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).

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• PhylomeDB: a database for genome-wide collections of gene phylogenies.

  PMID 17962297 · PMC2238872 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  PhylomeDB is a publicly accessible database storing complete, genome-wide collections of gene phylogenies (phylomes).

  seed homologous trimmed homology sequence neighbor

• Topological approximate Bayesian computation for parameter inference of an angiogenesis model.

  PMID 35191485 · PMC9048691 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 3 setups

  Has reproduction · 100

  TDA summary statistics can be combined with ABC to infer parameters (ρ, χ) of the Anderson–Chaplain angiogenesis model

  square simplicial simulated computational persistent approximate

• Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

  PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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  Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

  tuberculosis putative orthologous genomewide blastp clustal nei-gojobori

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Bayesian coestimation of phylogeny and sequence alignment.

  PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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  Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

  globin same four-sequence bayesian mcmc comparison

• Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

  PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

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  Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

  animals cdk encephalitozoon pfmrk comparative bayesian distance

• PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

  PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC

  homo peroxisomal bona eukaryotic annotation comparative sequence

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

  PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

  fish full-length tetraodon rt-pcr database molecular

• A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

  PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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  A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

  cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

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  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray

• Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

  PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

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  N. lactamica por is less diverse than meningococcal porB2 and porB3

  lactamica unique pcr distance-based population