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 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

• Epidemiology and phylogenomic characterization of the Clade IIb C.1 Mpox outbreak in Phnom Penh, Cambodia (2023-2024).

  PMID 41575511 · PMC12978180 · Emerging microbes & infections · 2026 · 8 claims · 8 setups

  Full-text index only

  All Cambodian Mpox genomes belong to lineage C.1, nested within Clade IIb

  skin mpxv-positive raw cambodian real-time viral bioinformatic

• Towards reliable whole genome sequencing for outbreak preparedness and response.

  PMID 35945497 · PMC9361258 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 84

  Amplicon-based Nanopore sequencing can rapidly generate whole genome sequences in samples with viral load up to Ct 33.

  culture aligned amplicon-based metagenomic capture-based

• CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

  PMID 34210356 · PMC8247108 · Genome biology · 2021 · 7 claims · 2 setups

  Full-text index only

  A centralised hub model built on the CLIMB compute infrastructure (CLIMB-COVID) can integrate SARS-CoV-2 genomic sequencing data and sample metadata from a decentralised, autonomous network of sequencing sites into a single canonical dataset.

  sars-cov-2 whole-genome pcr

• poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

  PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data

  porecov sars-cov-2 nanopore fastq gisaid workflow real-world