메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Steiner tree methods for optimal sub-network identification: An empirical study

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATE SOLUTION; BIOLOGICAL NETWORKS; CONTEXT IDENTIFICATION; EMPIRICAL STUDIES; ORDERS OF MAGNITUDE; PROTEIN-PROTEIN INTERACTION NETWORKS; STEINER TREE PROBLEM; SYSTEMATIC SIMULATION;

EID: 84876788441     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-144     Document Type: Article
Times cited : (32)

References (44)
  • 2
    • 38549126643 scopus 로고    scopus 로고
    • Kegg for linking genomes to life and the environment
    • Kanehisa M. Kegg for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:480-484.
    • (2008) Nucleic Acids Res , vol.36 , pp. 480-484
    • Kanehisa, M.1
  • 5
    • 1342330546 scopus 로고    scopus 로고
    • Functional topology in a network of protein interactions
    • 10.1093/bioinformatics/btg415, 14960460
    • Przulj N, Wigle D, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics 2004, 20(3):340-348. [http://bioinformatics.oxfordjournals.org/content/20/3/340.abstract], 10.1093/bioinformatics/btg415, 14960460.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 340-348
    • Przulj, N.1    Wigle, D.2    Jurisica, I.3
  • 9
    • 0003037529 scopus 로고
    • Reducibility among combinatorial problems
    • New York: Plenum Press, Miller T
    • Karp RM. Reducibility among combinatorial problems. Complexity of Computer Computations 1972, 85-103. New York: Plenum Press, Miller T.
    • (1972) Complexity of Computer Computations , pp. 85-103
    • Karp, R.M.1
  • 10
    • 20844436318 scopus 로고    scopus 로고
    • Identifying Regulatory Subnetworks for a Set of Genes
    • 10.1074/mcp.M400110-MCP200, 23734346
    • Scott MS, Perkins T, Bunnell S, Pepin F, Thomas DY, Hallett M. Identifying Regulatory Subnetworks for a Set of Genes. Molecular & Cellular Proteomics 2005, 4(5):683-692. [http://www.mcponline.org/content/4/5/683.abstract], 10.1074/mcp.M400110-MCP200, 23734346.
    • (2005) Molecular & Cellular Proteomics , vol.4 , Issue.5 , pp. 683-692
    • Scott, M.S.1    Perkins, T.2    Bunnell, S.3    Pepin, F.4    Thomas, D.Y.5    Hallett, M.6
  • 11
    • 70350452746 scopus 로고    scopus 로고
    • Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
    • Huang SSC, Fraenkel E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal 2009, 2(81):40. [http://dx.doi.org/10.1126/scisignal.2000350].
    • (2009) Sci Signal , vol.2 , Issue.81 , pp. 40
    • Huang, S.S.C.1    Fraenkel, E.2
  • 12
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein - protein interaction networks: an integrated exact approach
    • Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Maller T. Identifying functional modules in protein - protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24(13):223-231. [http://bioinformatics.oxfordjournals.org/content/24/13/i223.abstract].
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 223-231
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Maller, T.5
  • 13
    • 54049158517 scopus 로고    scopus 로고
    • Network integration and graph analysis in mammalian molecular systems biology
    • Ma'ayan A. Network integration and graph analysis in mammalian molecular systems biology. Systems Biology, IET 2008, 2(5):206-221.
    • (2008) Systems Biology, IET , vol.2 , Issue.5 , pp. 206-221
    • Ma'ayan, A.1
  • 14
    • 62549145762 scopus 로고    scopus 로고
    • Toward accurate reconstruction of functional protein networks
    • 2671920, 19293828
    • Yosef N, Ungar L, Zalckvar E, Kimchi A, Kupiec M, Ruppin E, Sharan R. Toward accurate reconstruction of functional protein networks. Mol Syst Biol 2009, 5:248. [http://dx.doi.org/10.1038/msb.2009.3], 2671920, 19293828.
    • (2009) Mol Syst Biol , vol.5 , pp. 248
    • Yosef, N.1    Ungar, L.2    Zalckvar, E.3    Kimchi, A.4    Kupiec, M.5    Ruppin, E.6    Sharan, R.7
  • 15
    • 79551658804 scopus 로고    scopus 로고
    • Finding undetected protein associations in cell signaling by belief propagation
    • 10.1073/pnas.1004751108, 3021011, 21187432
    • Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, Francois JM, Zecchina R. Finding undetected protein associations in cell signaling by belief propagation. Proc Natl Acad Sci U S A 2011, 108(2):882-887. [http://dx.doi.org/10.1073/pnas.1004751108], 10.1073/pnas.1004751108, 3021011, 21187432.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , Issue.2 , pp. 882-887
    • Bailly-Bechet, M.1    Borgs, C.2    Braunstein, A.3    Chayes, J.4    Dagkessamanskaia, A.5    Francois, J.M.6    Zecchina, R.7
  • 16
    • 77951972600 scopus 로고    scopus 로고
    • BioNet: an R-Package for the functional analysis of biological networks
    • 10.1093/bioinformatics/btq089, 20189939
    • Beisser D, Klau GW, Dandekar T, Muller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics 2010, 26(8):1129-1130. 10.1093/bioinformatics/btq089, 20189939.
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 1129-1130
    • Beisser, D.1    Klau, G.W.2    Dandekar, T.3    Muller, T.4    Dittrich, M.T.5
  • 17
    • 84864470208 scopus 로고    scopus 로고
    • SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways
    • Tuncbag N, McCallum S, Huang SSC, Fraenkel E. SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Res 2012, [http://dx.doi.org/10.1093/nar/gks445].
    • (2012) Nucleic Acids Res
    • Tuncbag, N.1    McCallum, S.2    Huang, S.S.C.3    Fraenkel, E.4
  • 18
    • 0000133156 scopus 로고
    • An approximate solution for the Steiner problem in graphs
    • Takahashi H, Matsuyama A. An approximate solution for the Steiner problem in graphs. Math. Jap 1980, 24:573-577.
    • (1980) Math. Jap , vol.24 , pp. 573-577
    • Takahashi, H.1    Matsuyama, A.2
  • 22
    • 65649116900 scopus 로고    scopus 로고
    • KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
    • 10.1093/bioinformatics/btp167, 2682514, 19307239
    • Zhang JD, Wiemann S. KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics 2009, 25(11):1470-1471. [http://bioinformatics.oxfordjournals.org/content/25/11/1470.abstract], 10.1093/bioinformatics/btp167, 2682514, 19307239.
    • (2009) Bioinformatics , vol.25 , Issue.11 , pp. 1470-1471
    • Zhang, J.D.1    Wiemann, S.2
  • 24
    • 84986958410 scopus 로고
    • Problem reduction methods and a tree generation algorithm for the Steiner network problem
    • Balakrishnan A, Patel NR. Problem reduction methods and a tree generation algorithm for the Steiner network problem. Networks 1987, 17:65-85.
    • (1987) Networks , vol.17 , pp. 65-85
    • Balakrishnan, A.1    Patel, N.R.2
  • 25
    • 84981632113 scopus 로고
    • The Steiner problem in graphs
    • Dreyfus RA SE. The Steiner problem in graphs. Networks 1971, 1:195-207.
    • (1971) Networks , vol.1 , pp. 195-207
    • Dreyfus, R.A.S.E.1
  • 26
    • 0001343881 scopus 로고
    • Algorithm for the shortest connection of a group of graph vertices
    • Levin AY. Algorithm for the shortest connection of a group of graph vertices. Sov. Math. Dokl 1971, 12:1477-1481.
    • (1971) Sov. Math. Dokl , vol.12 , pp. 1477-1481
    • Levin, A.Y.1
  • 28
    • 0020179202 scopus 로고
    • An algorithm for the Steiner problem in graphs
    • Shore LRF ML, Gibbons PB. An algorithm for the Steiner problem in graphs. Networks 1982, 12:323-333.
    • (1982) Networks , vol.12 , pp. 323-333
    • Shore, L.R.F.M.L.1    Gibbons, P.B.2
  • 29
    • 0021385377 scopus 로고
    • An algorithm for the Steiner problem in graphs
    • Beasley JE. An algorithm for the Steiner problem in graphs. Networks 1984, 14:147-159.
    • (1984) Networks , vol.14 , pp. 147-159
    • Beasley, J.E.1
  • 30
    • 84987012291 scopus 로고
    • An SST-based algorithm for the Steiner problem in graphs
    • Beasley JE. An SST-based algorithm for the Steiner problem in graphs. Networks 1989, 19:1-16.
    • (1989) Networks , vol.19 , pp. 1-16
    • Beasley, J.E.1
  • 32
    • 0015200656 scopus 로고
    • Steiner's problem in graphs and its implications
    • Hakimi SL. Steiner's problem in graphs and its implications. Networks 1971, 1(2):113-133. [http://dx.doi.org/10.1002/net.3230010203].
    • (1971) Networks , vol.1 , Issue.2 , pp. 113-133
    • Hakimi, S.L.1
  • 33
    • 0001850931 scopus 로고
    • Steiner 's problem in graphs: heuristic methods
    • Voss S. Steiner 's problem in graphs: heuristic methods. Discrete Applied Mathematics 1992, 40:45-72.
    • (1992) Discrete Applied Mathematics , vol.40 , pp. 45-72
    • Voss, S.1
  • 34
    • 0022781638 scopus 로고
    • On finding Steiner vertices
    • Rayward-Smith VJ, Clare A. On finding Steiner vertices. Networks 1986, 16:283-294.
    • (1986) Networks , vol.16 , pp. 283-294
    • Rayward-Smith, V.J.1    Clare, A.2
  • 35
    • 52449147871 scopus 로고
    • Path-distance heuristics for the Steiner problem in undirected networks
    • Winter P, Smith JM. Path-distance heuristics for the Steiner problem in undirected networks. Algorithmica 1992, 7:309-327.
    • (1992) Algorithmica , vol.7 , pp. 309-327
    • Winter, P.1    Smith, J.M.2
  • 37
  • 39
    • 1542383500 scopus 로고
    • Worst-case relative performances of heuristics for the Steiner problem in graphs
    • Plesnik J. Worst-case relative performances of heuristics for the Steiner problem in graphs. Acta Math. Univ Comenianae 1991, 60:269-284.
    • (1991) Acta Math. Univ Comenianae , vol.60 , pp. 269-284
    • Plesnik, J.1
  • 41
    • 34147116337 scopus 로고    scopus 로고
    • The Gene Ontology (GO) database and informatics resource
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research 2004, 32:58-261. The Gene Ontology Consortium.
    • (2004) Nucleic Acids Research , vol.32 , pp. 58-261
  • 42
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • 10.1093/bioinformatics/btl567, 17098774
    • Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23(2):257-258. [http://dx.doi.org/10.1093/bioinformatics/btl567], 10.1093/bioinformatics/btl567, 17098774.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 43
    • 0024316113 scopus 로고
    • Elevation of pi class glutathione S-transferase activity in human breast cancer cells by transfection of the GST pi gene and its effect on sensitivity to toxins
    • Moscow JA, Townsend AJ, Cowan KH. Elevation of pi class glutathione S-transferase activity in human breast cancer cells by transfection of the GST pi gene and its effect on sensitivity to toxins. Mol Pharmacol 1989, 36:22-28.
    • (1989) Mol Pharmacol , vol.36 , pp. 22-28
    • Moscow, J.A.1    Townsend, A.J.2    Cowan, K.H.3
  • 44
    • 79951997445 scopus 로고    scopus 로고
    • Insulin breast cancer connection: confirmatory data set the stage for better care
    • 10.1200/JCO.2010.32.3022, 21115871
    • DeCensi A, Gennari A. Insulin breast cancer connection: confirmatory data set the stage for better care. J Clin Oncol 2011, 29:7. 10.1200/JCO.2010.32.3022, 21115871.
    • (2011) J Clin Oncol , vol.29 , pp. 7
    • DeCensi, A.1    Gennari, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.