Function-preserving filters for sampling in biological networks

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

7 Citations (Scopus)

Abstract

Assays created to study systems of disease and aging can offer a whole new set of therapeutic targets. However, with experiments of this immense volume, data becomes unmanageable for many traditional analyses. Enter the biological network, a tool for modeling relationships among high-throughput data that is quickly rising in popularity. Small networks (in the order of hundreds to few thousands of nodes) use relationships between network structure to infer biological function; this relationship has been confirmed and used in many studies to advance the study of model organisms. Networks built for assessing entire genomes, or entire protein repertoires, however, tend to be very large and complex, having tens of thousands of nodes and in some cases upwards of millions of edges. Thus, network sampling techniques take an appropriate step to reduce complexity while modeling data. Here we present a new type of network sampling applied to biological correlations network, the spanning tree, designed to identify critical hub nodes in the model. We compare this filter to others previously used to identify structures in complex networks, chordal-based filters. The results of this work highlight the applicability for multiple filters based upon the graphic structure and biological result desired.

Original languageEnglish (US)
Title of host publicationProcedia Computer Science
PublisherElsevier
Pages587-595
Number of pages9
Volume9
DOIs
StatePublished - 2012
Event12th Annual International Conference on Computational Science, ICCS 2012 - Omaha, NB, United States
Duration: Jun 4 2012Jun 6 2012

Other

Other12th Annual International Conference on Computational Science, ICCS 2012
CountryUnited States
CityOmaha, NB
Period6/4/126/6/12

Fingerprint

Sampling
Complex networks
Data structures
Assays
Genes
Aging of materials
Throughput
Proteins
Experiments

Keywords

  • Biological networks
  • Chordal graphs
  • Spanning tree

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Function-preserving filters for sampling in biological networks. / Cooper, Kathryn M; Bhowmick, Sanjukta; Ali, Hesham H.

Procedia Computer Science. Vol. 9 Elsevier, 2012. p. 587-595.

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

Cooper, KM, Bhowmick, S & Ali, HH 2012, Function-preserving filters for sampling in biological networks. in Procedia Computer Science. vol. 9, Elsevier, pp. 587-595, 12th Annual International Conference on Computational Science, ICCS 2012, Omaha, NB, United States, 6/4/12. https://doi.org/10.1016/j.procs.2012.04.063
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