메뉴 건너뛰기




Volumn 102, Issue , 2016, Pages 57-63

Minimum dominating set-based methods for analyzing biological networks

Author keywords

Complex networks; Minimum dominating set; Network controllability; Protein protein interaction networks

Indexed keywords

UNTRANSLATED RNA;

EID: 84954285287     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.12.017     Document Type: Review
Times cited : (70)

References (41)
  • 1
    • 84876576325 scopus 로고    scopus 로고
    • Computational solutions for omics data
    • Berger B., Peng J., Singh M. Computational solutions for omics data. Nat. Rev. Genet. 2013, 14:333-346.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 333-346
    • Berger, B.1    Peng, J.2    Singh, M.3
  • 2
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • Vidal M., Cusick M.E., Barabási A.-L. Interactome networks and human disease. Cell 2011, 144:986-995.
    • (2011) Cell , vol.144 , pp. 986-995
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.-L.3
  • 3
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: a network-based approach to human disease
    • Barabási A.-L., Gulbahce N., Loscalzo J. Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 2011, 12:56-68.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 56-68
    • Barabási, A.-L.1    Gulbahce, N.2    Loscalzo, J.3
  • 5
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: the next paradigm in drug discovery
    • Hopkins A.L. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol. 2008, 4:682-690.
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 6
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of biological networks: a novel paradigm of drug discovery. A comprehensive review
    • Csermely P., Korcsmaros T., Kiss H.J.M., London G., Nussinov R. Structure and dynamics of biological networks: a novel paradigm of drug discovery. A comprehensive review. Pharmacol. Ther. 2013, 138:333-408.
    • (2013) Pharmacol. Ther. , vol.138 , pp. 333-408
    • Csermely, P.1    Korcsmaros, T.2    Kiss, H.J.M.3    London, G.4    Nussinov, R.5
  • 7
    • 48549092620 scopus 로고    scopus 로고
    • Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets
    • Chu L., Chen B.S. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. BMC Syst. Biol. 2008, 2:56.
    • (2008) BMC Syst. Biol. , vol.2 , pp. 56
    • Chu, L.1    Chen, B.S.2
  • 8
    • 78650345652 scopus 로고    scopus 로고
    • Proofs of concept: a review on how network and systems biology approaches aid in the discovery of potent anticancer drug combinations
    • Azmi A., Wang Z., Phillip P.A., Mohammad R.M., Sarkar F.H. Proofs of concept: a review on how network and systems biology approaches aid in the discovery of potent anticancer drug combinations. Mol. Cancer Ther. 2010, 9:3137-3144.
    • (2010) Mol. Cancer Ther. , vol.9 , pp. 3137-3144
    • Azmi, A.1    Wang, Z.2    Phillip, P.A.3    Mohammad, R.M.4    Sarkar, F.H.5
  • 10
    • 38549083508 scopus 로고    scopus 로고
    • Lower bounds and algorithms for dominating sets in web graphs
    • Cooper C., Klasing R., Zito M. Lower bounds and algorithms for dominating sets in web graphs. Internet Math. 2005, 2:275-300.
    • (2005) Internet Math. , vol.2 , pp. 275-300
    • Cooper, C.1    Klasing, R.2    Zito, M.3
  • 11
    • 84864367967 scopus 로고    scopus 로고
    • Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control
    • Nacher J.C., Akutsu T. Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control. New J. Phys. 2012, 14:073005.
    • (2012) New J. Phys. , vol.14 , pp. 073005
    • Nacher, J.C.1    Akutsu, T.2
  • 12
    • 84900503465 scopus 로고    scopus 로고
    • Controllability in protein interaction networks
    • Wuchty S. Controllability in protein interaction networks. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:7156-7160.
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 7156-7160
    • Wuchty, S.1
  • 13
    • 70349335853 scopus 로고    scopus 로고
    • A measure & conquer approach for the analysis of exact algorithms
    • Fomin F.V., Grandoni F., Kratsch D. A measure & conquer approach for the analysis of exact algorithms. J. ACM 2009, 56:25.
    • (2009) J. ACM , vol.56 , pp. 25
    • Fomin, F.V.1    Grandoni, F.2    Kratsch, D.3
  • 15
    • 84858377485 scopus 로고    scopus 로고
    • A faster algorithm for dominating set analyzed by the potential method
    • Iwata Y. A faster algorithm for dominating set analyzed by the potential method. Lect. Notes Comput. Sci. 2012, 7112:41-54.
    • (2012) Lect. Notes Comput. Sci. , vol.7112 , pp. 41-54
    • Iwata, Y.1
  • 16
    • 84861525639 scopus 로고    scopus 로고
    • Simulated annealing with stochastic local search for minimum dominating set problem
    • Hedar A.-R., Ismail R. Simulated annealing with stochastic local search for minimum dominating set problem. Int. J. Mach. Learn. Cyber. 2012, 3:97-109.
    • (2012) Int. J. Mach. Learn. Cyber. , vol.3 , pp. 97-109
    • Hedar, A.-R.1    Ismail, R.2
  • 17
    • 84969637246 scopus 로고    scopus 로고
    • CPLEX web site: (Sept. 1, 2015). http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/.
    • (2015)
  • 18
    • 84969710768 scopus 로고    scopus 로고
    • Gurobi web site: (Sept. 1)
    • Gurobi web site: (Sept. 1, 2015). http://www.gurobi.com/.
    • (2015)
  • 19
    • 84922774376 scopus 로고    scopus 로고
    • Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets
    • Nacher J.C., Akutsu T. Analysis of critical and redundant nodes in controlling directed and undirected complex networks using dominating sets. J. Comp. Network 2014, 2:394-412.
    • (2014) J. Comp. Network , vol.2 , pp. 394-412
    • Nacher, J.C.1    Akutsu, T.2
  • 23
    • 84875693642 scopus 로고    scopus 로고
    • Analysis on controlling complex networks based on dominating sets
    • Nacher J.C., Akutsu T. Analysis on controlling complex networks based on dominating sets. J. Phys. Conf. Ser. 2013, 410:012104.
    • (2013) J. Phys. Conf. Ser. , vol.410 , pp. 012104
    • Nacher, J.C.1    Akutsu, T.2
  • 26
  • 27
    • 0037481034 scopus 로고    scopus 로고
    • Characterization of generic properties of linear structured systems for efficient computations
    • Commault C., Dion J.-M., van der Woude J.W. Characterization of generic properties of linear structured systems for efficient computations. Kybernetika 2002, 38:503-520.
    • (2002) Kybernetika , vol.38 , pp. 503-520
    • Commault, C.1    Dion, J.-M.2    van der Woude, J.W.3
  • 28
    • 84863449762 scopus 로고    scopus 로고
    • Controlling edge dynamics in complex networks
    • Nepusz T., Vicsek T. Controlling edge dynamics in complex networks. Nat. Phys. 2012, 8:568-573.
    • (2012) Nat. Phys. , vol.8 , pp. 568-573
    • Nepusz, T.1    Vicsek, T.2
  • 30
    • 84881455921 scopus 로고    scopus 로고
    • Structural controllability of unidirectional bipartite networks
    • Nacher J.C., Akutsu T. Structural controllability of unidirectional bipartite networks. Sci. Rep. 2013, 3:1647.
    • (2013) Sci. Rep. , vol.3 , pp. 1647
    • Nacher, J.C.1    Akutsu, T.2
  • 31
    • 84921957339 scopus 로고    scopus 로고
    • Structurally robust control of complex networks
    • Nacher J.C., Akutsu T. Structurally robust control of complex networks. Phys. Rev. E 2015, 91:012826.
    • (2015) Phys. Rev. E , vol.91 , pp. 012826
    • Nacher, J.C.1    Akutsu, T.2
  • 32
    • 84923102593 scopus 로고    scopus 로고
    • Building damage-resilient dominating sets in complex networks against random and targeted attacks
    • Molnár F., Derzsy N., Szymanski B.K., Korniss G. Building damage-resilient dominating sets in complex networks against random and targeted attacks. Sci. Rep. 2015, 5:8321.
    • (2015) Sci. Rep. , vol.5 , pp. 8321
    • Molnár, F.1    Derzsy, N.2    Szymanski, B.K.3    Korniss, G.4
  • 33
    • 84929150654 scopus 로고    scopus 로고
    • Determining minimum set of driver nodes in protein-protein interaction networks
    • Zhang X.-F., Ou-Yang L., Zhu Y., Wu M.-Y., Dai D.-Q. Determining minimum set of driver nodes in protein-protein interaction networks. BMC Bioinform. 2015, 16:146.
    • (2015) BMC Bioinform. , vol.16 , pp. 146
    • Zhang, X.-F.1    Ou-Yang, L.2    Zhu, Y.3    Wu, M.-Y.4    Dai, D.-Q.5
  • 35
    • 84928580139 scopus 로고    scopus 로고
    • Essentiality and centrality in protein networks revisited
    • Khuri S., Wuchty S. Essentiality and centrality in protein networks revisited. BMC Bioinfor. 2015, 16:109.
    • (2015) BMC Bioinfor. , vol.16 , pp. 109
    • Khuri, S.1    Wuchty, S.2
  • 37
    • 13244284551 scopus 로고    scopus 로고
    • Dynamic complex formation during the yeast cell cycle
    • de Lichtenberg U., Jensen L., Brunak S., Bork P. Dynamic complex formation during the yeast cell cycle. Science 2005, 307:724-727.
    • (2005) Science , vol.307 , pp. 724-727
    • de Lichtenberg, U.1    Jensen, L.2    Brunak, S.3    Bork, P.4
  • 38
    • 0001173632 scopus 로고
    • An automatic method of solving discrete programming-problems
    • Land A.H., Doig A.G. An automatic method of solving discrete programming-problems. Econometrica 1960, 28:497-520.
    • (1960) Econometrica , vol.28 , pp. 497-520
    • Land, A.H.1    Doig, A.G.2
  • 39
    • 84944350960 scopus 로고    scopus 로고
    • Determining associations between human diseases and non-coding RNAs with critical roles in network control
    • Kagami H., Akutsu T., Maegawa S., Hosokawa H., Nacher J.C. Determining associations between human diseases and non-coding RNAs with critical roles in network control. Sci. Rep. 2015, 5:14577.
    • (2015) Sci. Rep. , vol.5 , pp. 14577
    • Kagami, H.1    Akutsu, T.2    Maegawa, S.3    Hosokawa, H.4    Nacher, J.C.5
  • 40
    • 84894266778 scopus 로고    scopus 로고
    • Controllability in cancer metabolic networks according to drug targets as driver nodes
    • Asgari Y., Salehzadeh-Yazdi A., Schreiber F., Masoudi-Nejad A. Controllability in cancer metabolic networks according to drug targets as driver nodes. PLoS One 2013, 8:e79397.
    • (2013) PLoS One , vol.8 , pp. e79397
    • Asgari, Y.1    Salehzadeh-Yazdi, A.2    Schreiber, F.3    Masoudi-Nejad, A.4
  • 41
    • 84941565303 scopus 로고    scopus 로고
    • Controllability and modularity of complex networks
    • Sun P.G. Controllability and modularity of complex networks. Inf. Sci. 2015, 325:20-32.
    • (2015) Inf. Sci. , vol.325 , pp. 20-32
    • Sun, P.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.