An introduction to artificial neural networks in bioinformatics--application to complex microarray and mass spectrometry datasets in cancer studies.
AffiliationClinical and Experimental Pharmacology, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, UK. firstname.lastname@example.org
MetadataShow full item record
AbstractApplications of genomic and proteomic technologies have seen a major increase, resulting in an explosion in the amount of highly dimensional and complex data being generated. Subsequently this has increased the effort by the bioinformatics community to develop novel computational approaches that allow for meaningful information to be extracted. This information must be of biological relevance and thus correlate to disease phenotypes of interest. Artificial neural networks are a form of machine learning from the field of artificial intelligence with proven pattern recognition capabilities and have been utilized in many areas of bioinformatics. This is due to their ability to cope with highly dimensional complex datasets such as those developed by protein mass spectrometry and DNA microarray experiments. As such, neural networks have been applied to problems such as disease classification and identification of biomarkers. This review introduces and describes the concepts related to neural networks, the advantages and caveats to their use, examples of their applications in mass spectrometry and microarray research (with a particular focus on cancer studies), and illustrations from recent literature showing where neural networks have performed well in comparison to other machine learning methods. This should form the necessary background knowledge and information enabling researchers with an interest in these methodologies, but not necessarily from a machine learning background, to apply the concepts to their own datasets, thus maximizing the information gain from these complex biological systems.
CitationAn introduction to artificial neural networks in bioinformatics--application to complex microarray and mass spectrometry datasets in cancer studies. 2009, 10 (3):315-29 Brief. Bioinformatics
JournalBriefings in Bioinformatics
- Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics.
- Authors: Phan JH, Quo CF, Wang MD
- Issue date: 2006
- Neural networks.
- Authors: Yang ZR
- Issue date: 2010
- Clinical bioinformatics.
- Authors: Chang PL
- Issue date: 2005 Apr
- Prediction of peptides observable by mass spectrometry applied at the experimental set level.
- Authors: Sanders WS, Bridges SM, McCarthy FM, Nanduri B, Burgess SC
- Issue date: 2007 Nov 1
- Machine learning in bioinformatics: a brief survey and recommendations for practitioners.
- Authors: Bhaskar H, Hoyle DC, Singh S
- Issue date: 2006 Oct