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).

• nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.

  PMID 42057295 · PMC13141149 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  nf-core/viralmetagenome is a Nextflow pipeline that automates untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation-capture data.

  real simulated seven pipeline metagenomic simulated clinical

• Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing.

  PMID 42274466 · PMC13256323 · Microbial genomics · 2026 · 8 claims · 8 setups

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  A novel ONT long-read sequencing laboratory and bioinformatic workflow rapidly identifies bacterial and fungal organisms and AMR determinants from positive blood cultures

  positive matching pure ont long-read short-read maldi-tof

• Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.

  PMID 41758556 · PMC12948150 · Microbial genomics · 2026 · 8 claims · 8 setups

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  Autocycler (consensus long-read-only assembler) circularised the most chromosomes, 95% (87/92), significantly more than Unicycler, Unicycler bold, Flye and Hybracter (hybrid)

  clinical enterobacterales assembled assembler-polisher nanopore illumina comparative

• Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.

  PMID 42224013 · PMC13225438 · Microbial genomics · 2026 · 8 claims · 6 setups

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  The H37Rv_ref reference genome, sequenced in 1998 with early technology, is incomplete relative to modern hybrid-sequenced assemblies

  tuberculosis h37rv_cn a2018772 publicly hybrid comparative functional

• Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

  PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups

  Has reproduction · 82

  An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis

  michiganensis a55848 african assembled whole-genome novo genome-based

• TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

  PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 43

  TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

  mdr-tb paired-end raw bam whole-genome kraken raw

• Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae.

  PMID 42113870 · PMC13183285 · PLoS pathogens · 2026 · 8 claims · 8 setups

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  Each N. gonorrhoeae genome has on average 7 distinct opa alleles at 9-12 opa loci

  gonorrhoeae complete opa non-gonorrhoeae long-read custom blast

• The dynamic distribution of genetic tandem amplifications in a heteroresistant Escherichia coli population revealed by ultra-deep long read sequencing.

  PMID 41760616 · PMC12953903 · Nature communications · 2026 · 8 claims · 6 setups

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  Ultra-deep Nanopore sequencing of I-SceI-linearized plasmid DNA can detect and quantify full tandem amplification arrays at single-molecule resolution down to frequencies of 10^-5

  coli ultra-deep short-read digital

• Transposable elements are driving rapid adaptation of Enterococcus faecium.

  PMID 42020750 · PMC13216065 · Nature · 2026 · 8 claims · 8 setups

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  E. faecium has the highest IS density among ESKAPEE pathogens, dominated by replicative ISL3 family elements

  eskapee faecium ncbi single-hospital large-scale chromosome core