Login

Join for Free!
114035 members
table of contents table of contents

A recent definition of a reference set of proteins essential for the …


Biology Articles » Immunobiology » Efficiency of the immunome protein interaction network increases during evolution » References

References
- Efficiency of the immunome protein interaction network increases during evolution

  1. Vespignani A: Evolution thinks modular.

    Nat Genet 2003, 35:118-119.

  2. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: simple building blocks of complex networks.

    Science 2002, 298:824-827.

  3. Shen-Orr SS, Milo R, Mangan S, Alon U: Network motifs in the transcriptional regulation network of Escherichia coli.

    Nat Genet 2002, 31:64-68. 

  4. Wuchty S, Oltvai ZN, Barabasi AL: Evolutionary conservation of motif constituents in the yeast protein interaction network.

    Nat Genet 2003, 35:176-179. 

  5. Mazurie A, Bottani S, Vergassola M: An evolutionary and functional assessment of regulatory network motifs.

    Genome Biol 2005, 6:R35

  6. Berg J, Lassig M, Wagner A: Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications.

    BMC Evol Biol 2004, 4:51.

  7. Beltrao P, Serrano L: Specificity and evolvability in eukaryotic protein interaction networks.

    PLoS Comput Biol 2007, 3:e25. 

  8. Bloom JD, Adami C: Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets.

    BMC Evol Biol 2003, 3:21. 

  9. Jordan IK, Wolf YI, Koonin EV: No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly.

    BMC Evol Biol 2003, 3:1.

  10. Plotkin JB, Fraser HB: Assessing the determinants of evolutionary rates in the presence of noise.

    Mol Biol Evol 2007, 24:1113-1121.

  11. Drummond DA, Raval A, Wilke CO: A single determinant dominates the rate of yeast protein evolution.

    Mol Biol Evol 2006, 23:327-337. 

  12. Stumpf MP, Kelly WP, Thorne T, Wiuf C: Evolution at the system level: the natural history of protein interaction networks.

    Trends Ecol Evol 2007, 22:366-373. 

  13. Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG: A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network.

    BMC Syst Biol 2007, 1:34.

  14. Qin H, Lu HH, Wu WB, Li WH: Evolution of the yeast protein interaction network.

    Proc Natl Acad Sci USA 2003, 100:12820-12824. 

  15. Litman GW, Cooper MD: Why study the evolution of immunity?

    Nat Immunol 2007, 8:547-548. 

  16. Ortutay C, Siermala M, Vihinen M: Molecular characterization of the immune system: emergence of proteins, processes, and domains.

    Immunogenetics 2007, 59:333-348. 

  17. Ortutay C, Vihinen M: A reference set of genes and proteins for systems biology of the human immune system.

    Cell Immunol 2006, 244:87-89. 

  18. Ortutay C, Siermala M, Vihinen M: ImmTree: Database of evolutionary relationships of genes and proteins in the human immune system.

    Immunome Res 2007, 3:4.

  19. Mathivanan S, Periaswamy B, Gandhi TK, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A: An evaluation of human protein-protein interaction data in the public domain.

    BMC Bioinformatics 2006, 7(Suppl 5):S19. 

  20. Bales ME, Johnson SB: Graph theoretic modeling of large-scale semantic networks.

    J Biomed Inform 2006, 39:451-464.

  21. Amaral LA, Scala A, Barthelemy M, Stanley HE: Classes of small-world networks.

    Proc Natl Acad Sci USA 2000, 97:11149-11152.

  22. Doherty IA, Padian NS, Marlow C, Aral SO: Determinants and consequences of sexual networks as they affect the spread of sexually transmitted infections.

    J Infect Dis 2005, 191(Suppl 1):S42-54

  23. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions.

    Nature 2002, 417:399-403

  24. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW: Evolutionary rate in the protein interaction network.

    Science 2002, 296:750-752.

  25. Pastor-Satorras R, Vespignani A: Epidemic spreading in scale-free networks.

    Phys Rev Lett 2001, 86:3200-3203.

  26. Schintler L, Gorman S, Reggiani A, Patuelli R, Gillespie A, Nijkamp P, Rutherford J: Complex network phenomena in telecommunication systems.

    Network Spatial Econ 2005, 5:351-370.

  27. Onnela JP, Saramaki J, Hyvonen J, Szabo G, Lazer D, Kaski K, Kertesz J, Barabasi AL: Structure and tie strengths in mobile communication networks.

    Proc Natl Acad Sci USA 2007, 104:7332-7336.

  28. Albert R, Jeong H, Barabasi AL: Error and attack tolerance of complex.

    Nature 2000, 406:378-382.

  29. Xulvi-Brunet R, Sokolov IM: Growing networks under geographical constraints.

    Phys Rev E Stat Nonlin Soft Matter Phys 2007, 75:046117

  30. Barabasi AL, Albert R: Emergence of scaling in random networks.

    Science 1999, 286:509-512.

  31. Dorogovtsev SN, Mendes JF: Scaling properties of scale-free evolving networks: continuous approach.

    Phys Rev E Stat Nonlin Soft Matter Phys 2001, 63:056125

  32. Koonin EV, Wolf YI, Karev GP: The structure of the protein universe and genome evolution.

    Nature 2002, 420:218-223.

  33. Eisenberg E, Levanon EY: Preferential attachment in the protein network evolution.

    Phys Rev Lett 2003, 91:138701.

  34. Eriksen KA, Hornquist M: Scale-free growing networks imply linear preferential attachment.

    Phys Rev E Stat Nonlin Soft Matter Phys 2002, 65:017102.

  35. Wuchty S, Ravasz E, Barabasi AL: The Architecture of Biological Networks. In Complex Systems in Biomedicine. Edited by: Deisboeck TS YKJ, Kepler TB. New York: Kluwer Academic Publishing; 2003.

  36. Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization.

    Nat Rev Genet 2004, 5:101-113. 

  37. Yook SH, Oltvai ZN, Barabasi AL: Functional and topological characterization of protein interaction networks.

    Proteomics 2004, 4(4):929-842.

  38. Dorogovtsev S, Mendes J: Evolution of networks: from biological nets to the Internet and WWW. Oxford: Oxford University Press; 2003.

  39. Palla G, Barabasi AL, Vicsek T: Quantifying social group evolution.

    Nature 2007, 446:664-667.

  40. Wuchty S: Evolution and topology in the yeast protein interaction network.

    Genome Res 2004, 14:1310-1314.

  41. Wuchty S, Barabasi AL, Ferdig MT: Stable evolutionary signal in a yeast protein interaction network.

    BMC Evol Biol 2006, 6:8. 

  42. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R: IntAct-open source resource for molecular interaction data.

    Nucleic Acids Research 2006, 35:D561-565.

  43. Colland F, Jacq X, Trouplin V, Mougin C, Groizeleau C, Hamburger A, Meil A, Wojcik J, Legrain P, Gauthier J: Functional proteomics mapping of a human signaling pathway.

    Genome Research 2004, 14:1324-1332.

  44. Yu H, Luscombe N, Lu H, Zhu X, Xia Y, Han J, Bertin N, Chung S, Vidal M, Gerstein M: Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

    Genome Research 2004, 14:1107-1118.

  45. Liang Z, Xu M, Teng M, Niu L: Comparison of protein interaction networks reveals species conservation and divergence.

    BMC Bioinformatics 2006, 7:457.

  46. Hurst LD, Smith NG: Do essential genes evolve slowly?

    Curr Biol 1999, 9:747-750.

  47. Mirny L, Shakhnovich E: Evolutionary conservation of the folding nucleus.

    J Mol Biol 2001, 308:123-129.

  48. Latora V, Marchiori M: Efficient behavior of small-world networks.

    Phys Rev Lett 2001, 87:198701.

  49. Gol'dshtein V, Koganov G, Surdutovich G: Vulnerability and hierarchy of complex networks.

    Arxiv preprint cond-mat/0409298 2004.

  50. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks.

    Genome Res 2003, 13:2498-2504.

  51. Csardi G, Nepusz T: The igraph software package for complex network research.

    InterJournal Complex Systems 2006, 1695.


rating: 0.00 from 0 votes | updated on: 20 Jul 2009 | views: 5506 |

Rate article:







excellent!bad…