Biology Reference
In-Depth Information
REFERENCES
[1] Alm E, Arkin A. Biological networks. Current Opinion in
Structural Biology 2003;13:193
e
202.
[2] Barab´si AL, Oltvai ZN. Network biology: understanding the
cell's
[21] Tong AHY, Lesage G, Bader GD, Ding H, Xu H, Xin X, et al.
Global mapping of the yeast genetic interaction network. Science
1999;286:509
e
21.
[22] Salgado H, Gama-Castro S, Peralta-Gil M, D´az-Peredo E, S´n-
chez-Solano F, Santos-Zavaleta A, et al. RegulonDB (version
5.0): Escherichia coli K-12 transcriptional regulatory network,
operon organization, and growth conditions. Nucleic Acids
Research 2006;34:D394
e
7.
[23] Farkas I, Jeong H, Vicsek T, Barab´si AL, Oltvai ZN. The
topology of the transcription regulatory network in the yeast,
Sacchromyces cervisiae. Physica A 2003;318:601
e
12.
[24] Erd
T
sP,R´nyi A. On Random Graphs I. Publicationes Mathe-
maticae 1959;6:290
e
7.
[25] Erd
T
sP,R
´
nyi A. The Evolution of Random Graphs. Magyar Tud
Akad Mat Kutat
´
Int. K¨zl 1960;5:17
e
61.
[26] Gilbert EN. Random Graphs. Annals of Mathematical Statistics
1959;30:1141
e
4.
[27] Newman MEJ. Networks
e
an Introduction. 1st ed. New York:
Oxford University Press; 2010.
[28] Holland PW, Leinhardt S. Transitivity in structural models of
small groups. Comparative Group Studies 1971;2:107
e
24.
[29] Luce RD, Perry AD. A method of matrix analysis of group
structure. Psychometrika 1949;14:95
e
116.
[30] Watts DJ, Strogatz S. Collective dynamics of small-world
networks. Nature 1998;393:440
e
2.
[31] Jeong H, Tombor B, Albert R, Oltvai ZN, Barab´si AL. The large-
scale organization of metabolic networks. Nature 2000;407:651
e
5.
[32] Yook S, Oltvai ZN, Barab´si AL. Functional and topological charac-
terization of protein interaction networks. Proteomics 2004;4:928
e
42.
[33] Xu K, Bezakova I, Bunimovich L, Yi SV. Path lengths in protein-
protein interaction networks and biological complexity. Proteo-
mics 2011;11:1857
e
67.
[34] Wagner A, Fell DA. The small world inside large metabolic
networks. Proc. Biological Science 2001;268:1803
e
10.
[35] Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barab´si AL.
Hierarchical organization of modularity in metabolic networks.
Science 2002;297:1551
e
6.
[36] Barab
´
si AL, Albert R. Emergence of scaling in random
networks. Science 1999;286:509
e
21.
[37] Mason O, Verwoerd M. Graph theory and networks in Biology.
IET Systems Biology 2007;1:89
e
119.
[38] Guelzim N, Bottani S, Bourgine P, K
´
p
`
s F. Topological and
causal structure of the yeast transcriptional regulatory network.
Nature Genetics 2002;31:60
e
3.
[39] Wagner A. The yeast protein interaction network evolves rapidly
and contains few redundant duplicate genes. Molecular Biology
and Evolution 2001;18:1283
e
92.
[40] Arita M. Scale-Freeness and Biological Networks. J. Biochem-
istry 2005;138:1
e
4.
[41] Jeong H, Mason SP, Barab´si AL, Oltvai ZN. Lethality and
centrality in protein networks. Nature 2001;411:41
e
3.
[42] Wuchty S. Scale-free behavior in protein domain networks.
Molecular Biology and Evolution 2001;18. 1964
e
1702.
[43] Apic G, Gough J, Teichmann SA. An insight
functional organization. Nature Reviews
e
Genetics
2004;5:101
e
13.
[3] Bray D. Molecular networks:
the top-down view. Science
2003;301:1864
e
5.
[4] Vidal M, Cusick ME, Barab´si AL. Interactome networks and
human disease. Cell 2011;144:986
e
98.
[5] Albert R, Barab´si AL. The statistical mechanics of complex
networks. Review of Modern Physics 2002;74:47
e
97.
[6] Newman M. The structure and function of complex networks.
SIAM Reviews 2003;45:167
e
256.
[7] Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D,
et al. An integrative genomics approach to infer causal associa-
tions between gene expression and disease. Nature Genetics
2005;37:710
e
7.
[8] Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based
classification of breast cancer metastasis. Molecular Systems
Biology 2007;3:140
e
50.
[9] Fran¸ois K. Biological Network. Complex Systems and Interdis-
ciplinary Science
e
Volume 3. 1st ed. Hackensak, New-Jersey:
World Scientific Publishing Company; 2007.
[10]
Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N.
Revealing modular organization in the yeast
transcriptional
network. Nature Genetics 2002;31:370
e
7.
[11] Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH,
Goehler H, et al. A human protein-protein interaction network:
a resource for annotating the proteome. Cell 2005;122:957
e
68.
[12] Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR,
et al. A comprehensive analysis of protein-protein interactions in
Saccharomyces cerevisiae. Nature 2000;403:623
e
30.
[13] Rain JC, Selig L, De-Reuse H, Battaglia V, Reverdy C, Simon S,
et al. The protein-protein interaction map of Helicobacter pylori.
Nature 2001;409:211
e
6.
[14] Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, et al.
A Protein Interaction Map of Drosophila melanogaster. Science
2003;302:1727
e
36.
[15] Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A
comprehensive two-hybrid analysis to explore the yeast protein
interactome. Proc. Natl. Acad. Sci. USA 2001;98:4569
e
74.
[16] Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P,
Robertson LS, et al. YPD, PombePD andWormPD: model organism
volumes of the BioKnowledge library, an integrated resource for
protein information. Nucleic Acids Res 2001;29:75
e
84.
[17] Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, et al.
A map of the interactome network of the metazoan Caeno-
rhabditis elegans. Science 2004;303:540
e
3.
[18] CostanzoM, Baryshnikova A, Bellay J, KimY, Spear ED, Sevier CS.
The genetic landscape of a cell. Science 2010;327:425
e
56.
[19] De-Las Rivas J, Fontanillo C. Protein-protein interactions essen-
tials: key concepts to building and analyzing interactome
networks. PLoS Computational Biology 2010;6:e100807.
[20] Stumpf MP, Thorne T, de-Silva E, Stewart R, An HJ, Lappe M,
et al. Estimating the size of the human interactome. Proc Natl
Acad Sci 2008;105:6959
e
64.
into domain
combinations. Bioinformatics 2001;17:S83
e
9.
[44] Featherstone DE, Broadie K. Wrestling with pleiotropy: genomic
and topological analysis of the yeast gene expression network.
Bioessays 2002;24:267
e
74.
