메뉴 건너뛰기




Volumn 9, Issue 1, 2015, Pages

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity

Author keywords

Metabolic networks; Modularity; Substrate cycles

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; HUMAN; LIVER; METABOLISM; METABOLOMICS; PROCEDURES; TRANSPORT AT THE CELLULAR LEVEL;

EID: 84925111519     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/s12918-015-0146-2     Document Type: Article
Times cited : (6)

References (30)
  • 1
    • 33751013018 scopus 로고    scopus 로고
    • Synthetic biology-putting engineering into biology
    • Heinemann M, Panke S. Synthetic biology-putting engineering into biology. Bioinformatics. 2006;22:2790-9.
    • (2006) Bioinformatics , vol.22 , pp. 2790-2799
    • Heinemann, M.1    Panke, S.2
  • 3
    • 81355154070 scopus 로고    scopus 로고
    • Identification of biochemical network modules based on shortest retroactive distances
    • Sridharan GV, Hassoun S, Lee K. Identification of biochemical network modules based on shortest retroactive distances. PLoS Comput Biol. 2011;7:e1002262.
    • (2011) PLoS Comput Biol , vol.7 , pp. e1002262
    • Sridharan, G.V.1    Hassoun, S.2    Lee, K.3
  • 4
    • 0036084819 scopus 로고    scopus 로고
    • Accelerated substrate cycling: a new energy-wasting role for leptin in vivo
    • Reidy SP, Weber J-M. Accelerated substrate cycling: a new energy-wasting role for leptin in vivo. Am J Physiol Metab. 2002;282:E312-7.
    • (2002) Am J Physiol Metab , vol.282 , pp. E312-E317
    • Reidy, S.P.1    Weber, J.-M.2
  • 6
    • 77953169046 scopus 로고    scopus 로고
    • Cellular bioenergetics as a target for obesity therapy
    • Tseng Y-H, Cypess AM, Kahn CR. Cellular bioenergetics as a target for obesity therapy. Nat Rev Drug Discov. 2010;9:465-82.
    • (2010) Nat Rev Drug Discov , vol.9 , pp. 465-482
    • Tseng, Y.-H.1    Cypess, A.M.2    Kahn, C.R.3
  • 7
    • 77954248039 scopus 로고    scopus 로고
    • Altered metabolism in cancer
    • Locasale J, Cantley L. Altered metabolism in cancer. BMC Biol. 2010;8:88.
    • (2010) BMC Biol , vol.8 , pp. 88
    • Locasale, J.1    Cantley, L.2
  • 8
    • 84865224842 scopus 로고    scopus 로고
    • Detecting and investigating substrate cycles in a genome-scale human metabolic network
    • Gebauer J, Schuster S, de Figueiredo LF, Kaleta C. Detecting and investigating substrate cycles in a genome-scale human metabolic network. FEBS J. 2012;279:3192-202.
    • (2012) FEBS J , vol.279 , pp. 3192-3202
    • Gebauer, J.1    Schuster, S.2    de Figueiredo, L.F.3    Kaleta, C.4
  • 9
    • 84856560417 scopus 로고    scopus 로고
    • EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks
    • Kaleta C, de Figueiredo LF, Behre J, Schuster S. EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks. Lect Notes Inform. 2009;P-157:179-89.
    • (2009) Lect Notes Inform , vol.157 , pp. 179-189
    • Kaleta, C.1    de Figueiredo, L.F.2    Behre, J.3    Schuster, S.4
  • 10
    • 77956407882 scopus 로고    scopus 로고
    • HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology
    • Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol. 2010;6:411.
    • (2010) Mol Syst Biol , vol.6 , pp. 411
    • Gille, C.1    Bölling, C.2    Hoppe, A.3    Bulik, S.4    Hoffmann, S.5    Hübner, K.6
  • 11
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
    • 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;18:351-61.
    • (2002) Bioinformatics , vol.18 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3    Koch, I.4    Dandekar, T.5
  • 12
    • 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
    • Kaleta C, de Figueiredo LF, 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 Res. 2009;19:1872-83.
    • (2009) Genome Res , vol.19 , pp. 1872-1883
    • Kaleta, C.1    de Figueiredo, L.F.2    Schuster, S.3
  • 13
    • 84871603597 scopus 로고    scopus 로고
    • Metabolic flux-based modularity using shortest retroactive distances
    • Sridharan GV, Yi M, Hassoun S, Lee K. Metabolic flux-based modularity using shortest retroactive distances. BMC Syst Biol. 2012;6:155.
    • (2012) BMC Syst Biol , vol.6 , pp. 155
    • Sridharan, G.V.1    Yi, M.2    Hassoun, S.3    Lee, K.4
  • 14
    • 33745012299 scopus 로고    scopus 로고
    • Modularity and community structure in networks
    • Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci. 2006;103:8577-82.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 8577-8582
    • Newman, M.E.J.1
  • 15
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • Terzer M, Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics. 2008;24:2229-35.
    • (2008) Bioinformatics , vol.24 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 16
    • 34547469442 scopus 로고    scopus 로고
    • Network motif discovery using subgraph enumeration and symmetry-breaking
    • Springer
    • Grochow JA, Kellis M. Network motif discovery using subgraph enumeration and symmetry-breaking. In: Research in Computational Molecular Biology. Springer; 2007. p92-106
    • (2007) Research in Computational Molecular Biology , pp. 92-106
    • Grochow, J.A.1    Kellis, M.2
  • 17
    • 0028339522 scopus 로고
    • Proton-translocating transhydrogenase and NAD-and NADP-linked isocitrate dehydrogenases operate in a substrate cycle which contributes to fine regulation of the tricarboxylic acid cycle activity in mitochondria
    • Sazanov LA, Jackson JB. Proton-translocating transhydrogenase and NAD-and NADP-linked isocitrate dehydrogenases operate in a substrate cycle which contributes to fine regulation of the tricarboxylic acid cycle activity in mitochondria. FEBS Lett. 1994;344:109-16.
    • (1994) FEBS Lett , vol.344 , pp. 109-116
    • Sazanov, L.A.1    Jackson, J.B.2
  • 18
    • 29544450610 scopus 로고    scopus 로고
    • Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis
    • Nolan RP, Fenley AP, Lee K. Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis. Metab Eng. 2006;8:30-45.
    • (2006) Metab Eng , vol.8 , pp. 30-45
    • Nolan, R.P.1    Fenley, A.P.2    Lee, K.3
  • 19
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • Beard DA, Liang S, Qian H. Energy balance for analysis of complex metabolic networks. Biophys J. 2002;83:79-86.
    • (2002) Biophys J , vol.83 , pp. 79-86
    • Beard, D.A.1    Liang, S.2    Qian, H.3
  • 20
    • 0036100243 scopus 로고    scopus 로고
    • Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis
    • Price ND, Papin JA, Palsson BØ. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 2002;12:760-9.
    • (2002) Genome Res , vol.12 , pp. 760-769
    • Price, N.D.1    Papin, J.A.2    Palsson, B.3
  • 21
    • 84864048927 scopus 로고    scopus 로고
    • A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks
    • De Martino D, Figliuzzi M, De Martino A, Marinari E. A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. PLoS Comput Biol. 2012;8:e1002562.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002562
    • De Martino, D.1    Figliuzzi, M.2    De Martino, A.3    Marinari, E.4
  • 22
    • 79551676901 scopus 로고    scopus 로고
    • Elimination of thermodynamically infeasible loops in steady-state metabolic models
    • Schellenberger J, Lewis NE, Palsson BØ. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J. 2011;100:544-53.
    • (2011) Biophys J , vol.100 , pp. 544-553
    • Schellenberger, J.1    Lewis, N.E.2    Palsson, B.3
  • 23
    • 0029556146 scopus 로고
    • Triiodothyronine treatment increases substrate cycling between pyruvate carboxylase and malic enzyme in perfused rat liver
    • Petersen KF, Blair JB, Shulman GI. Triiodothyronine treatment increases substrate cycling between pyruvate carboxylase and malic enzyme in perfused rat liver. Metabolism. 1995;44:1380-3.
    • (1995) Metabolism , vol.44 , pp. 1380-1383
    • Petersen, K.F.1    Blair, J.B.2    Shulman, G.I.3
  • 24
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
    • Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular 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    Korcsmáros, T.2    Kiss, H.J.M.3    London, G.4    Nussinov, R.5
  • 26
    • 33744953147 scopus 로고    scopus 로고
    • Rosiglitazone controls fatty acid cycling in human adipose tissue by means of glyceroneogenesis and glycerol phosphorylation
    • Leroyer SN, Tordjman J, Chauvet G, Quette J, Chapron C, Forest C, et al. Rosiglitazone controls fatty acid cycling in human adipose tissue by means of glyceroneogenesis and glycerol phosphorylation. J Biol Chem. 2006;281:13141-9.
    • (2006) J Biol Chem , vol.281 , pp. 13141-13149
    • Leroyer, S.N.1    Tordjman, J.2    Chauvet, G.3    Quette, J.4    Chapron, C.5    Forest, C.6
  • 27
    • 12544254470 scopus 로고    scopus 로고
    • Effect of cancer cachexia on triacylglycerol/fatty acid substrate cycling in white adipose tissue
    • Beck SA, Tisdale MJ. Effect of cancer cachexia on triacylglycerol/fatty acid substrate cycling in white adipose tissue. Lipids. 2004;39:1187-9.
    • (2004) Lipids , vol.39 , pp. 1187-1189
    • Beck, S.A.1    Tisdale, M.J.2
  • 28
    • 26844582185 scopus 로고    scopus 로고
    • Molecular pathways leading to cancer cachexia
    • Tisdale MJ. Molecular pathways leading to cancer cachexia. Physiology. 2005;20:340-8.
    • (2005) Physiology , vol.20 , pp. 340-348
    • Tisdale, M.J.1
  • 29
    • 80054969621 scopus 로고    scopus 로고
    • A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology
    • Bordbar A, Feist A, Usaite-Black R, Woodcock J, Palsson B, Famili I. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. BMC Syst Biol. 2011;5:180.
    • (2011) BMC Syst Biol , vol.5 , pp. 180
    • Bordbar, A.1    Feist, A.2    Usaite-Black, R.3    Woodcock, J.4    Palsson, B.5    Famili, I.6
  • 30
    • 84897947195 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
    • El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst Biol. 2014;8:41.
    • (2014) BMC Syst Biol , vol.8 , pp. 41
    • El-Semman, I.E.1    Karlsson, F.H.2    Shoaie, S.3    Nookaew, I.4    Soliman, T.H.5    Nielsen, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.