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).

• 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

• Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.

  PMID 42038409 · PMC13107125 · NAR genomics and bioinformatics · 2026 · 7 claims · 7 setups

  Has reproduction · 78

  Long-read shotgun metagenomic sequencing of eDNA can simultaneously detect and quantify organismal DNA from viruses to mammals in a single assay

  river edna extracted raw edna concentration quantitative

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid

• Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

  PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 50

  BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

  bovine direct amplified synthetic

• Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

  PMID 41563441 · PMC13007207 · Diabetes · 2026 · 8 claims · 7 setups

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  5′ single-cell library preparation protocols outperform 3′ protocols for transcript identification and read length

  lines pancreatic spleen dtc single-cell bulk ngs

• Whole genome sequences of Yersinia pestis strains of ancient phylogenetic branch 0.ANT5 isolated in the 21st century in the Tien-Shan in Kyrgyzstan.

  PMID 39206953 · PMC11478111 · Microbiology resource announcements · 2024 · 6 claims · 5 setups

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  Eleven Yersinia pestis strains of the ancient phylogenetic branch 0.ANT5, isolated in the Tien Shan focus (Kyrgyzstan) in 1952, 1971, and 2013–2023, were hybrid-sequenced (MGI short reads + ONT long reads)

  yersinia whole-genome hybrid plasmid

• The genome sequence of a rove beetle, Tachyporus hypnorum (Fabricius, 1775) (Coleoptera: Staphylinidae).

  PMID 41993728 · PMC13080330 · Wellcome open research · 2026 · 6 claims · 8 setups

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  A chromosome-level genome assembly was generated for Tachyporus hypnorum, the first high-quality genome for the genus Tachyporus.

  tachyporus barcoding high pacbio

• The genome sequence of the Figwort Mason Wasp, Symmorphus gracilis (Brulle, 1832) (Hymenoptera: Vespidae).

  PMID 42109708 · PMC13153769 · Wellcome open research · 2026 · 6 claims · 8 setups

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  A chromosome-level genome assembly was generated for Symmorphus gracilis, comprising two haplotypes (220.03 Mb and 217.14 Mb), with haplotype 1 scaffolded to 6 chromosomal pseudomolecules

  symmorphus head genomic hifi barcoding hmw pacbio

• The genome sequence of a hoverfly , Melangyna compositarum (Verrall, 1873) (Diptera: Syrphidae).

  PMID 41971599 · PMC13069379 · Wellcome open research · 2026 · 7 claims · 8 setups

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  A genome assembly was generated for a single male Melangyna compositarum hoverfly specimen (idMelComo1) as part of the Darwin Tree of Life project.

  melangyna barcoding high pacbio

• Optimized library preparation, sequencing, and data analysis protocols for the generation of orbivirus consensus sequences.

  PMID 41527034 · PMC12809950 · BMC genomics · 2026 · 8 claims · 8 setups

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  Optimized sample and library preparation protocols achieved comparable results to established methods while requiring simpler sample preparation.

  btv17 purification carrier dnase