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Volumn 5, Issue , 2011, Pages

A new computational method to split large biochemical networks into coherent subnets

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 79551619614     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-25     Document Type: Article
Times cited : (17)

References (28)
  • 2
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • 10.1023/A:1020390132244, 12241063
    • Klamt S, Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep 2002, 29:233-236. 10.1023/A:1020390132244, 12241063.
    • (2002) Mol Biol Rep , vol.29 , pp. 233-236
    • Klamt, S.1    Stelling, J.2
  • 3
    • 52949098408 scopus 로고    scopus 로고
    • Large scale computation of elementary flux modes with bit pattern trees
    • 10.1093/bioinformatics/btn401, 18676417
    • Terzer M, Stelling J. Large scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24:2229-2235. 10.1093/bioinformatics/btn401, 18676417.
    • (2008) Bioinformatics , vol.24 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 4
    • 75849164426 scopus 로고    scopus 로고
    • Computing the shortest elementary flux modes in genome-scale metabolic networks
    • 10.1093/bioinformatics/btp564, 19793869
    • de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics 2009, 25:3158-3165. 10.1093/bioinformatics/btp564, 19793869.
    • (2009) Bioinformatics , vol.25 , pp. 3158-3165
    • de Figueiredo, L.F.1    Podhorski, A.2    Rubio, A.3    Kaleta, C.4    Beasley, J.E.5    Schuster, S.6    Planes, F.J.7
  • 5
    • 70349636598 scopus 로고    scopus 로고
    • Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
    • 10.1101/gr.090639.108, 2765277, 19541909
    • Kaleta C, de Figueiredo L, Schuster S. Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. Genome Research 2009, 19:1872-1883. 10.1101/gr.090639.108, 2765277, 19541909.
    • (2009) Genome Research , vol.19 , pp. 1872-1883
    • Kaleta, C.1    de Figueiredo, L.2    Schuster, S.3
  • 6
    • 77956649528 scopus 로고    scopus 로고
    • Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
    • 10.1016/j.copbio.2010.07.002, 20692823
    • Ruppin E, Papin JA, de Figueiredo LF, Schuster S. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Current Opinion in Biotechnology 2010, 21:502-510. 10.1016/j.copbio.2010.07.002, 20692823.
    • (2010) Current Opinion in Biotechnology , vol.21 , pp. 502-510
    • Ruppin, E.1    Papin, J.A.2    de Figueiredo, L.F.3    Schuster, S.4
  • 7
    • 67650904950 scopus 로고    scopus 로고
    • Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation
    • 10.1371/journal.pcbi.1000410, 2690837, 19521528
    • Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ. Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation. PLoS Comput Biol 2009, 5:e1000410. 10.1371/journal.pcbi.1000410, 2690837, 19521528.
    • (2009) PLoS Comput Biol , vol.5
    • Teusink, B.1    Wiersma, A.2    Jacobs, L.3    Notebaart, R.A.4    Smid, E.J.5
  • 8
    • 36048998568 scopus 로고    scopus 로고
    • An algorithm for modularization of MAPK and calcium signaling pathways: Comparative analysis among different species
    • 10.1016/j.jbi.2007.05.007, 17591461
    • Nayak L, De RK. An algorithm for modularization of MAPK and calcium signaling pathways: Comparative analysis among different species. Journal of Biomedical Informatics 2007, 40:726-749. 10.1016/j.jbi.2007.05.007, 17591461.
    • (2007) Journal of Biomedical Informatics , vol.40 , pp. 726-749
    • Nayak, L.1    De, R.K.2
  • 9
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • 10.1093/nar/30.7.1575, 101833, 11917018
    • Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucl Acids Res 2002, 30:1575-1584. 10.1093/nar/30.7.1575, 101833, 11917018.
    • (2002) Nucl Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 10
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • 10.1038/nature03288, 2175124, 15729348
    • Guimera R, Nunes Amaral LA. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900. 10.1038/nature03288, 2175124, 15729348.
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimera, R.1    Nunes Amaral, L.A.2
  • 11
    • 0037345719 scopus 로고    scopus 로고
    • Subnetwork hierarchies of biochemical pathways
    • 10.1093/bioinformatics/btg033, 12611809
    • Holme P, Huss M, Jeong HW. Subnetwork hierarchies of biochemical pathways. Bioinformatics 2003, 19:532-538. 10.1093/bioinformatics/btg033, 12611809.
    • (2003) Bioinformatics , vol.19 , pp. 532-538
    • Holme, P.1    Huss, M.2    Jeong, H.W.3
  • 12
    • 0038281450 scopus 로고    scopus 로고
    • Hierarchical analysis of dependency in metabolic networks
    • 10.1093/bioinformatics/btg115, 12761067
    • Gagneur J, Jackson D, Casari G. Hierarchical analysis of dependency in metabolic networks. Bioinformatics 2003, 19:1027-1034. 10.1093/bioinformatics/btg115, 12761067.
    • (2003) Bioinformatics , vol.19 , pp. 1027-1034
    • Gagneur, J.1    Jackson, D.2    Casari, G.3
  • 13
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
    • 10.1093/bioinformatics/18.2.351, 11847093
    • Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 2002, 18:351-361. 10.1093/bioinformatics/18.2.351, 11847093.
    • (2002) Bioinformatics , vol.18 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3    Koch, I.4    Dandekar, T.5
  • 14
    • 25444515956 scopus 로고    scopus 로고
    • YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
    • 10.1186/1471-2105-6-135, 1175843, 15929789
    • Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T. YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics 2005, 6:135. 10.1186/1471-2105-6-135, 1175843, 15929789.
    • (2005) BMC Bioinformatics , vol.6 , pp. 135
    • Schwarz, R.1    Musch, P.2    von Kamp, A.3    Engels, B.4    Schirmer, H.5    Schuster, S.6    Dandekar, T.7
  • 15
    • 4444234772 scopus 로고    scopus 로고
    • Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
    • 10.1093/bioinformatics/bth167, 15037506
    • Ma HW, Zhao XM, Yuan YJ, Zeng AP. Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 2004, 20:1870-1876. 10.1093/bioinformatics/bth167, 15037506.
    • (2004) Bioinformatics , vol.20 , pp. 1870-1876
    • Ma, H.W.1    Zhao, X.M.2    Yuan, Y.J.3    Zeng, A.P.4
  • 17
    • 67049098922 scopus 로고    scopus 로고
    • Hypergraphs and Cellular Networks
    • 10.1371/journal.pcbi.1000385, 2673028, 19478865
    • Klamt S, Haus U-U, Theis F. Hypergraphs and Cellular Networks. PLoS Comput Biol 2009, 5:e1000385. 10.1371/journal.pcbi.1000385, 2673028, 19478865.
    • (2009) PLoS Comput Biol , vol.5
    • Klamt, S.1    Haus, U.-U.2    Theis, F.3
  • 19
    • 0037249498 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    • 10.1093/nar/gkg076, 165523, 12519987
    • Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 2003, 31:224-228. 10.1093/nar/gkg076, 165523, 12519987.
    • (2003) Nucleic Acids Research , vol.31 , pp. 224-228
    • Rhee, S.Y.1    Beavis, W.2    Berardini, T.Z.3    Chen, G.4    Dixon, D.5    Doyle, A.6    Garcia-Hernandez, M.7    Huala, E.8    Lander, G.9    Montoya, M.10
  • 22
    • 79952006713 scopus 로고    scopus 로고
    • Dissecting metabolic networks into functional subnets
    • Brisbane: iConceptPress, Fung GPC
    • Verwoerd WS. Dissecting metabolic networks into functional subnets. A Practical Guide to Bioinformatics Analysis 2010, 0000:79-98. Brisbane: iConceptPress, Fung GPC.
    • (2010) A Practical Guide to Bioinformatics Analysis , vol.0 , pp. 79-98
    • Verwoerd, W.S.1
  • 23
    • 67651209209 scopus 로고    scopus 로고
    • On the Reconstruction of the Mus musculus Genome-Scale Metabolic Network Model
    • full_text, 19425150
    • Quek L-E, Nielsen LK. On the Reconstruction of the Mus musculus Genome-Scale Metabolic Network Model. Genome Informatics 2008, 21:89-100. full_text, 19425150.
    • (2008) Genome Informatics , vol.21 , pp. 89-100
    • Quek, L.-E.1    Nielsen, L.K.2
  • 24
    • 58049211936 scopus 로고    scopus 로고
    • Can sugars be produced from fatty acids? A test case for pathway analysis tools
    • 10.1093/bioinformatics/btn621, 19117076
    • de Figueiredo LF, Schuster S, Kaleta C, Fell DA. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 2009, 25:152-158. 10.1093/bioinformatics/btn621, 19117076.
    • (2009) Bioinformatics , vol.25 , pp. 152-158
    • de Figueiredo, L.F.1    Schuster, S.2    Kaleta, C.3    Fell, D.A.4
  • 25
    • 0004062749 scopus 로고    scopus 로고
    • Mathematica
    • Mathematica. , http://www.wolfram.com
  • 28
    • 79952007314 scopus 로고    scopus 로고
    • Percolation threshold
    • Percolation threshold. , http://en.wikipedia.org/wiki/Percolation_threshold


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.