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).

• 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

• Genomics against flatulence.

  PMID 17635535 · PMC1974822 · Environmental microbiology · 2007 · 8 claims · 8 setups

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  Methanogenic archaea (not bacteria) in the human gut, chiefly Methanobrevibacter smithii, produce the methane component of intestinal gas, most of which is released via the large intestine (up to 0.5 l day−1) rather than in breath.

  methanobrevibacter fecal metallosphaera pyrobaculum whole-genome serial respiratory

• The past and future of tuberculosis research.

  PMID 19855821 · PMC2745564 · PLoS pathogens · 2009 · 8 claims · 6 setups

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  Integrating systems biology with epidemiology ('systems epidemiology') will be required to better predict TB's trajectory and eliminate the disease

  clinical mycobacterium mtbc patients fingerprinting whole-genome microarray

• PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.

  PMID 35338232 · PMC8956664 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  Two computational approaches (sub-sampling and phenotype-simulation) can be implemented to perform power calculations for bacterial GWAS using existing genome collections, packaged as the PowerBacGWAS pipeline

  enterococcus klebsiella mycobacterium faecium pan-genome burden variant

• The impact of low-cost, genome-wide resequencing on association studies.

  PMID 16004723 · PMC3525269 · Human genomics · 2005 · 8 claims · 4 setups

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  The HapMap project provides more than 500,000 SNPs across three major human populations, enabling genome-wide association studies via linkage disequilibrium tagging.

  bacterial phi-x case genome massively genome snp

• 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

• Molecular genomic approaches to infectious diseases in resource-limited settings.

  PMID 19855820 · PMC2745561 · PLoS medicine · 2009 · 8 claims · 5 setups

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  Researchers in most developing countries lack the technology, resources, and capacity to participate fully in genomics research.

  clinical mycobacterium trypanosoma theileria pcr-based molecular whole-genome

• Using DNA microarrays to study host-microbe interactions.

  PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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  DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

  streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene

• Versatile and open software for comparing large genomes.

  PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

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  MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

  escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level

• Have microarrays failed to deliver for developmental biology?

  PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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  Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

  drosophila caenorhabditis developing xenopus cdna genome-wide microarray