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).

• Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.

  PMID 32111840 · PMC7048732 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 95

  SuSr-D1 encodes Med15b.D, a subunit of the Mediator complex

  wheat flow-sorted uninoculated med15 seedling plant flow-sorted

• Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

  PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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  APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

  magi pbmc 293t supt1 sensitive rt-pcr western

• Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history.

  PMID 18507832 · PMC2427034 · BMC microbiology · 2008 · 7 claims · 6 setups

  Full-text index only

  A2143G point mutation of the H. pylori 23S rRNA gene causes clarithromycin resistance

  fasting subjects serum pylori pcr 13c-urea elisa

• Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

  PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups

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  Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode

  generic simulated hiv-1 stochastic dynamic regression

• Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

  PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 71

  CAI is positively correlated with translational efficiency, validating its use as a proxy for translational efficiency at the elongation level.

  unstimulated cd4+ kidney liver bulk single-cell

• 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

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

  PMID 12589088 · PMC3054991 · Journal of Korean medical science · 2003 · 6 claims · 5 setups

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  The t-PA I/D or D/D genotype is significantly associated with duodenal (vs gastric) ulcer location

  genomic randomly patients endoscopic allele-specific pcr logistic

• Initial characterization of Chlamydophila (Chlamydia) pneumoniae cultured from the late-onset Alzheimer brain.

  PMID 18829386 · PMC2730674 · International journal of medical microbiology : IJMM · 2009 · 6 claims · 7 setups

  Full-text index only

  C. pneumoniae was cultured from two late-onset AD brain tissue samples (Tor-1 from hippocampus, Phi-1 from temporal cortex) from different North American regions.

  tor-1 brain hep-2 pcr culture immunofluorescence

• Impact of RTS,S/AS02(A) and RTS,S/AS01(B) on genotypes of P. falciparum in adults participating in a malaria vaccine clinical trial.

  PMID 19924281 · PMC2773849 · PloS one · 2009 · 7 claims · 4 setups

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  Both RTS,S/AS02A and RTS,S/AS01B vaccines reduce multiplicity of infection (MOI) of breakthrough P. falciparum infections

  falciparum malaria-experienced blood csp msp-1 randomized

• Genomic signatures of human versus avian influenza A viruses.

  PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

  Full-text index only

  52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

  throat clinical 401-genome avian rt-pcr immunofluorescent sequence

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

  PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

  Full-text index only

  tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

  clinical pcr-negative representative whole-cell conventional colony locus-specific

• Early days: genomics and human responses to infection.

  PMID 16679048 · PMC7108404 · Current opinion in microbiology · 2006 · 8 claims · 8 setups

  Full-text index only

  DNA microarray-based transcript profiling of primate/human responses to infection has begun to yield new insights into host-pathogen interactions but is limited by unresolved methodological challenges.

  peripheral liver gastric brain microarray

• Charting and probing the activity of ADARs in human development and cell-fate specification.

  PMID 39537590 · PMC11561244 · Nature communications · 2024 · 8 claims · 6 setups

  Has reproduction · 100

  RNA editing (AEI) and ADAR/ADARB1/ADARB2 expression show organ-specific dynamic shifts across fetal-to-adult developmental stages in human forebrain, hindbrain, heart, liver, kidney, and testis

  organ same 8-week-old week alu site-specific gene

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

  Full-text index only

  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• 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

• 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

• 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

• Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

  PMID 15545352 · PMC2211924 · The Journal of experimental medicine · 2004 · 7 claims · 4 setups

  Full-text index only

  CD8+ CTL responses contribute to containment of viral replication in acute/early HIV-1 infection, and HIV-1 rapidly selects escape variants within epitope-containing regions beginning within weeks of infection.

  pbmcs autologous vaccinia plasma ifn-γ 51cr recombinant