single-cell RNA sequencing data.

  PMID 41940310 · PMC12914865 · Computational and structural biotechnology journal · 2026 · 8 claims · 5 setups

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  scCopulaGNN combines copula theory with graph neural network representation learning for scRNA-seq cell type classification

  brain pancreas kidney turtle scrna-seq simulated

• Partial domain adaptation enables cross domain cell type annotation between scRNA-seq and snRNA-seq.

  PMID 42090457 · PMC13170964 · PLoS computational biology · 2026 · 7 claims · 5 setups

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  ScNucAdapt is a partial domain adaptation framework that enables cross-domain cell type annotation between paired or unpaired scRNA-seq and snRNA-seq datasets.

  bladder kidney cortex frozen scrna-seq snrna-seq

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• Annexin A13 Protects Against Acute Kidney Injury by Inactivating TGF-β/Smad3 Signaling.

  PMID 41486854 · PMC12915081 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  ANXA13 is selectively downregulated in the kidneys of AKI patients and IRI- or cisplatin-induced AKI mice, primarily in proximal tubular cells

  kidney aki renal hek293t rna-seq immunohistochemistry serum

• sCellST predicts single-cell gene expression from H& E images.

  PMID 41513659 · PMC12858858 · Nature communications · 2026 · 7 claims · 6 setups

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  sCellST is a weakly supervised (Multiple Instance Learning) deep learning framework that predicts single-cell gene expression from H&E images alone, trained using paired spatial transcriptomics (Visium) and H&E slides

  ovarian kidney prostate breast simulation spot-level nucleus