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).

• Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

  PMID 24987116 · PMC4299494 · Molecular systems biology · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  MinSpan, a mixed-integer linear optimization algorithm, computes the shortest, linearly independent pathways (sparsest basis of the null space of the stoichiometric matrix S) for genome-scale metabolic networks, which convex approaches (extreme pathways, elementary flux modes) cannot do at genome scale.

  simplified genome-scale cerevisiae coli minspan spearman comparative

• Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

  PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 7 claims · 7 setups

  Has reproduction · 89

  STEC are prevalent in surface waters of four Lower Mainland BC watersheds, recovered from 21.6, 23.2, 19.5, and 9.2% of samples across sites, with seasonal variation (13.3% in fall to 34.3% in winter).

  surface coli presumptive confirmed hydrophobic sandwich monoplex

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

  PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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  Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

  chromosome genomic pbmc multi-species phylogenetic bisulphite

• Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

  PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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  Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

  yeast specified normal coli chip-on-chip chip-sequencing correlation-based

• The key role of genomics in modern vaccine and drug design for emerging infectious diseases.

  PMID 19855822 · PMC2752168 · PLoS genetics · 2009 · 8 claims · 8 setups

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  Reverse vaccinology (in silico genome screening for surface/secreted proteins) can identify vaccine candidates far faster than conventional approaches, as demonstrated by the MenB project.

  neisseria streptococcus coli vibrio reverse pan-genomic comparative

• Shaken not stirred: a global research cocktail served in Hinxton.

  PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups

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  Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process

  budding caenorhabditis drosophila escherichia two-color double chip-chip

• Harnessing the HGP of public health.

  PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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  The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

  carnation cirv blood rice x-ray site-directed mass

• International sequencing consortium.

  PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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  The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

  cirv blood sampled rice x-ray site-directed mass

• Cryptosporidium: genomic and biochemical features.

  PMID 19187778 · PMC2819285 · Experimental parasitology · 2010 · 8 claims · 8 setups

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  C. parvum lacks a plastid and mitochondrial genome, unlike other apicomplexans, limiting plastid-targeted drug strategies

  parvum yeast recombinant gp40 pulsed-field happy genome

• Helicobacter Pylori's plasticity zones are novel transposable elements.

  PMID 19727398 · PMC2731543 · PloS one · 2009 · 8 claims · 8 setups

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  Plasticity zones are a novel class of transposable elements (named TnPZs), flanked by direct repeats of 5'AAGAATG and inserted at multiple discrete chromosomal sites

  pylori shimaa model mammalian pcr-based genome pcr