Bioinformatics mining and modeling methods for the identification of disease mechanisms in neurodegenerative disorders

Martin Hofmann-Apitius*, Gordon Ball, Stephan Gebel, Shweta Bagewadi, Bernard De Bono, Reinhard Schneider, Matt Page, Alpha Tom Kodamullil, Erfan Younesi, Christian Ebeling, Jesper Tegnér, Luc Canard

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

34 Scopus citations

Abstract

Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies—data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI); which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations (EFPIA) and the European Commission (EC).

Original languageEnglish (US)
Pages (from-to)29179-29206
Number of pages28
JournalInternational Journal of Molecular Sciences
Volume16
Issue number12
DOIs
StatePublished - Dec 7 2015

Keywords

  • Bioinformatics
  • Data integration
  • Disease models
  • Genetics
  • Graphical models
  • Knowledge-based modeling
  • Mechanism-identification
  • Multiscale
  • Neurodegeneration

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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