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

• pTARGET: a web server for predicting protein subcellular localization.

  PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups

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  pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)

  eukaryotic complete pfam amino subcellular

• Automatic discovery of cross-family sequence features associated with protein function.

  PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

  non-redundant same evolved eukaryotic self-supervised experiment self-organizing

• Evolutionary origins of human apoptosis and genome-stability gene networks.

  PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

  apoptosis fully same orthologous protein-protein comparative orthology

• Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton.

  PMID 37098087 · PMC10128935 · PloS one · 2023 · 8 claims · 3 setups

  Has reproduction · 38

  Genes encoding superoxide (O2•−) scavenging are ubiquitous across phytoplankton, but their fractional gene allocation decreases with increasing cell radius, consistent with a nearly fixed core gene set.

  diverse annotated same comparative enzyme trait

• 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

• The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

  PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

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  P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

  sequences orthomcl yeast orthomcl jaccard phylogenetic

• 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

• Reconstructing the evolution of the mitochondrial ribosomal proteome.

  PMID 17604309 · PMC1950548 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  The ancestral mitoribosome was of alpha-proteobacterial descent and more than doubled its protein content in most eukaryotic lineages.

  proteomes eukaryotic aligned alignments iterative hmm-based neighbor-joining

• Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

  PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

  est gene worm fly blat-based transcription comparative

• 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

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Linking disease-associated genes to regulatory networks via promoter organization.

  PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

  orthologous eukaryotic genomatix pubmed promoter model additional

• What defines a photosynthetic microbial mat in western Antarctica?

  PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions

  microbial quality-filtered overflowing shotgun taxonomic alpha

• 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

• Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

  PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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  Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

  nine animals completed fungal combined sequence biochemical

• 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