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).

• 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

• Single-cell landscape of piglet lung response with Actinobacillus pleuropneumoniae.

  PMID 41843736 · PMC13014559 · Virulence · 2026 · 8 claims · 8 setups

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  scRNA-seq of piglet lungs identified 18 cell subpopulations with distinct phenotypes in infected vs control lungs

  piglet monocytes bronchoalveolar single-cell hematoxylin-and-eosin immunohistochemistry

• Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals the transcriptome profile of Microtus fortis immune cells during the early phase of infection with Schistosoma japonicum.

  PMID 41675929 · PMC12886473 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 2 setups

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  Both innate and adaptive immune responses were activated in M. fortis peripheral blood at 10 dpi, while activation was not obvious in Kunming mice at the same time point

  pbmcs single-cell qpcr

• ZFP148 is a transcriptional repressor of cytolytic effector CD8(+) T cell differentiation.

  PMID 41896465 · PMC13043298 · Nature immunology · 2026 · 8 claims · 8 setups

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  ZFP148 is enriched in CD8+ T progenitor (T PRO) cells and its expression declines during differentiation into effector (T EFF) and exhausted (T EX) cells

  p14 splenic cd8+ b16-gp scrna-seq flow tcr

• AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PM(2.5) exposure.

  PMID 41912520 · PMC13194984 · Nature communications · 2026 · 8 claims · 6 setups

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  A fine-tuned Geneformer (single-cell transcriptomics transformer) model classifies PM2.5 exposure status and generalizes better than BERT models trained from scratch, especially with limited data.

  lung fine-tuned biobank single-cell bulk gene

• Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

  PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 51

  Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

  pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl

• Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.

  PMID 41729083 · PMC12956012 · JCI insight · 2026 · 8 claims · 7 setups

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  A clonally expanded CD8+GZMK+IFNG+ T cell population (subdivided into IFNGhi and IFNGint groups) is enriched in the EM lesion and shows an inflammatory, tissue-resident phenotype (GZMBlo/PRF1-) resembling tissue-enriched GZMK+ TteK cells

  whole-skin cd8+gzmk+ifnghi identified skin scrna-seq pseudobulk immune

• Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.

  PMID 41560697 · PMC13042525 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  Mitochondrial somatic mutations from scRNA-seq can be repurposed as endogenous genetic barcodes for lineage tracing in hPSC-derived organoids.

  hpsc hemo larry-barcoded pdgfrα+ scrna-seq mitochondrial cospar

• Exploring phenotype-related single-cells through attention-enhanced representation learning.

  PMID 41566378 · PMC12906058 · Genome medicine · 2026 · 6 claims · 5 setups

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  scPhase, an attention-based multiple instance learning (AMIL) framework with Mixture-of-Experts aggregation, predicts sample-level clinical phenotypes from raw scRNA-seq data and generalizes across patient cohorts

  pbmcs brain tumor scrna-seq

• Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in mice.

  PMID 41922840 · PMC13171603 · Nature microbiology · 2026 · 8 claims · 7 setups

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  Inflammatory macrophages accumulate in joint-associated tissue during the chronic stage of CHIKV infection and show an activated, pro-inflammatory, MHC-II+ transcriptional programme

  ankle ipsilateral computational pfa-fixed rt-qpcr single-cell gene

• Tree shrew immune cell atlas identifies NR1H3⁺ tissue macrophages with conserved anti-inflammatory function.

  PMID 41957356 · PMC13223331 · Nature communications · 2026 · 8 claims · 8 setups

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  A single-cell/single-nucleus RNA-seq atlas across 12 tree shrew tissues identifies 39 distinct immune and non-immune cell types, providing a reference resource for tree shrew immunology

  tree single-cell scrna-seq cross-species functional

• Single-cell RNA-sequencing highlights a curtailed NK cell function in convalescent COVID-19 pregnant women.

  PMID 40661959 · PMC12257036 · Frontiers in immunology · 2025 · 7 claims · 5 setups

  Has reproduction · 87

  NK cells show a sustained reduction during active SARS-CoV-2 infection and persisting after recovery in pregnant women

  pbmcs serum 14-color single-cell 13-plex

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.

  PMID 42121287 · PMC13162514 · Genome biology · 2026 · 8 claims · 8 setups

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  scArchon is a reproducible, modular, Snakemake-based benchmarking platform that evaluates perturbation response prediction tools in a standardized, containerized, extensible manner.

  pbmcs epithelial liver glioblastoma scrna-seq gene dimensionality

• Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

  PMID 41489684 · PMC12767585 · The Journal of experimental medicine · 2026 · 8 claims · 8 setups

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  MMP1+CXCL5+ fibroblasts and SPP1+ macrophages are linked to TB disease and TB lung granuloma and reveal targetable cellular cross talk underlying TB immunopathology

  lung ffpe lymph nonhuman scrna-seq spatial bulk

• Venezuelan equine encephalitis virus infection causes chronic neurobehavioral outcomes, cellular remodeling, and hippocampal single-cell transcriptomic changes.

  PMID 41950299 · PMC13089902 · PLoS pathogens · 2026 · 7 claims · 8 setups

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  VEEV infection causes persistent motor dysfunction, memory impairment, and reduced anxiety-like behavior up to 106 DPI

  c57bl pooled hippocampal scrna-seq elevated novel modified

• Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.

  PMID 42010620 · PMC13227897 · Journal of neuroinflammation · 2026 · 8 claims · 5 setups

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  Morphine-dependent macaques show increased CD4+ TCM and Treg cell proportions and decreased CD8+ TEM cell proportions in CSF at the pre-infection timepoint compared to saline controls

  csf scrna-seq necropsy single-cell flow cell-cell

• Helicobacter pylori-induced PPFIA4 orchestrates immune network-promoting gastritis and gastric bacterial colonization.

  PMID 42065246 · PMC13132368 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  PPFIA4 is increased in GECs from gastric mucosa of H. pylori-infected patients and mice

  ags gastric il33 slam-seq scrna-seq western

• Dynamics of lung-infiltrating virus-specific T cells associated with age-dependent SARS-CoV-2 pneumonia severity.

  PMID 41533733 · PMC12829949 · PLoS pathogens · 2026 · 8 claims · 8 setups

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  Aged Nr4a3-Tocky mice develop more severe pneumonia and delayed body weight recovery after SARS-CoV-2 infection than adult mice

  nr4a3-tocky bronchoalveolar lung left viral histopathology immunohistochemistry

• Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.

  PMID 41593733 · PMC12918531 · Genome biology · 2026 · 8 claims · 5 setups

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  Generated the first single-cell transcriptome atlas (scRNA-seq + spRNA-seq) of grapevine leaves during P. viticola infection across four early time points (0, 3, 6, 12 hpi)

  vitis guard cabernet tissue-specific single-cell spatial pseudo-time