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).

• Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

  PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

  Has reproduction

  The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

  ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional

• In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

  PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 8 setups

  Has reproduction · 89

  SARS-CoV-2 infection induces a strong interferon-driven antiviral response in the nasopharynx, with up-regulation of viral sensors, T cell/NK chemokines, and antiviral effectors

  nasopharyngeal airway patient-matched swab shotgun gsea biological

• 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

• Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

  PMID 37243151 · PMC10224212 · Viruses · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  An exhaustive-search workflow can recover intra-host co-existing SARS-CoV-2 strains from the reference-genome read set (SRR11092062) that de Bruijn-graph assemblers discard.

  sars-cov-2 spike predicted california short-read read sequence

• Optimizing data-driven excellence: Canada's approach to using pathogen test datasets for quality control, pipeline development and training initiatives.

  PMID 41591806 · PMC12847982 · Microbial genomics · 2026 · 8 claims · 5 setups

  Full-text index only

  Standardized SARS-CoV-2 test datasets (Illumina and Nanopore) were developed as benchmarks for validating sequencing/bioinformatics pipelines across Canadian public health labs

  sars-cov-2 extracted nasopharyngeal bioinformatic whole-genome triplex extraction

• Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

  PMID 41663577 · PMC12982125 · Nature methods · 2026 · 6 claims · 3 setups

  Full-text index only

  Most SARS-CoV-2 genomes were sequenced using tiled amplicon methods, which introduce systematic errors unless assembly software is aware of the amplicon scheme and the error modes of amplicon sequencing

  sars-cov-2 amplicon-aware simulation global

• 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

• eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.

  PMID 34019643 · PMC8218201 · Nucleic acids research · 2021 · 8 claims · 7 setups

  Has reproduction · 82

  eVITTA is a web-based toolbox with three integrated modules (easyGEO, easyGSEA, easyVizR) for GEO data access, functional profiling, and multi-dataset comparison

  nasopharyngeal elegans bulk pre-ranked microarray

• Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.

  PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups

  Has reproduction · 71

  Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.

  nasopharyngeal heart leukocytes blood bulk pathway machine

• 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

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• VGEA: an RNA viral assembly toolkit.

  PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline

  sars-cov-2 lassa hiv-1 ngs-based computational comparative

• Betacoronavirus-specific alternate splicing.

  PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Genes differentially spliced during SARS-CoV-2 infection show a similar functional (GO) profile to those differentially spliced in SARS-CoV and MERS infection, affecting a diverse set of genes tied to virus biology.

  mrc5 calu-3 nasal lung bulk

• EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

  PMID 35561186 · PMC9113274 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 5 setups

  Has reproduction · 49

  EDGE COVID-19 (EC-19) is a web-based platform that automates QC, reference-based variant/consensus calling, lineage determination, and submission of SARS-CoV-2 genomes and metadata to GenBank, GISAID and INSDC for both Illumina and ONT data.

  sars-cov-2 srr illumina ont amplicon lineage cross-workflow

• Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

  PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

  Has reproduction · 75

  RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

  pbmcs pbmc aligned bulk read transcript

• Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

  PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

  Has reproduction · 50

  Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

  sars-cov-2 publicly simulated simulated amplicon-based variant

• Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.

  PMID 41609640 · PMC12856159 · Microbial genomics · 2026 · 8 claims · 8 setups

  Full-text index only

  Sample PH-RITM-1395 represents a Delta–Omicron co-infection, confirmed by convergent evidence from Nextclade, bammix, Freyja, VirStrain, AAF analysis and amplicon sorting rather than contamination

  consensus aligned raw bam nextclade nucleotide strain-level

• Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.

  PMID 41680899 · PMC12903587 · Genome medicine · 2026 · 7 claims · 6 setups

  Full-text index only

  A novel batch-effect correction method (log-normal gene usage modeling, Z-score normalization, and roulette-wheel resampling) allows combining AIRR-seq data from different batches and protocols.

  blood peripheral batch-corrected airr-seq airr-seq hla tcrβ

• WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.

  PMID 41911220 · PMC13048486 · PLoS computational biology · 2026 · 8 claims · 5 setups

  Full-text index only

  WEPP is a pathogen-agnostic pipeline that uses phylogenetic placement of sequencing reads onto mutation-annotated trees (MATs) to identify candidate haplotypes and estimate their abundances

  sars-cov-2 mutation-annotated simulated synthetic real-world

• Virus variant quantification with Orthanq.

  PMID 41639627 · PMC12930645 · BMC bioinformatics · 2026 · 8 claims · 6 setups

  Full-text index only

  Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, including in samples with mixed infections

  simulated real mixture sequencing sequencing-based pangenome variant