Page 78 - GPD-1-2
P. 78
Gene & Protein in Disease Recent advances and challenges of network biology
46. Fessenden M, 2017, Protein maps chart the causes of disease. hypertextual web search engine. Comput Networks ISDN
Nature, 549(7671): 293–295. Syst, 30: 107–117.
https://doi.org/10.1038/549293a https://doi.org/10.1016/S0169-7552(98)00110-X
47. Wang P, Lü JH, Yu XH, 2014, Identification of important 59. Lü LY, Chen DB, Ren XL, et al., 2016, Vital nodes
nodes in directed biological networks: A network motif identification in complex networks. Phys Rep, 650: 1–63.
approach. PLoS One, 9(8): e106132.
https://doi.org/10.1016/j.physrep.2016.06.007
https://doi.org/10.1371/journal.pone.0106132
60. Xu S, Wang P, 2017, Identifying important nodes by adaptive
48. Bracken CP, Scott HS, Goodall GJ, 2016, A network-biology LeaderRank. Physica A, 469: 654–664.
perspective of microRNA function and dysfunction in https://doi.org/10.1016/j.physa.2016.11.034
cancer. Nat Rev Genet, 17(12): 719–732.
61. Xu S, Wang P, Zhang CX, et al., 2019, Spectral learning
https://doi.org/10.1038/nrg.2016.134
algorithm reveals propagation capability of complex
49. Chen LN, Liu R, Liu ZP, et al., 2012, Detecting early-warning network. IEEE Trans Cybern, 49(12): 4253–4261.
signals for sudden deterioration of complex diseases by https://doi.org/10.1109/TCYB.2018.2861568
dynamical network biomarkers. Sci Rep, 2: 342.
62. Watts DJ, Strogatz SH, 1998, Collective dynamics of ‘small-
https://doi.org/10.1038/srep00342
world’ networks. Nature, 393(6684): 440–442.
50. Azhagesan K, Ravindran B, Raman K, 2018, Network-based https://doi.org/10.1038/30918
features enable prediction of essential genes across diverse
organisms. PLoS One, 13(12): e0208722. 63. Humphries MD, Gurney K, 2008, Network ‘small-worldness:
A quantitative method for determining canonical network
https://doi.org/10.1371/journal.pone.0208722
equivalence. PLoS One, 3(4): e0002051.
51. Carson MB, Lu H, 2015, Network-based prediction and https://doi.org/10.1371/journal.pone.0002051
knowledge mining of disease genes. BMC Med Genomics,
8(Suppl 2): S9. 64. Barabási Al, Albert R, 1999, Emergence of scaling in random
networks. Science, 286(5439): 509–512.
https://doi.org/10.1186/1755-8794-8-S2-S9
https://doi.org/10.1126/science.286.5439.509
52. Hou L, Chen M, Cho J, et al., 2014, Guilt-by-rewiring: Gene
prioritization through network rewiring in genome wide 65. Yu HY, Braun P, Yildirim MA, et al., 2008, High-quality
association studies. Hum Mol Genet, 23(10): 2780–2790. binary protein interaction map of the yeast interactome
network. Science, 322(5898): 104–110.
https://doi.org/10.1093/hmg/ddt668
https://doi.org/10.1126/science.1158684
53. Li XY, Li WK, Zeng M, et al., 2020, Network-based methods
for predicting essential genes or proteins: A survey. Brief 66. Wang P, Lü JH, Yu XH, et al., 2015, Duplication and
Bioinforma, 21(2): 566–583. divergence effect on network motifs in undirected bio-
molecular networks. IEEE Trans Biomed Circuits Syst, 9(3):
https://doi.org/10.1093/bib/bbz017
312–320.
54. Newman ME, 2003, The structure and function of complex https://doi.org/10.1109/TBCAS.2014.2343620
networks. SIAM Rev, 45(2): 167–256.
67. Stark C, Breitkreutz BJ, Reguly T, et al., 2006, BioGRID:
https://doi.org/10.1137/S003614450342480
A general repository for interaction datasets. Nucl Acids Res,
55. Ulrik B, 2001, A faster algorithm for betweenness centrality. 34(90001): D535–D539.
J Math Sociol, 25(2): 163–177.
https://doi.org/10.1093/nar/gkj109
https://doi.org/10.1080/0022250X.2001.9990249
68. Hamosh A, Scott AF, Amberger JS, et al., 2005, Online
56. Shai C, Shlomo H, Scott K, et al., 2007, A model of Internet mendelian inheritance in man (OMIM), a knowledgebase
topology using k-shell decomposition. Proc Natl Acad Sci of human genes and genetic disorders. Nucl Acids Res, 33(1):
U S A, 104(27): 11150–11154. D514–D517.
https://doi.org/10.1073/pnas.0701175104 https://doi.org/10.1093/nar/gki033
57. Chen DB, Lü LY, Shang MS, et al., 2012, Identifying 69. Fields S, Song O, 1989, A novel genetic system to detect
influential nodes in complex networks. Physica A Stat Mech protein-protein interactions. Nature, 340(6230): 245–246.
Appl, 391(4): 1777–1787.
https://doi.org/10.1038/340245a0
https://doi.org/10.1016/j.physa.2011.09.017
70. SenGupta DJ, Zhang B, Kraemer B, et al., 1996, A three-
58. Sergey B, Lawrence P, 1998, The anatomy of a large-scale hybrid system to detect RNA-protein interactions in vivo.
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