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).

• Reconstruction of human protein interolog network using evolutionary conserved network.

  PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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  A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

  ppi sequences interaction predicted interolog orthology quasi-clique

• A survey of integral alpha-helical membrane proteins.

  PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.

  pfam-a organisms 34-genome integral transmembrane comparative sequence

• 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

• g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

  PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

  input 1000-bp microarray organisms functional transcription gene

• MODBASE: a database of annotated comparative protein structure models and associated resources.

  PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

  uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain

• PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

  PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

  sequences query swiss-prot naive-bayes blast feature

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

  PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

  sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining