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).

• Having a BLAST with bioinformatics (and avoiding BLASTphemy).

  PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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  BLAST is the most widely used tool for searching biological sequences for regions of local similarity

  superfamilies blocks query pairwise phylogenetic sequence heuristic

• Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

  PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

  non-identical gene3d cath whole-gene domain transmembrane

• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

  PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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  Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

  consensus sap query all-against-all blast cross-database

• InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

  PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

  eukaryotic homo sequence species pairwise algorithm low-complexity

• A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.

  PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups

  Has reproduction · 69

  Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.

  mus chuniphyes hormiphora pleuromamma rna-seq homology

• Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

  PMID 12890320 · PMC3023423 · Emerging infectious diseases · 2003 · 8 claims · 4 setups

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  Lateral gene transfer (LGT) produced roughly three times as many nucleotide changes as point mutation among the 96 O139 isolates.

  vibrio same novel aligned multilocus pcr blast