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).

• A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.

  PMID 41513996 · PMC12872441 · Nature microbiology · 2026 · 8 claims · 7 setups

  Full-text index only

  The global cellular tRNA pool is not substantially altered during APMV infection, despite the virus encoding its own tRNA genes.

  acanthamoeba apmv rna-seq ribo-seq mim-trna-seq

• Tissue-resident macrophage and dendritic cells drive type I IFN immunity to enteroviruses in the liver.

  PMID 41592119 · PMC12858076 · PLoS pathogens · 2026 · 8 claims · 6 setups

  Full-text index only

  Type I IFN signaling (Ifnar1), but not type III IFN signaling (Ifnlr1), is essential for survival and for limiting viral replication in the liver during echovirus infection

  neonatal liver survival viral h&e

• Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms.

  PMID 41654489 · PMC12923905 · Translational psychiatry · 2026 · 7 claims · 6 setups

  Full-text index only

  MIA induces enduring epigenetic reprogramming of gene regulatory networks in the developing brain that persists into adulthood

  sorted frontal rna-seq mia-responsive chip-seq rna-seq facs

• α4 Integrin blockade impairs CD8+ T cell neuroimmune surveillance following SIV infection.

  PMID 41734020 · PMC13078879 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

  Full-text index only

  α4 blockade preserves CD4+ Th1 cell access to brain parenchyma but impairs CD8 effector recruitment, disrupting antiviral control

  siv-infected live macaque cd4-δitga4 flow antibody single-cell

• The macrophage entry mechanism of SARS-CoV-2 mediated by surface CD98/TMPRSS11E complex is associated with the cellular tropism toward proinflammatory M1 and pathogenesis.

  PMID 41877147 · PMC13137717 · Respiratory research · 2026 · 8 claims · 8 setups

  Full-text index only

  CD98 (CD98hc/SLC3A2) is a novel receptor for the SARS-CoV-2 Spike protein

  thp-1-derived 293t structures thp-1 co-ip co-immunoprecipitation molecular

• 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

  Full-text index only

  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

• De novo transcriptome assembly and annotation of Penaeus monodon hemocytes under WSSV infection and STAT knockdown.

  PMID 41942475 · PMC13233909 · Scientific data · 2026 · 8 claims · 7 setups

  Full-text index only

  A validated de novo hemocyte transcriptome assembly and 12-library RNA-seq dataset for P. monodon under WSSV infection and PmSTAT knockdown is provided as a public resource.

  penaeus monodon assembled predicted bulk novo busco

• Dietary conjugated linoleic acid enhances resistance to Salmonella infection by promoting PPARγ-mediated metabolic reprogramming and effector function in CD8⁺ T cells.

  PMID 41964110 · PMC13078244 · Gut microbes · 2026 · 8 claims · 12 setups

  Full-text index only

  Dietary CLA supplementation enhances host resistance to Salmonella Typhimurium infection

  ileal mice serum culture 16s untargeted bulk

• Limited protection against early-life lung murine cytomegalovirus infection results from deficiency of cytotoxic CD8 T cells.

  PMID 42008567 · PMC13128127 · PLoS pathogens · 2026 · 9 claims · 9 setups

  Full-text index only

  Expansion of endogenous MCMV-specific CD8 T cells is delayed in early life due to a low precursor frequency of peripheral αβ T cells

  peripheral spleen polyclonal neonatal pmhc-i mhc-ii flow

• 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

  Full-text index only

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

  ags gastric il33 slam-seq scrna-seq western

• PDLIM2 repression: a common mechanism in viral lung infection.

  PMID 41904702 · PMC13168810 · ImmunoHorizons · 2026 · 8 claims · 7 setups

  Full-text index only

  PDLIM2 expression is repressed in blood leukocytes, BAL cells, and lung tissue of patients infected with influenza or SARS-CoV-2 compared to uninfected controls

  peripheral blood bal influenza gene bulk single-cell

• Mitochondrial D-loop mutations and deletion profiles of cancerous and noncancerous liver tissue in hepatitis B virus-infected liver.

  PMID 15785740 · PMC2361973 · British journal of cancer · 2005 · 8 claims · 2 setups

  Full-text index only

  D-loop mutation frequency is significantly higher in both noncancerous and tumour liver tissue of HCC/HBV patients than in normal control liver

  liver pcr

• A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

  PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 94

  A 4-gene signature (ITGB4, ITGA7, IFI27, FAM20A) derived from whole blood RNA-seq discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90

  hospitalized adults pediatric blood bulk rna-seq microarray

• Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control.

  PMID 40758707 · PMC12333995 · PLoS pathogens · 2025 · 8 claims · 7 setups

  Has reproduction · 90

  Six viral promoters (UL5, UL72, EP3, UL57-AS, US16-AS, US30-S) are ≥50-fold more active in D-NT2 than in HFF at 96 h post-infection and are classified as viral long promoters.

  d-nt2 hcmv-infected hcmv pro-seq dff-chip promoter

• The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.

  PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 6 setups

  Has reproduction · 100

  SMCs show high gene expression for mucus-secreted proteins (Tff1, Gkn1, Gkn2, Psca, Muc5ac), mitoribosome RNA, and cytoskeleton proteins

  laser-microdissected gastric ffpe oct-embedded sequencing glycomics immunofluorescence

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 84

  ChIRP-MS of SARS-CoV-2 RNA in infected Huh7.5 and Vero E6 cells identifies a comprehensive set of 309 host proteins that bind the viral RNA during active infection

  huh7.5 vero schmidt lung chirp-ms chirp-rna-seq sds-page

• Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

  PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

  lung c57bl pbmcs macrophages bulk metabolomics histopathology

• Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.

  PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups

  Has reproduction · 64

  A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs

  peripheral genome blood bulk illumina ion

• Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

  PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

  vero calu-3 genes direct pcr poly

• An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

  PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

  liver hcv-infected serum bulk chip-seq serum