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[45] Barab´si AL, Dezs
Z, Ravasz E, Yook SH, Oltvai Z. Scale-free
and hierarchical structures in complex networks. AIP Conference
Proceedings 2003;661:1 e 16.
[46] Chung F, Lu L. The average distance in random graphs with given
expected degrees. Proc. Natl. Acad. Sci. USA 2002;99:15879 e 82.
[47] Bollob´s B, Riordan O. The diameter of a scale-free random
graph. Combintorica 2004;24:5 e 34.
[48] Chen F, Chen Z, Wang X, Yuan Z. The average path length of
scale-free networks. Communications in Nonlinear Science and
Numerical Simulation 2008;13:1405 e 10.
[49] Cohen R, Havlin S. Scale-free networks are ultra-small. Physical
Review Letters 2003;90:058701:1 e 058701:4.
[50] Winzler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K,
Andre B, et al. Functional characterization of the Saccharomyces
cerevisiae genome by gene deletion and parallel analysis. Science
1999;285:901 e 6.
[51] Giaever G, Chu AM, Ni L, Connelly C, Riles L, V ´ ronneau S,
et al. Functional profiling of the Saccharomyces cerevisiae
genome. Nature 2002;418:387 e 91.
[52] Gerdes SY, Scholle MD, Campbell JW, Bal ´ zsi G, Ravasz E,
Daugherty MD, et al. Experimental determination and system-
level analysis of essential genes in Escherichia coli MG1655. J
Bacteriology 2003;185:5673 e 84.
[53] Yu BJ, Sung BH, Koob MD, Lee CH, Lee JH, Lee WH, et al.
Minimization of the Escherichia coli genome using a Tn5-tar-
geted Cre/loxP excitation
[66] Rzhetsky A, Gomez SM. Birth of scale-free molecular networks
and the number of distinct DNA and protein domains per genome.
Bioinformatics 2001;17:988 e 96.
[67] Qian J, Luscombe NM, Gerstein M. Protein family and fold
occurrence in genomes: power-law behavior and evolutionary
model. J. Molecular Biology 2001;313:673 e 81.
[68] Bhan A, Galas DJ, Dewey TG. A duplication growth model of
gene expression networks. Bioinformatics 2002;18:1486 e 93.
[69] Pastor-Satorras R, Smith E, Sole R. Evolving protein interaction
networks
T
through gene duplication.
J Theoretical Biology
2003;222:199 e 210.
[70] Vazquez A, Flammini A, Maritan A, Vespignani A. Modeling of
protein interaction networks. ComPlexUs 2003;1:38 e 44.
[71] Kim J, Krapivsky PL, Kahng B, Redner S. Infinite-order perco-
lation and giant fluctuations in a protein interaction network.
Physical Review E 2002;66:055101.
[72] Wagner A. How the global structure of protein interaction networks
evolves. Proc Royal Society of London B 2003;270:457 e 66.
[73] Eisenberg E, Levanon EY. Preferential attachment in the protein
network evolution. Physical Review Letters 2003;91:138701.
[74] Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular
to modular cell biology. Nature 1999;402:C47 e 52.
[75] Wall ME, Hlavacek WS, Savageau MA. Design of gene circuits:
lessons from bacteria. Nature Reviews Genetics 2004;5:34 e 42.
[76] Alon U. Biological networks: the tinkerer as an engineer. Science
2003;301:1866 e 7.
[77] Alberts B. The cell as a collection of protein machines: preparing
the next generation of molecular biologists. Cell 1998;92:291 e 4.
[78] Ravasz E, Barab´si AL. Hierarchical organization in complex
networks. Physical Review E Statistical Nonlinear Soft Matter
Physics 67 2003;026112.
[79] Deisboeck TS, Yasha-Kresh J, Kepler TB. Complex Systems in
Biomedicine. 1st ed. New York, New York: Kluwer Academic
Publishing; 2005.
[80] Dorogovtsev SN, Goltsev AV, Mendes JFF. Pseudofractal scale-
free web. Physical Review E Statistical Nonlinear Soft Matter
Physics 2002;65:066122.
[81] Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV,
et al. Evidence for dynamically organized modularity in the yeast
protein-protein interaction network. Nature 2004;430:88 e 93.
[82] Maslov S, Sneppen K. Specificity and stability in topology of
protein networks. Science 2002;296:910 e 3.
[83] Newman MEJ. Assortative mixing in networks. Physical Review
Letters 2002;89:208701.
[84] V ´ zquez A, Pastor-Satorras R, Vespignani A. Large-scale topo-
logical and dynamical properties of the Internet. Physical Review
E 2002;65:066130 e 42.
[85] Colliza V, Flammini A, Maritan A, Vespignani A. Characteriza-
tion and modeling of protein-protein interaction networks. Phys-
ica A 2005;352:1 e 27.
[86] Goh K, Cusick ME, Valle D, Childs B, Vidal M, Barab´si AL.
The human disease network. Proc Natl Acad Sci USA
2007;104:8685 e 90.
[87] Oti M, Snel B, Huynen MA, Brunner HG. Predicting disease
genes using protein-protein interactions. J Medical Genetics
2006;43:691 e 8.
[88] Lage K, Karlberg EO, Størling ZM, Olason PI, Pedersen AG,
Rigina O, et al. A human phenome interactome network of protein
system. Nature Biotechnology
2002;20:1018 e 23.
[54] Kolysnychenko V, Plunkett G, Herring CD, Feh´rT,P´sfai J,
Blattner FR, et al. Engineering a reduced Escherichia coli
genome. Genome Research 2002;12:640 e 7.
[55] Albert R, Jeong H, Barab´si AL. Error and attack tolerance of
complex networks. Nature 2000;406:378 e 82.
[56] He X, Zhang J. Why do hubs tend to be essential in protein
networks? PLoS Genetics 2006;2:826 e 34.
[57] Havlin S, Cohen R. Complex Networks e Structure, Robustness and
Function. 1st ed. New York: Cambridge University Press; 2010.
[58] Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Genomic
analysis of essentiality within protein networks. Trends in
Genetics 2004;20:227 e 31.
[59] Hahn MW, Kern AD. Comparative genomics of centrality and
essentiality in three eukaryotic protein-interaction networks.
Molecular Biology and Evolution 2005;22:803 e 9.
[60] Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M,
et al. Systematic functional analysis of the Caenorhabditis elegans
genome using RNAi. Nature 2003;421:231 e 8.
[61] Prachumwat A, Li WH. Protein function, connectivity, and
duplicability in yeast. Molecular Biology and Evolution
2006;23:30 e 9.
[62] Yamada T, Bork P. Evolution of biomolecular networks: lessons
from metabolic and protein interactions. Nature Reviews Molec-
ular Cell Biology 2009;10:791 e 803.
[63] Liang H, Li WH. Gene essentiality, gene duplicability and protein
connectivity in human and mouse. Trends
in Genetics
2007;23:375 e 83.
[64] Wuchty S. Evolution and topology in the yeast protein interaction
network. Genome Research 2004;14:1310 e 4.
[65] Fraser HB. Modularity and evolutionary constraint on proteins.
Nature Genetics 2005;37:351 e 3.
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