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).

• Comparative genomics and understanding of microbial biology.

  PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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  GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

  completed same sequenced mycobacterium whole-genome comparative phylogenomic

• A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

  PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 71

  MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples

  3h-labeled imr-90 lambda saliva scintillation genome restriction

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Massively parallel pyrosequencing in HIV research.

  PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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  Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

  mammoth hiv hiv-infected honey pyrosequencing pcr 16s

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

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  Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

  gastrointestinal acid ocean group metagenomic shotgun comparative

• Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.

  PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups

  Has reproduction · 65

  eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.

  edna khumbu genome metabarcoding satellite

• Unlocking the microbial studies through computational approaches: how far have we reached?

  PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

  Has reproduction

  Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

  clinical bacteriophage vaginal hbv ngs random whole-genome

• Viruses take center stage in cellular evolution.

  PMID 16787527 · PMC1779534 · Genome biology · 2006 · 8 claims · 6 setups

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  A large poxvirus-like dsDNA virus may have become the eukaryotic nucleus after being taken in by an ancestral cell (viral eukaryogenesis)

  acanthamoeba coccolithovirus nucleocytoplasmic dsdna whole-genome phylogenetic comparative