Modeling information flow in biological networks

Physical Biology

Volumn 8, Issue 3, 2011, Pages

  Kim, Yoo Ah ^a   Przytycki, Jozef H ^b   Wuchty, Stefan ^a   Przytycka, Teresa M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b GEORGE WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; GENETICS; GENOTYPE; HUMAN; METHODOLOGY; PHENOTYPE; PHYSIOLOGY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; REVIEW;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENOTYPE; HUMANS; MODELS, BIOLOGICAL; PHENOTYPE; PROTEIN BINDING; PROTEIN INTERACTION MAPS;

EID: 79956222534     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/8/3/035012     Document Type: Article

References (26)

1. Ewing R M et al 2007 Large-scale mapping of human protein-protein interactions by mass spectrometry Mol. Syst. Biol. 3 89
2. Rual J F et al 2005 Towards a proteome-scale map of the human protein-protein interaction network Nature 437 1173-8
3. Stelzl U et al 2005 A human protein-protein interaction network: a resource for annotating the proteome Cell 122 957-68 (Pubitemid 41345212)
4. Gavin A C et al 2006 Proteome survey reveals modularity of the yeast cell machinery Nature 440 631-6
5. Giot L et al 2003 A protein interaction map of Drosophila melanogaster Science 302 1727-36 (Pubitemid 37505730)
6. Krogan N J et al 2006 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440 637-43
7. Li S et al 2004 A map of the interactome network of the metazoan C. elegans Science 303 540-3 (Pubitemid 38120855)
8. Kim Y A, Wuchty S and Przytycka T M 2011 Identifying causal genes and dysregulated pathways in complex diseases PLoS Comput. Biol. at press
9. Kim Y A, Wuchty S and Przytycka T M 2010 Simultaneous identification of causal genes and dys-regulated pathways in complex diseases Lecture Notes on Computer Science vol 6044 pp 263-80
10. Missiuro P V et al 2009 Information flow analysis of interactome networks PLoS Comput. Biol. 5 e1000350
11. Newman M 2005 A measure of betweenness centrality based on random walks Soc. Netw. 27 39-54 (Pubitemid 40272648)
12. Suthram S et al 2008 eQED: an efficient method for interpreting eQTL associations using protein networks Mol. Syst. Biol. 4 162
13. Tu Z et al 2006 An integrative approach for causal gene identification and gene regulatory pathway inference Bioinformatics 22 e489-96
14. Doyle P G and Snell J 2000 Random walks and electric networks Am. Math. Mon. 94 202
15. Yeger-Lotem E et al 2009 Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity Nat. Genet. 41 316-23
16. Lee E et al 2009 Analysis of AML genes in dysregulated molecular networks BMC Bioinformatics 10 (Suppl. 9) S2
17. Brem R B and Kruglyak L 2005 The landscape of genetic complexity across 5700 gene expression traits in yeast Proc. Natl Acad. Sci. USA 102 1572-7 (Pubitemid 40209209)
18. Ahuja R K, Magnanti T L and Orlin J B 1993 Network Flows : Theory, Algorithms, and Applications (Englewood Cliffs, NJ: Prentice Hall)
19. Kohler S et al 2008 Walking the interactome for prioritization of candidate disease genes Am. J. Hum. Genet. 82 949-58
20. Vanunu O and Sharan R 2008 A propagation-based algorithm for inferring gene-disease associations German Conf. on Bioinformatics (Lecture Notes in Informatics vol P-136) pp 54-63
21. Stojmirovic A and Yu Y K 2007 Information flow in interaction networks J. Comput. Biol. 14 1115-43 (Pubitemid 350073529)
22. Nabieva E et al 2005 Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps Bioinformatics 21 (Suppl. 1) i302-10
23. Tutte W T 2001 Graph Theory (Cambridge: Cambridge University Press)
24. Zotenko E et al 2008 Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality PLoS Comput. Biol. 4 e1000140
25. Potokina E et al 2008 Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation Plant J. 53 90-101 (Pubitemid 350265242)
26. Carlson D H 1986 What are Schur complements, anyway? Linear Alg. Appl. Rep. 74 257-75