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).

• The global landscape of sequence diversity.

  PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups

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  Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.

  fully eukaryotic complete gene blast-based est gene

• 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

• Pseudofam: the pseudogene families database.

  PMID 18957444 · PMC2686518 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  Pseudofam is an online database of pseudogene families built by mapping pseudogenes to Pfam protein families, providing query tools, statistics, and sequence alignments

  eukaryotic over pseudogenes pseudogene blast family sequence

• 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

• An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage.

  PMID 15606920 · PMC544558 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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  SVD-based analysis of tetrapeptide frequency vectors can compare whole eukaryotic proteomes without pre-defining orthologs or aligning homologous sites

  predicted nine svd-derived ras svd species bootstrap

• 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

• The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

  PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.

  est clustered sequences sequence est sequence orf

• Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

  PMID 35288549 · PMC8921327 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 58

  P. cf. balticum produces carbon-rich 'mucospheres' that attract, capture and immobilise a wide range of prokaryotic and eukaryotic prey

  balticum xenic tara prokaryotic its lc-ms 18s

• Gene duplication: the genomic trade in spare parts.

  PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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  Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

  great genome recently yeast genome-wide molecular comparative