Biology Reference
In-Depth Information
[199] Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol
2012;8:565.
[200] Han JD, Bertin N, et al. Evidence for dynamically organized
modularity in the yeast protein-protein interaction network.
Nature 2004;430(6995):88
e
93.
[201] Ekman D, Light S, et al. What properties characterize the hub
proteins of the protein
e
protein interaction network of Saccha-
romyces cerevisiae? Genome Biol 2006;7(6):R45.
[202] Kim PM, Sboner A, et al. The role of disorder in interaction
networks: a structural analysis. Mol Syst Biol 2008;4:179.
[203] Kim SH, Yi SV. Correlated asymmetry of sequence and functional
divergence between duplicate proteins of Saccharomyces cer-
evisiae. Mol Biol Evol 2006;23(5):1068
e
75.
[204] Taylor IW, Linding R, et al. Dynamic modularity in protein
interaction networks predicts breast cancer outcome. Nat Bio-
technol 2009;27(2):199
e
204.
[205] Huh WK, Falvo JV, et al. Global analysis of protein localization in
budding yeast. Nature 2003;425(6959):686
e
91.
[206] Kumar A, Agarwal S, et al. Subcellular localization of the yeast
proteome. Genes Dev 2002;16(6):707
e
19.
[207] Kiemer L, Cesareni G. Comparative interactomics: comparing
apples and pears? Trends Biotechnol 2007;25(10):448
e
54.
[208] Cesareni G, Ceol A, et al. Comparative interactomics. FEBS Lett
2005;579(8):1828
e
33.
[209] Gandhi TK, Zhong J, et al. Analysis of the human protein inter-
actome and comparison with yeast, worm and fly interaction
datasets. Nat Genet 2006;38(3):285
[220] Zarrinpar A, Park SH, et al. Optimization of specificity in
a cellular protein interaction network by negative selection.
Nature 2003;426(6967):676
80.
[221] Wagner A. The yeast protein interaction network evolves rapidly
and contains few redundant duplicate genes. Mol Biol Evol
2001;18(7):1283
e
92.
[222] Pastor-Satorras R, Smith E, et al. Evolving protein interaction
networks through gene duplication. J Theor Biol 2003;222(2):
199
e
210.
[223] Vazquez A. Growing network with local rules: preferential
attachment, clustering hierarchy, and degree correlations. Phys
Rev E Stat Nonlin Soft Matter Phys 2003;67(5 Pt 2):056104.
[224] Musso G, Zhang Z, et al. Retention of protein complex
membership by ancient duplicated gene products in budding
yeast. Trends Genet 2007;23(6):266
e
9.
[225] Pereira-Leal JB, Levy ED, et al. Evolution of protein complexes
by duplication of homomeric interactions. Genome Biol 2007;
8(4):R51.
[226] Bochtler M, Ditzel L, et al. The proteasome. Annu Rev Biophys
Biomol Struct 1999;28:295
e
317.
[227] Ispolatov I, Krapivsky PL, et al. Duplication-divergence model of
protein interaction network. Phys Rev E Stat Nonlin Soft Matter
Phys 2005;71(6 Pt 1):061911.
[228] Maslov S, Sneppen K, et al. Upstream plasticity and downstream
robustness in evolution of molecular networks. BMC Evol Biol
2004;4:9.
[229] Presser A, Elowitz MB, et al. The evolutionary dynamics of the
Saccharomyces cerevisiae protein interaction network after
duplication. Proc Natl Acad Sci U S A 2008;105(3):950
e
4.
[230] Wagner A. How the global structure of protein interaction
networks evolves. Proc Biol Sci 2003;270(1514):457
e
66.
[231] Conant GC, Wagner A. Asymmetric sequence divergence of
duplicate genes. Genome Res 2003;13(9):2052
e
8.
[232] He X, Zhang J. Rapid subfunctionalization accompanied by
prolonged and substantial neofunctionalization in duplicate gene
evolution. Genetics 2005;169(2):1157
e
64.
[233] Wagner A. Asymmetric functional divergence of duplicate genes
in yeast. Mol Biol Evol 2002;19(10):1760
e
8.
[234] Sharan R, Ideker T. Modeling cellular machinery through bio-
logical network comparison. Nat Biotechnol 2006;24(4):427
e
33.
[235] Wuchty S, Oltvai ZN, et al. Evolutionary conservation of motif
constituents in the yeast protein interaction network. Nat Genet
2003;35(2):176
e
9.
[236] Kuchaiev O, Milenkovic T, et al. Topological network alignment
uncovers biological function and phylogeny. J R Soc Interface
2010;7(50):1341
e
54.
[237] Fernandez A, Lynch M. Non-adaptive origins of interactome
complexity. Nature 2011;474(7352):502
e
5.
[238] O'Donoghue SI, Goodsell DS, et al. Visualization of macromo-
lecular structures. Nat Methods 2010;7(Suppl. 3):S42
e
93.
[210] Matthews LR, Vaglio P, et al. Identification of potential interac-
tion networks using sequence-based searches for conserved
protein
e
protein interactions or 'interologs'. Genome Res 2001;
11(12):2120
e
6.
[211] Suthram S, Sittler T, et al. The Plasmodium protein network
diverges from those of other eukaryotes. Nature 2005;438(7064):
108
e
12.
[212] Beltrao P, Serrano L. Specificity and evolvability in eukaryotic
protein interaction networks. PLoS Comput Biol 2007;3(2):e25.
[213] Shou C, Bhardwaj N, et al. Measuring the evolutionary rewiring
of biological networks. PLoS Comput Biol 2011;7(1):e1001050.
[214] Roguev A, Bandyopadhyay S, et al. Conservation and rewiring of
functional modules revealed by an epistasis map in fission yeast.
Science 2008;322(5900):405
e
10.
[215] Teichmann SA. The constraints protein
e
protein interactions place
on sequence divergence. J Mol Biol 2002;324(3):399
e
407.
[216] Jensen LJ, Jensen TS, et al. Co-evolution of transcriptional and
post-translational cell-cycle regulation. Nature 2006;443(7111):
594
e
7.
[217] Mika S, Rost B. Protein-protein interactions more conserved within
species than across species. PLoS Comput Biol 2006;2(7):e79.
[218] Fraser HB. Modularity and evolutionary constraint on proteins.
Nat Genet 2005;37(4):351
e
2.
[219] Kim PM, Lu LJ, et al. Relating three-dimensional structures to
protein networks provides evolutionary insights. Science 2006;
314(5807):1938
55.
[239] Stein A, Mosca R, et al. Three-dimensional modeling of protein
interactions and complexes is going 'omics. Curr Opin Struct Biol
2011;21(2):200
e
e
41.
8.
e
e
