A gene network for navigating the literature

By Robert Hoffmann, Alfonso Valencia. Nature Genetics, 2004

548 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4b2bf55b01a632d2b85197114c8f7e76ec4d76e6

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In Molecular Biology

Citations in the corpus

ALSoD: A user‐friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics (2012, background): “, 2009], iHop [Hoffmann and Valencia, 2004], Pathway in KEGG [Kanehisa et al.”
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks (2008, background): “We have added this capability, enabling direct connection with the following databases: • BioModels: database of annotated computational models [14](10); • SGD: Saccharomyces Genome Database [17](11); • DBGET: database retrieval system for a diverse range of molecular biology databases [18](12); • i”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, background): “In a similar vein, additional functional relationships will undoubtedly be uncovered by different experimental and computational procedures, such as high-throughput comparative analysis of mutant cellular phenotypes [2], genome-wide genetic interaction screens [88,89], and automated text mining [90,”
Biomedical text mining and its applications in cancer research (2013, unknown): “iHOP [70,71,153] Information Hyperlinked over Proteins (iHOP) can generate a network of concurring genes and proteins from millions of PubMed abstracts.”
Text-mining and information-retrieval services for molecular biology (2005, methodology): “One system that extracts annotations and detects interactions is the iHOP system that we have implemented at the Spanish National Biotechnology Center [40].”
Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses (2011, unknown): “Analysis of the established annotation resources, such as SwissProt (UniProt Consortium, 2007), GeneCards (www.genecards. org), WikiGenes (www.wikigenes.org), and IHOP (Hoffmann and Valencia, 2004), suggests that a significant fraction of genes in the identified network either play a well-defined fu”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “Annotated pathway knowledge is mostly kept in a separate set of resources (22–24) and yet other interactions can be found in various organism-speciﬁc databases (25,26) or text-mining resources (27,28).”
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D (2009, background): “Several systems have been developed to make the curation ∗To whom correspondence should be addressed. process more accurate, faster and effective (Donaldson et al., 2003; Hoffmann and Valencia, 2004).”
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort (2013, background): “org/), NCBI’s Entrez Gene (25), iHOP (26), Gene Cards (27) or NCBI’s PubMed (http://www.”
Implementing the iHOP concept for navigation of biomedical literature (2005, background): “The iHOP concept (Information Hyperlinked over Proteins) has recently been introduced to potential users (Hoffmann and Valencia, 2004); here, we discuss its feasibility and technical implementation.”
Extracting interactions between proteins from the literature (2008, unknown): “After that, researchers in biomedical domain contribute to the curation process by subsequent edits cbioc.eas.asu.edu Chilibot Chilibot [24] is a search software for MEDLINE literature database to rapidly identify relationships between genes, proteins, or any keywords that the user might be interest”