메뉴 건너뛰기




Volumn 6, Issue 5, 2012, Pages 164-174

Building blocks of biological networks: a review on major network motif discovery algorithms

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; BUILDING BLOCKES; COMPLEX NETWORKS; COMPUTATIONAL ASPECTS; FUNCTIONAL ABILITIES; FUNCTIONAL UNITS; HARD PROBLEMS; LOCAL PROPERTY; NETWORK MOTIF; PATTERN GROWTH; SAMPLING METHOD; SUBGRAPHS;

EID: 84867951060     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2011.0011     Document Type: Article
Times cited : (71)

References (34)
  • 1
    • 33745998748 scopus 로고    scopus 로고
    • Are network motifs the sprandrels of cellular complexity?
    • 10.1016/j.tree.2006.05.013
    • Sole, R.V., and Valverde, S.: 'Are network motifs the sprandrels of cellular complexity?', Trends Ecol. Evol., 2006, 21, (8), p. 419-42210.1016/j.tree.2006.05.013
    • (2006) Trends Ecol. Evol. , vol.21 , Issue.8 , pp. 419-422
    • Sole, R.V.1    Valverde, S.2
  • 2
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: simple building blocks of complex networks
    • 10.1126/science.298.5594.824, 0036-8075
    • Milo, R., Shen-Orr, S.S., Itzkovitz, S., Kashtan, N., Chklovskii, D., and Alon, U.: 'Network motifs: simple building blocks of complex networks', Science, 2002, 298, (5594), p. 824-82710.1126/science.298.5594.824 0036-8075
    • (2002) Science , vol.298 , Issue.5594 , pp. 824-827
    • Milo, R.1    Shen-Orr, S.S.2    Itzkovitz, S.3    Kashtan, N.4    Chklovskii, D.5    Alon, U.6
  • 3
    • 28844434073 scopus 로고    scopus 로고
    • An evolutionary and functional assessment of regulatory network motifs
    • R3510.1186/gb-2005-6-4-r35
    • Mazurie, A., Bottani, S., and Vergassola, M.: 'An evolutionary and functional assessment of regulatory network motifs', Genome Biol., 2005, 6, (4), p. R3510.1186/gb-2005-6-4-r35
    • (2005) Genome Biol. , vol.6 , Issue.4
    • Mazurie, A.1    Bottani, S.2    Vergassola, M.3
  • 4
    • 33746922321 scopus 로고    scopus 로고
    • Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence
    • 10.1016/j.biosystems.2006.01.004
    • Dwight Kuo, P., Banzhaf, W., and Leier, A.: 'Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence', Biosystems, 2006, 85, (3), p. 177-20010.1016/j.biosystems.2006.01.004
    • (2006) Biosystems , vol.85 , Issue.3 , pp. 177-200
    • Dwight Kuo, P.1    Banzhaf, W.2    Leier, A.3
  • 5
    • 84956630545 scopus 로고    scopus 로고
    • An introduction to systems biology: design principles of biological circuits
    • Chapman & Hall/CRC, Boca Raton, FL, London )
    • Alon, U.: 'An introduction to systems biology: design principles of biological circuits', (Chapman & Hall/CRC, Boca Raton, FL, London 2006)
    • (2006)
    • Alon, U.1
  • 6
    • 0003491368 scopus 로고    scopus 로고
    • Handbook of graphs and networks: from the genome to the Internet
    • Weinheim: Wiley-VCH )
    • Bornholdt, S., and Schuster, H.G.: 'Handbook of graphs and networks: from the genome to the Internet', (Weinheim: Wiley-VCH 2003)
    • (2003)
    • Bornholdt, S.1    Schuster, H.G.2
  • 7
    • 0034633749 scopus 로고    scopus 로고
    • Classes of small-world network
    • 10.1073/pnas.200327197
    • Amaral, L.A.N., Scala, A., and Barthélémy, M.: et al. 'Classes of small-world network', Proc. Natl. Acad. Sci., 2000, 97, (21), p. 11149-1115210.1073/pnas.200327197
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , Issue.21 , pp. 11149-11152
    • Amaral, L.A.N.1    Scala, A.2    Barthélémy, M.3
  • 8
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • 10.1103/RevModPhys.74.47, 0034-6861
    • Albert, R., and Barabási, A.L.: 'Statistical mechanics of complex networks', Rev. Mod. Phys., 2002, 74, p. 47-9710.1103/RevModPhys.74.47 0034-6861
    • (2002) Rev. Mod. Phys. , vol.74 , pp. 47-97
    • Albert, R.1    Barabási, A.L.2
  • 9
    • 0035420732 scopus 로고    scopus 로고
    • Random graphs with arbitrary degree distributions and their applications
    • 10.1103/PhysRevE.64.026118
    • Newman, M.E.J., Strogatz, S.H., and Watts, D.J.: 'Random graphs with arbitrary degree distributions and their applications', Phys. Rev. E, 2001, 64, p. 02611810.1103/PhysRevE.64.026118
    • (2001) Phys. Rev. E , vol.64 , pp. 026118
    • Newman, M.E.J.1    Strogatz, S.H.2    Watts, D.J.3
  • 10
    • 0000664045 scopus 로고
    • The asymptotic number of labeled graphs with given degree sequences
    • 10.1016/0097-3165(78)90059-6, 0097-3165
    • Bender, E.A., and Canfield, E.R.: 'The asymptotic number of labeled graphs with given degree sequences', J. Comb. Theory A, 1978, 24, p. 296-30710.1016/0097-3165(78)90059-6 0097-3165
    • (1978) J. Comb. Theory A , vol.24 , pp. 296-307
    • Bender, E.A.1    Canfield, E.R.2
  • 11
    • 0016870630 scopus 로고
    • An algorithm for sub-graph isomorphism
    • 10.1145/321921.321925, 0004-5411
    • Ullmann, J.R.: 'An algorithm for sub-graph isomorphism', J. ACM, 1976, 23, (1), p. 31-4210.1145/321921.321925 0004-5411
    • (1976) J. ACM , vol.23 , Issue.1 , pp. 31-42
    • Ullmann, J.R.1
  • 12
    • 0003677229 scopus 로고    scopus 로고
    • Graph theory
    • Springer-Verlag, Heidelberg, New York ), lsquo;Graduate texts in mathematics'
    • Diestel, R.: 'Graph theory', (Springer-Verlag, Heidelberg, New York 2005), 173, 'Graduate texts in mathematics'
    • (2005) , vol.173
    • Diestel, R.1
  • 13
    • 1542287343 scopus 로고    scopus 로고
    • Superfamilies of designed and evolved networks
    • 10.1126/science.1089167, 0036-8075
    • Milo, R., Itzkovitz, S., and Kashtan, N.: et al. 'Superfamilies of designed and evolved networks', Science, 2004, 303, (5663), p. 1538-154210.1126/science.1089167 0036-8075
    • (2004) Science , vol.303 , Issue.5663 , pp. 1538-1542
    • Milo, R.1    Itzkovitz, S.2    Kashtan, N.3
  • 14
    • 67649859943 scopus 로고    scopus 로고
    • Network motifs
    • Junker, B.H., Schreiber, F.H., Analysis of biological networks, John Wiley & Sons, New Jersey )
    • Schwobbermeyer, H.: 'Network motifs', Junker, B.H., Schreiber, F.H., Analysis of biological networks, (John Wiley & Sons, New Jersey 2008), p. 85-108
    • (2008) , pp. 85-108
    • Schwobbermeyer, H.1
  • 15
    • 44349107818 scopus 로고    scopus 로고
    • A review on models and algorithms for motif discovery in protein-protein interaction networks
    • 10.1093/bfgp/eln015
    • Ciriello, G., and Guerra, C.: 'A review on models and algorithms for motif discovery in protein-protein interaction networks', Briefings Funct. Genomics Proteomics, 2008, 7, (2), p. 147-15610.1093/bfgp/eln015
    • (2008) Briefings Funct. Genomics Proteomics , vol.7 , Issue.2 , pp. 147-156
    • Ciriello, G.1    Guerra, C.2
  • 16
    • 4444268694 scopus 로고    scopus 로고
    • Efficient sampling algorithm for estimating sub-graph concentrations and detecting network motifs
    • 10.1093/bioinformatics/bth163
    • Kashtan, N., Itzkovitz, S., Milo, R., and Alon, U.: 'Efficient sampling algorithm for estimating sub-graph concentrations and detecting network motifs', Bioinformatics, 2004, 20, (11), p. 1746-175810.1093/bioinformatics/bth163
    • (2004) Bioinformatics , vol.20 , Issue.11 , pp. 1746-1758
    • Kashtan, N.1    Itzkovitz, S.2    Milo, R.3    Alon, U.4
  • 17
    • 33845676319 scopus 로고    scopus 로고
    • Efficient detection of network motifs
    • 10.1109/TCBB.2006.51, 1545-5963
    • Wernicke, S.: 'Efficient detection of network motifs', IEEE/ACM Trans. Comput. Biol. Bioinf., 2006, 3, (4), p. 347-35910.1109/TCBB.2006.51 1545-5963
    • (2006) IEEE/ACM Trans. Comput. Biol. Bioinf. , vol.3 , Issue.4 , pp. 347-359
    • Wernicke, S.1
  • 18
    • 39449128256 scopus 로고    scopus 로고
    • Assessing the exceptionality of network motifs
    • 10.1089/cmb.2007.0137
    • Picard, F., Daudin, J.-J., Schbath, S., and Robin, S.: 'Assessing the exceptionality of network motifs', J. Comput. Biol., 2008, 15, (1), p. 1-2010.1089/cmb.2007.0137
    • (2008) J. Comput. Biol. , vol.15 , Issue.1 , pp. 1-20
    • Picard, F.1    Daudin, J.2    Schbath, S.3    Robin, S.4
  • 19
    • 49749111671 scopus 로고    scopus 로고
    • Frequency concepts and pattern detection for the analysis of motifs in networks
    • 10.1007/11599128_7
    • Schreiber, F., and Schwobbermeyer, H.: 'Frequency concepts and pattern detection for the analysis of motifs in networks', Trans. Comput. Syst. Biol. III, 2005, 3, p. 89-10410.1007/11599128_7
    • (2005) Trans. Comput. Syst. Biol. III , vol.3 , pp. 89-104
    • Schreiber, F.1    Schwobbermeyer, H.2
  • 20
    • 24144495559 scopus 로고    scopus 로고
    • MAVisto: a tool for the exploration of network motifs
    • 10.1093/bioinformatics/bti556
    • Schreiber, F., and Schwobbermeyer, H.: 'MAVisto: a tool for the exploration of network motifs', Bioinformatics, 2005, 21, (17), p. 3572-357410.1093/bioinformatics/bti556
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3572-3574
    • Schreiber, F.1    Schwobbermeyer, H.2
  • 21
    • 0002603293 scopus 로고
    • Practical graph isomorphism
    • McKay, B.D.: 'Practical graph isomorphism', Congr. Numer., 1981, 30, p. 45-87
    • (1981) Congr. Numer. , vol.30 , pp. 45-87
    • McKay, B.D.1
  • 22
    • 0001540056 scopus 로고    scopus 로고
    • Isomorph-free exhaustive generation
    • 10.1006/jagm.1997.0898, 0196-6774
    • McKay, B.D.: 'Isomorph-free exhaustive generation', J. Algorithms, 1998, 26, p. 306-32410.1006/jagm.1997.0898 0196-6774
    • (1998) J. Algorithms , vol.26 , pp. 306-324
    • McKay, B.D.1
  • 23
  • 25
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • 10.1038/35001009, 0028-0836
    • Uetz, P., Giot, L., and Cagney, G.: et al. 'A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae', Nature, 2000, 403, (6770), p. 623-62710.1038/35001009 0028-0836
    • (2000) Nature , vol.403 , Issue.6770 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3
  • 26
    • 34547469442 scopus 로고    scopus 로고
    • Network motif discovery using sub-graph enumeration and symmetry-breaking
    • Grochow, J.A., and Kellis, M.: 'Network motif discovery using sub-graph enumeration and symmetry-breaking', RECOMB, 2007, p. 92-106
    • (2007) RECOMB , pp. 92-106
    • Grochow, J.A.1    Kellis, M.2
  • 27
    • 84872670210 scopus 로고    scopus 로고
    • 'Massachusetts institute of technology. dept. of electrical engineering and computer science.: on the structure and evolution of protein interaction networks', 2006, MEng, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science
    • Grochow, J.A.: 'Massachusetts institute of technology. dept. of electrical engineering and computer science.: on the structure and evolution of protein interaction networks', 2006, MEng, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science
    • Grochow, J.A.1
  • 28
    • 84975860562 scopus 로고    scopus 로고
    • Biomolecular network motif counting and discovery by color coding
    • i241-i24910.1093/bioinformatics/btn163
    • Alon, N., Dao, P., Hajirasouliha, I., Hormozdiari, F., and Sahinalp, S.C.: 'Biomolecular network motif counting and discovery by color coding', Bioinformatics, 2008, 24, pp., p. i241-i24910.1093/bioinformatics/btn163
    • (2008) Bioinformatics , pp. 24
    • Alon, N.1    Dao, P.2    Hajirasouliha, I.3    Hormozdiari, F.4    Sahinalp, S.C.5
  • 29
    • 76749118079 scopus 로고    scopus 로고
    • MODA: an efficient algorithm for network motif discovery in biological networks
    • 10.1266/ggs.84.385
    • Omidi, S., Schreiber, F., and Masoudi-Nejad, A.: 'MODA: an efficient algorithm for network motif discovery in biological networks', Genes Genet. Syst., 2009, 84, (5), p. 385-39510.1266/ggs.84.385
    • (2009) Genes Genet. Syst. , vol.84 , Issue.5 , pp. 385-395
    • Omidi, S.1    Schreiber, F.2    Masoudi-Nejad, A.3
  • 30
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • 10.1126/science.286.5439.509, 0036-8075
    • Barabasi, A.L., and Albert, R.: 'Emergence of scaling in random networks', Science, 1999, 286, (5439), p. 509-51210.1126/science.286.5439.509 0036-8075
    • (1999) Science , vol.286 , Issue.5439 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 31
    • 11144248635 scopus 로고    scopus 로고
    • The topological relationship between the large-scale attributes and local interaction patterns of complex networks
    • 10.1073/pnas.0406024101
    • Vázquez, A., Dobrin, R., and Sergi, D.: et al. 'The topological relationship between the large-scale attributes and local interaction patterns of complex networks', Proc. Natl. Acad. Sci., 2004, 101, (52), p. 17940-1794510.1073/pnas.0406024101
    • (2004) Proc. Natl. Acad. Sci. , vol.101 , Issue.52 , pp. 17940-17945
    • Vázquez, A.1    Dobrin, R.2    Sergi, D.3
  • 32
    • 70449631149 scopus 로고    scopus 로고
    • Kavosh: a new algorithm for finding network motifs
    • 10.1186/1471-2105-10-318
    • Kashani, Z.R., Ahrabian, H., and Elahi, E.: et al. 'Kavosh: a new algorithm for finding network motifs', BMC Bioinf., 2009, 10, p. 31810.1186/1471-2105-10-318
    • (2009) BMC Bioinf. , vol.10 , pp. 318
    • Kashani, Z.R.1    Ahrabian, H.2    Elahi, E.3
  • 33
    • 0002603293 scopus 로고
    • Practical graph isomorphism
    • McKay, B.D.: 'Practical graph isomorphism', Congr. Numer., 1981, 30, p. 45-87
    • (1981) Congr. Numer. , vol.30 , pp. 45-87
    • McKay, B.D.1
  • 34
    • 77954747857 scopus 로고    scopus 로고
    • G-tries: an efficient data structure for discovering network motifs
    • Ribeiro, P., and Silva, F.: 'G-tries: an efficient data structure for discovering network motifs', ACM, 2010
    • (2010) ACM
    • Ribeiro, P.1    Silva, F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.