GIANT: A cytoscape plugin for modular networks

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Cumbo, Fabio ^a   Paci, Paola ^a,b   Santoni, Daniele ^a   Di Paola, Luisa ^c   Giuliani, Alessandro ^d  

^a CNR   (Italy)

^b SysBio Centre for Systems Biology   (Italy)

^c UNIVERSITY CAMPUS BIO MEDICO   (Italy)

^d ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN;

ALGORITHM; ARTICLE; CALCULATION; CHEMISTRY; COMPUTER PREDICTION; COMPUTER PROGRAM; FRUIT RIPENING; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GRAPE; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MATHEMATICAL ANALYSIS; NONHUMAN; PLANT GENE; PROTEIN STRUCTURE; SIMULATION; VITIS;

ALGORITHMS; CHEMISTRY; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENETICS; HEMOGLOBINS; HUMANS; SOFTWARE; VITIS;

EID: 84907487776     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0105001     Document Type: Article

References (25)

1. Han J, Bertin N, Hao T., Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein protein interaction network. Nature 430: 88-93.
2. Jeong H, Mason S, Barabàsi A, Oltvai Z (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
3. Oliva G, Di Paola L, Giuliani A, Pascucci F., Setola R (2013) Assessing protein resilience via a complex network approach. In: Network Science Workshop (NSW), 2013 IEEE 2nd. IEEE, pp. 131-137.
4. Csermely P, Korcsmáros T, Kiss H., London G, Nussinov R (2013) Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 138: 333-408.
5. Guimerà R, Amaral LAN (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
6. Bassett D, Meyer-Lindenberg A, Achard S., Duke T, Bullmore E (2006) Adaptive reconfiguration of fractal small-world human brain functional networks. Nat Rev Neurosci 103: 19518-19523.
7. Pessoa L (2008) On the relationship between emotion and cognition. Nat Rev Neurosci 9: 148-158.
8. Guimerà R, Mossa S, Turtschi A, Amaral L (2005) The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles. PNAS 102: 7794-7799.
9. Di Paola L, De Ruvo M, Paci P, Santoni D., Giuliani A (2013) Proteins contact networks: an emerging paradigm in chemistry. Chem Rev 113: 1598-1613.
10. De Ruvo M, Giuliani A, Paci P., Santoni D, Di Paola L (2012) Shedding light on protein-ligand binding by graph theory: The topological nature of allostery. Biophys Chem 165-166: 21-29.
11. Krishnan A, Zbilut JP, Tomita M, Giuliani A (2008) Proteins as networks: usefulness of graph theory in protein science. Curr Protein Pept Sc 9: 28-38.
12. Tasdighian S, Di Paola L, De Ruvo M, Paci P, Santoni D, et al. (2013) Modules identification in protein structures: the topological and geometrical solutions. J Chem Inf Model 54: 159-168.
13. Morris J, Apeltsin L, Newman A., Baumbach J, Wittkop T, et al. (2011) clusterMaker: a multi-algorithm clustering plugin for cytoscape. BMC Bioinformatics 12.
14. Shannon P, Markiel A, Ozier O., Baliga N, Wang J, et al. (2003) Cytoscape: a software environment for integra ted models of biomolecular interaction networks. Genome Res 13: 2498-2504.
15. Meila M, Shi J (2001) Learning segmentation by random walks. Neural Information Processing Systems 13: 873-879.
16. Dongen SV (1997) Graph Clustering by Flow Simulation. Ph.D. thesis, University of Utrecht, The Netherlands.
17. Jain A (2009) Data clustering: 50 years beyond k-means. Pattern Recogn Lett 31: 651-666.
18. Guimerà R, Sales-Pardo M, Amaral LAN (2006) Classes of complex networks defined by role-to-role connectivity profiles. Nat Phys 3: 63-69.
19. Hardison R, Chui D, Giardine B., Riemer C, Patrinos G, et al. (2002) HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Human mutation 19: 225-233.
20. Monod J, Wyman J, Changeux J (1965) On the nature of allosteric transitions: a plausible model. J Mol Biol 12: 88-118.
21. Paci P, Di Paola L, Santoni D, De Ruvo M, Giuliani A (2012) Structural and functional analysis of hemoglobin and serum albumin through protein longrange interaction networks. Curr Proteomics 9: 160-166.
22. Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663-76.
23. Fasoli M, Santo SD, Zenoni S, Tornielli G., Farina L, et al. (2012) The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program. The Plant Cell 24: 3489-3505.
24. Bollobas B (1985) Random Graphs. Cambridge Studies in Advanced Mathematics. New York: Academic Press.
25. Barabàsi A, Albert R (1999) Emergence of scaling in random networks. Science 286: 509.