Separating drivers from passengers in whole genome analysis

identification of combinatorial effects of genes by mining knowledge sources

Enrico W. Coiera, Stephen Anthony, Vitali Sintchenko

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contribution

Abstract

This study aimed to develop a new informatics platform for the discovery, recovery and multi-level analysis of the effects of individual genes and multiple gene combinations on pathophenotypes of bacteria. Natural language processing algorithms were employed to extract gene-disease associations from PubMed literature and annotated genomes of bacteria with epidemic potential. From these associations gene virulence profiles were generated enabling the comparison of gene signatures within and across genomes. It allowed the identification of virulence genes and construction of their association networks as well as the detection of knowledge gaps. This proof-of-concept study confirmed the feasibility of our original approach for integrating bacterial genome level knowledge with published observations from clinical settings.
Original languageEnglish
Title of host publicationBiotechno 2011
Subtitle of host publicationthe Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies : proceedings
EditorsPei-Yuan Qian, Son V. Nghiem
Place of PublicationUnited States
PublisherIARIA
Pages6-11
Number of pages6
ISBN (Print)9781612081373
Publication statusPublished - 2011
Externally publishedYes
EventBiotechno 2011 : the Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies - Venice/Mestre, Italy
Duration: 22 May 201127 May 2011

Conference

ConferenceBiotechno 2011 : the Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies
CityVenice/Mestre, Italy
Period22/05/1127/05/11

Keywords

  • structural bioinformatics
  • whole genome analysis
  • text mining
  • infectious diseases
  • knowledge discovery

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  • Cite this

    Coiera, E. W., Anthony, S., & Sintchenko, V. (2011). Separating drivers from passengers in whole genome analysis: identification of combinatorial effects of genes by mining knowledge sources. In P-Y. Qian, & S. V. Nghiem (Eds.), Biotechno 2011: the Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies : proceedings (pp. 6-11). United States: IARIA.