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).

• The sequence and de novo assembly of the giant panda genome.

  PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

  Full-text index only

  A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

  giant panda whole-genome novo read

• HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

  PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups

  Has reproduction · 58

  HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers

  bacillus mycobacterium rhodobacter vibrio novo contigs-combining re-assembly

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

  zymobiomics assembled assembler-generated novo reference-based contig

• Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.

  PMID 31346012 · PMC6658682 · Microbiology resource announcements · 2019 · 6 claims · 7 setups

  Has reproduction · 92

  Draft genome sequences of three multidrug-resistant Shigella clinical isolates from Pakistan (two S. flexneri, one S. sonnei) are reported as a resource for AMR surveillance.

  shigella bacterial antimicrobial whole-genome

• Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

  PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 8 claims · 8 setups

  Has reproduction · 86

  HPVN24 is E. coli APEC serotype O78:H9, sequence type ST23

  coli hemolysis antibiotic whole-genome

• Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.

  PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups

  Has reproduction · 85

  An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.

  salmonella ncbi-pd illumina empirical coverage

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome.

  PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens

  gibbsiella lonsdalea brenneria miseq genome novo comparative

• Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality.

  PMID 35136576 · PMC8804904 · F1000Research · 2021 · 8 claims · 6 setups

  Has reproduction · 98

  metashot/prok-quality is a container-enabled Nextflow pipeline for quality assessment and dereplication of draft prokaryotic genomes

  draft filtered chimeric genome chimerism ribosomal