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).

• Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2.

  PMID 32333836 · PMC7181998 · Cell · 2020 · 8 claims · 7 setups

  Has reproduction · 87

  Clinical-grade hrsACE2 significantly inhibits SARS-CoV-2 infection of Vero-E6 cells in a dose-dependent manner

  nasopharyngeal vero-e6 ipsc-derived embryonic viral qrt-pcr organoid

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.

  garlic pepper pear grapevine rna-seq mrna-seq transcriptome

• 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

• Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

  PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses

  pooled individual liver serum viral pcr strand-specific

• Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.

  PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.

  th-cre awake ibat plasma retrograde chemogenetic indirect

• Molecular epidemiology of measles viruses in the United States, 1997-2001.

  PMID 12194764 · PMC2732556 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

  Full-text index only

  The diversity of measles virus genotypes observed in the US from 1997–2001 reflects multiple imported sources of virus, indicating no strain of measles is endemic in the United States.

  b95a clinical pcr measles viral extraction rt-pcr

• Viral and host determinants of RNA virus vector replication and expression.

  PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups

  Full-text index only

  BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.

  bmv saccharomyces wild-type immunogold genome-wide northern

• Thirty years into the genomics era: tumor viruses led the way.

  PMID 17940630 · PMC1994808 · The Yale journal of biology and medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  Restriction endonuclease-based analysis and sequencing of small tumor virus genomes (SV40, phiX174) established the technical framework later used to sequence bacterial and human genomes

  sv40 bacteriophage epstein-barr aids-associated restriction recombinant sequencing

• SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes.

  PMID 17169995 · PMC1802603 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  SECIS elements located within coding regions of selenoprotein mRNAs support functional Sec insertion in mammalian cells

  viral hek293 hepatoma tblastn computational western

• Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

  PMID 16916263 · PMC7121524 · Methods in molecular biology (Clifton, N.J.) · 2006 · 7 claims · 7 setups

  Full-text index only

  PCR-based amplification and direct sequencing of SARS-CoV genome fragments is feasible from uncultured clinical specimens (serum, nasopharyngeal aspirate, stool), avoiding culture-derived artifacts and biohazard risk.

  sars-cov extracted cdna pcr viral reverse real-time

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

  Full-text index only

  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal

• A bioinformatic pipeline for simulating viral integration data.

  PMID 35496474 · PMC9046613 · Data in brief · 2022 · 7 claims · 3 setups

  Has reproduction · 96

  A snakemake-based pipeline was developed to simulate integration of a viral or vector genome into a host genome, including sub-genomic fragment integration, structural variation, and host-site deletions.

  aav2 host simulated integration simulated junction-crossing

• 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

• HIV-1 evolution following transmission to an HLA-B*5801-positive patient.

  PMID 19909081 · PMC2779566 · The Journal of infectious diseases · 2009 · 8 claims · 8 setups

  Full-text index only

  Multiple escape mutations developed rapidly in HLA-B*5801-restricted epitopes in Gag, Nef, and Pol following transmission

  plasma transmitter subject genomic full-length population ifn-γ

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• The VIZIER project: preparedness against pathogenic RNA viruses.

  PMID 18083241 · PMC7114271 · Antiviral research · 2008 · 8 claims · 6 setups

  Full-text index only

  Almost all newly emerging human pathogenic viruses are RNA viruses, largely because their error-prone RNA-dependent RNA polymerases and zoonotic reservoirs allow rapid adaptation to new hosts.

  viruses virus coli soluble large-scale bioinformatic recombinant

• 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

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class Random Forest models built from meta-analyzed blood gene expression data can predict infection state (bacterial/viral/none) with high accuracy, correctly classifying 93% of bacterial and 89% of viral samples in the best model.

  blood merged affymetrix-trained microarray random gene

• Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

  PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

  Has reproduction · 81

  A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

  lung sequencing assembled deer high-throughput metagenomic reference

• Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

  PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

  Has reproduction · 68

  viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

  transgenic elegans four gfp genetic template-independence