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).

• Empirical codon substitution matrix.

  PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

  orthologous million codon same pairwise empirical comparative

• From genomics to chemical genomics: new developments in KEGG.

  PMID 16381885 · PMC1347464 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  KEGG BRITE has been formally added as a fourth main KEGG database to establish a logical foundation for functional interpretation and pathway reconstruction.

  enzymatic substrate kegg complete chemical number ortholog

• Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

  PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

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  Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

  proteomes predicted long prokaryotic coiled-coil all-against-all sequence

• Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

  PMID 15757514 · PMC1084347 · BMC microbiology · 2005 · 8 claims · 7 setups

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  PSI-BLAST identified several novel homologies between LEE-encoded and Ysc-Yop-associated proteins

  lee-encoded escc sepq escd psi-blast blastp domain

• Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

  PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 8 setups

  Has reproduction · 99

  Verrucomicrobia is highly prevalent in north-temperate freshwater lakes, on average the 4th most abundant phylum (range 1.7–41.7%).

  southeastern lake muskegon lake-type 16s within-phylum phylogenetic

• Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

  PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups

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  HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.

  proteome homo domains hmm-hmm hmm subtractive

• From single cells to whole organisms.

  PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

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  The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

  saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai