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).

• Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

  PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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  Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

  swissprot nssnp-containing nssnps machine single-attribute sequence

• Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

  PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

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  Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

  pdb obligatory same psi-blast solvent residue

• Computational verification of protein-protein interactions by orthologous co-expression.

  PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

  cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous

• 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

• The cohesin complex: sequence homologies, interaction networks and shared motifs.

  PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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  Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

  smc1 smc3 mmip1 smc psi-blast phylogenetic sequence

• targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

  PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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  A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

  tuberculosis mtb protein-protein flux transposon

• What makes species unique? The contribution of proteins with obscure features.

  PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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  POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

  eukaryotic animal cerevisiae homo hmmpfam blast tblastn

• NovelFam3000--uncharacterized human protein domains conserved across model organisms.

  PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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  NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

  lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining

• The European Bioinformatics Institute's data resources: towards systems biology.

  PMID 15608238 · PMC539980 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Since 2003 the EBI has launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI)

  proteins varies vertebrate newly macromolecular microarray protein-protein

• hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

  PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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  hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

  mgc cloned orfs genome gateway orf blat