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).

• Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

  PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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  Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

  medline annotated interactions consolidated conditional co-citation bayesian

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

  PMID 19756916 · PMC2778706 · Targeted oncology · 2009 · 8 claims · 5 setups

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  Genomic/gene expression profiling alone is insufficient to identify tumors with molecular pathway changes predictive of treatment outcome; protein-level functional assessment (activation states, PTMs, interactions) is also required

  microarray ffpe models cancer immunohistochemistry fret fret-flim

• 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

• Assembling a jigsaw puzzle with 20,000 parts.

  PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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  Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.

  yeast caenorhabditis escherichia proteome-wide microarray yeast rnai

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Systems biology: where it's at in 2005.

  PMID 16086862 · PMC1273629 · Genome biology · 2005 · 8 claims · 8 setups

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  High-throughput genetic-interaction and physical-interaction maps show only minimal overlap with each other, whereas literature-derived genetic and physical interaction maps share a much greater fraction of edges

  saccharomyces drosophila environmental literature systematic genome-wide

• Ontological visualization of protein-protein interactions.

  PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

  gene interacting interaction annotation yeast co-immunoprecipitation

• InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

  PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

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  InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

  saccharomyces homo bank computational yeast tandem

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

  PMID 19649302 · PMC2709445 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  A computational framework can build disease-specific drug-protein connectivity maps by integrating protein interaction networks and PubMed literature mining, without gene expression profiles from drug perturbation experiments

  seed ad-related retrieved combined protein-protein network-based pubmed

• 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

• Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.

  PMID 19779549 · PMC2739292 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  Human disease genes are much closer to aging genes in the PPI network than expected by chance

  protein-protein randomized dan aging network degree-conserved closeness

• 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

• Pathway analysis of kidney cancer using proteomics and metabolic profiling.

  PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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  31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

  ccrcc rcc computational random gel immunoblotting immunohistochemistry

• The role of positive selection in determining the molecular cause of species differences in disease.

  PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

  orthologous omim meta-database panther comparative disease protein-protein

• Proteomics and genomics: perspectives on drug and target discovery.

  PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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  Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma

  proteins blood carbohydrate medicinal x-ray microarrays glycan

• Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

  PMID 15882449 · PMC1134656 · BMC genomics · 2005 · 8 claims · 4 setups

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  A predictive computational screen covering ~40% of annotated protein-coding genes identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory motifs.

  upstream co-expression pre-b microarray-based motif gene

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• Interactome networks: the state of the science.

  PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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  Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

  genes tnfα orf proteins yeast tandem interference