Not all scale free networks are born equal: The role of the seed graph in PPI network emulation

Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pržulj, Cenk Sahinalp

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

Abstract

The (asymptotic) degree distributions of the best known "scale free" network models are all similar and are independent of the seed graph used. Hence it has been tempting to assume that networks generated by these models are similar in general. In this paper we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the "right" seed graph, the duplication model captures many topological features of publicly available PPI networks very well.

Original languageEnglish (US)
Title of host publicationSystems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers
Pages1-13
Number of pages13
StatePublished - Dec 1 2007
Externally publishedYes
EventJoint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics - San Diego, CA, United States
Duration: Dec 1 2006Dec 3 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4532 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherJoint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics
CountryUnited States
CitySan Diego, CA
Period12/1/0612/3/06

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Hormozdiari, F., Berenbrink, P., Pržulj, N., & Sahinalp, C. (2007). Not all scale free networks are born equal: The role of the seed graph in PPI network emulation. In Systems Biology and Computational Proteomics - Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics, Revised Selected Papers (pp. 1-13). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4532 LNBI).