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).

• Protein length in eukaryotic and prokaryotic proteomes.

  PMID 15951512 · PMC1150220 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  Eukaryotic proteins are significantly longer than prokaryotic proteins across virtually all functional categories and the majority of protein families

  eukaryotic proteins genomic cog comparative orthology domain

• InParanoid 6: eukaryotic ortholog clusters with inparalogs.

  PMID 18055500 · PMC2238924 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  InParanoid 6 is an updated eukaryotic ortholog database covering 35 species (34 eukaryotes plus E. coli as outgroup), providing pairwise ortholog clusters with inparalogs for all species pairs.

  eukaryotic pairwise average pairwise inparanoid upgma

• The human phylome.

  PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

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  Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

  proteome proteins neighbor-joining maximum bayesian

• From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

  PMID 17983265 · PMC2062474 · PLoS computational biology · 2007 · 8 claims · 7 setups

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  There has been a large turnover of the mitochondrial proteome during evolution: cell envelope synthesis proteins virtually disappeared, and replication, transcription, cell division, transport, regulation, and signal transduction proteins were replaced by eukaryotic proteins

  alpha-proteobacterial reclinomonas reconstructed yeast comparative phylogenomic cog

• Inparanoid: a comprehensive database of eukaryotic orthologs.

  PMID 15608241 · PMC540061 · Nucleic acids research · 2005 · 8 claims · 4 setups

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  The Inparanoid algorithm identifies true ortholog clusters by seeding on reciprocal best-matching pairs, gathering inparalogs (post-speciation duplicates) while excluding outparalogs (pre-speciation duplicates)

  eukaryotic pairwise uniprot sequences whole-genome inparanoid redundancy

• Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

  PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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  The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

  cerevisiae mitocarta mitochondrial tissues comparative subcellular gene

• 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

• DBD--taxonomically broad transcription factor predictions: new content and functionality.

  PMID 18073188 · PMC2238844 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  DBD is a database of predicted sequence-specific DNA-binding transcription factors covering over 700 publicly available proteomes, up from 150 in the initial version.

  proteomes eukaryotic genomes hmm-based comparative heatmap

• Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

  PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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  Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

  mitoproteome orthologous liver mitochondrial sequence-based computational literature