Global network alignment in the context of aging

Tijana Milenković, Han Zhao, Fazle E. Faisal

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

Abstract

Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2)Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human between aligned network regions. By doing so, we produce novel agingrelated information, which complements currently available information about aging that has been obtained mainly by sequence alignment, especially in human. To our knowledge, we are the first to use NA to learn more about aging.

Original languageEnglish (US)
Title of host publication2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Pages23-32
Number of pages10
DOIs
StatePublished - 2013
Externally publishedYes
Event2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 - Wshington, DC, United States
Duration: Sep 22 2013Sep 25 2013

Publication series

Name2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013

Other

Other2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Country/TerritoryUnited States
CityWshington, DC
Period9/22/139/25/13

Keywords

  • Aging
  • Network alignment
  • Protein function prediction

ASJC Scopus subject areas

  • Bioengineering
  • Biomedical Engineering
  • Health Informatics

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