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Volumn 6, Issue , 2012, Pages

VANTED v2: A framework for systems biology applications

Author keywords

Omics; Biological networks; Data analysis; Data integration; Data visualization; Model simulation

Indexed keywords

ARABIDOPSIS; ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; CYTOLOGY; ENZYMOLOGY; METABOLISM; METHODOLOGY; SYSTEMS BIOLOGY;

EID: 84868514445     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-139     Document Type: Article
Times cited : (138)

References (63)
  • 1
    • 77951168442 scopus 로고    scopus 로고
    • Omics meet networks - using systems approaches to infer regulatory networks in plants
    • Moreno-Risueno MA, Busch W, Benfey PN. Omics meet networks - using systems approaches to infer regulatory networks in plants. Curr Opin Plant Biol 2010, 13(2):126-131.
    • (2010) Curr Opin Plant Biol , vol.13 , Issue.2 , pp. 126-131
    • Moreno-Risueno, M.A.1    Busch, W.2    Benfey, P.N.3
  • 3
    • 35748962289 scopus 로고    scopus 로고
    • Tools for visually exploring biological networks
    • Suderman M, Hallett MT. Tools for visually exploring biological networks. Bioinformatics 2007, 23(20):2651-2659.
    • (2007) Bioinformatics , vol.23 , Issue.20 , pp. 2651-2659
    • Suderman, M.1    Hallett, M.T.2
  • 4
    • 33645241830 scopus 로고    scopus 로고
    • VANTED: a system for advanced data analysis and visualization in the context of biological networks
    • Junker BH, Klukas C, Schreiber F. VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 2006, 7:109. 1-13.
    • (2006) BMC Bioinformatics , vol.7
    • Junker, B.H.1    Klukas, C.2    Schreiber, F.3
  • 6
    • 77953515457 scopus 로고    scopus 로고
    • Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism
    • Hofmann J, Ashry AENE, Anwar S, Erban A, Kopka J, Grundler F. Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism. Plant J 2010, 62(6):1058-1071.
    • (2010) Plant J , vol.62 , Issue.6 , pp. 1058-1071
    • Hofmann, J.1    Ashry, A.E.N.E.2    Anwar, S.3    Erban, A.4    Kopka, J.5    Grundler, F.6
  • 9
    • 48549101307 scopus 로고    scopus 로고
    • Metabolic and developmental adaptations of growing potato tubers in response to specific manipulations of the adenylate energy status
    • Riewe D, Grosman L, Zauber H, Wucke C, Fernie AR, Geigenberger P. Metabolic and developmental adaptations of growing potato tubers in response to specific manipulations of the adenylate energy status. Plant Physiol 2008, 146(4):1579-1598.
    • (2008) Plant Physiol , vol.146 , Issue.4 , pp. 1579-1598
    • Riewe, D.1    Grosman, L.2    Zauber, H.3    Wucke, C.4    Fernie, A.R.5    Geigenberger, P.6
  • 11
    • 68949086653 scopus 로고    scopus 로고
    • An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis
    • Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S. An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. Biophys J 2009, 96(11):4542-4551.
    • (2009) Biophys J , vol.96 , Issue.11 , pp. 4542-4551
    • Gupta, S.1    Maurya, M.R.2    Stephens, D.L.3    Dennis, E.A.4    Subramaniam, S.5
  • 14
    • 0025489075 scopus 로고
    • The Self-Organizing Map
    • Kohonen T. The Self-Organizing Map. Proc IEEE 1990, 78:1464-1480.
    • (1990) Proc IEEE , vol.78 , pp. 1464-1480
    • Kohonen, T.1
  • 15
    • 33847320742 scopus 로고    scopus 로고
    • Dynamic exploration and editing of KEGG pathway diagrams
    • Klukas C, Schreiber F. Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics 2007, 23(3):344-350.
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 344-350
    • Klukas, C.1    Schreiber, F.2
  • 18
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 22
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets.
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012, 40(Database issue):D109-D114.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 27
    • 80053645387 scopus 로고    scopus 로고
    • DBE2- Management of experimental data for the VANTED system
    • Mehlhorn H, Schreiber F. DBE2- Management of experimental data for the VANTED system. J Integrative Bioinf 2011, 8(2):162.1-10.
    • (2011) J Integrative Bioinf , vol.8 , Issue.2
    • Mehlhorn, H.1    Schreiber, F.2
  • 28
    • 33645348241 scopus 로고    scopus 로고
    • The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
    • Cote R, Jones P, Apweiler R, Hermjakob H. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 2006, 7:97.1-7.
    • (2006) BMC Bioinformatics , vol.7
    • Cote, R.1    Jones, P.2    Apweiler, R.3    Hermjakob, H.4
  • 29
    • 77956549590 scopus 로고    scopus 로고
    • Editing, Validating, and Translating of SBGN Maps
    • Czauderna T, Klukas C, Schreiber F. Editing, Validating, and Translating of SBGN Maps. Bioinformatics 2010, 26(18):2340-2341.
    • (2010) Bioinformatics , vol.26 , Issue.18 , pp. 2340-2341
    • Czauderna, T.1    Klukas, C.2    Schreiber, F.3
  • 32
    • 27644483321 scopus 로고    scopus 로고
    • JFreeChart, a free Java class library for generating charts
    • Gilbert D, Morgner T. JFreeChart, a free Java class library for generating charts.
    • Gilbert, D.1    Morgner, T.2
  • 33
    • 84862157783 scopus 로고    scopus 로고
    • FluxMap: a VANTED Add-on for the visual exploration of flux distributions in biological networks
    • Rohn H, Hartmann A, Junker A, Junker BH, Schreiber F. FluxMap: a VANTED Add-on for the visual exploration of flux distributions in biological networks. BMC Syst Biol 2012, 6:33.1-9.
    • (2012) BMC Syst Biol , vol.6
    • Rohn, H.1    Hartmann, A.2    Junker, A.3    Junker, B.H.4    Schreiber, F.5
  • 34
    • 79959462235 scopus 로고    scopus 로고
    • Creating views on integrated multidomain data
    • Rohn H, Klukas C, Schreiber F. Creating views on integrated multidomain data. Bioinformatics 2011, 27(13):1839-1845.
    • (2011) Bioinformatics , vol.27 , Issue.13 , pp. 1839-1845
    • Rohn, H.1    Klukas, C.2    Schreiber, F.3
  • 37
    • 84875678685 scopus 로고    scopus 로고
    • Automated metabolic pathway reconstruction based on structural grammars
    • De RK, Tagore S. Automated metabolic pathway reconstruction based on structural grammars. J Comput Sci Syst Biol 2012, 5:116-127.
    • (2012) J Comput Sci Syst Biol , vol.5 , pp. 116-127
    • De, R.K.1    Tagore, S.2
  • 38
    • 70350029519 scopus 로고    scopus 로고
    • FBASimViz: interactive visualization of constraint-based metabolic models
    • Grafahrend-Belau E, Klukas C, Junker BH, Schreiber F. FBASimViz: interactive visualization of constraint-based metabolic models. Bioinformatics 2009, 25(20):2755-2757.
    • (2009) Bioinformatics , vol.25 , Issue.20 , pp. 2755-2757
    • Grafahrend-Belau, E.1    Klukas, C.2    Junker, B.H.3    Schreiber, F.4
  • 40
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering 2003, 5:264-276.
    • (2003) Metabolic Engineering , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 41
    • 0034519221 scopus 로고    scopus 로고
    • Robustness analysis of the Escherichia coli metabolic network
    • Edwards JSuBP
    • Edwards JSuBP Robustness analysis of the Escherichia coli metabolic network. Biotechnol Progress 2000, 16:927-939. Edwards JSuBP.
    • (2000) Biotechnol Progress , vol.16 , pp. 927-939
  • 42
    • 78649903919 scopus 로고    scopus 로고
    • Petri nets for modelling metabolic pathways: a survey
    • Baldan P, Cocco N, Marin A, Simeoni M. Petri nets for modelling metabolic pathways: a survey. Natural Computing 2010, 9(4):955-989.
    • (2010) Natural Computing , vol.9 , Issue.4 , pp. 955-989
    • Baldan, P.1    Cocco, N.2    Marin, A.3    Simeoni, M.4
  • 44
    • 84871727664 scopus 로고    scopus 로고
    • Guiding the interactive exploration of metabolic pathway interconnections
    • Jusufi I, Klukas C, Kerren A, Schreiber F. Guiding the interactive exploration of metabolic pathway interconnections. Information Visualization 2012, 11(2):136-150.
    • (2012) Information Visualization , vol.11 , Issue.2 , pp. 136-150
    • Jusufi, I.1    Klukas, C.2    Kerren, A.3    Schreiber, F.4
  • 45
    • 0029488555 scopus 로고
    • High dimensional brushing for interactive exploration of multivariate data
    • Martin AR, Ward MO. High dimensional brushing for interactive exploration of multivariate data. Proceedings on Visualization 1995, 271-278.
    • (1995) Proceedings on Visualization , pp. 271-278
    • Martin, A.R.1    Ward, M.O.2
  • 46
    • 84859760346 scopus 로고    scopus 로고
    • CentiLib: comprehensive analysis and exploration of network centralities
    • Gräßler J, Koschützki D, Schreiber F. CentiLib: comprehensive analysis and exploration of network centralities. Bioinformatics 2012, 28(8):1178-1179.
    • (2012) Bioinformatics , vol.28 , Issue.8 , pp. 1178-1179
    • Gräßler, J.1    Koschützki, D.2    Schreiber, F.3
  • 47
    • 0001231470 scopus 로고
    • The distribution of the ratio, in a single, normal sample, of range to standard deviation
    • David H, Hartley H, Pearson E. The distribution of the ratio, in a single, normal sample, of range to standard deviation. Biometrika 1954, 41(3-4):482-493.
    • (1954) Biometrika , vol.41 , Issue.3-4 , pp. 482-493
    • David, H.1    Hartley, H.2    Pearson, E.3
  • 48
    • 84984996500 scopus 로고    scopus 로고
    • The Gene Ontology project in 2008
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium The Gene Ontology project in 2008. Nucleic Acids Res 2008, 36(Database issue):D440-D444. The Gene Ontology Consortium.
    • (2008) Nucleic Acids Res , vol.36 , Issue.DATABASE ISSUE
  • 49
    • 77952315185 scopus 로고    scopus 로고
    • Integration of -omics data and networks for biomedical research
    • Klukas C, Schreiber F. Integration of -omics data and networks for biomedical research. J Integrative Bioinf 2010, 7(2):112.1-6.
    • (2010) J Integrative Bioinf , vol.7 , Issue.2
    • Klukas, C.1    Schreiber, F.2
  • 51
    • 33747856186 scopus 로고    scopus 로고
    • Metatool 5.0: fast and flexible elementary modes analysis
    • von Kamp A, Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 2006, 22(15):1930-1931.
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1930-1931
    • von Kamp, A.1    Schuster, S.2
  • 52
    • 84861726485 scopus 로고    scopus 로고
    • Creating interactive, web-based and data-enriched maps using the Systems Biology Graphical Notation
    • Junker A, Rohn H, Czauderna T, Klukas C, Hartmann A, Schreiber F. Creating interactive, web-based and data-enriched maps using the Systems Biology Graphical Notation. Nat Protocols 2012, 7:579-593.
    • (2012) Nat Protocols , vol.7 , pp. 579-593
    • Junker, A.1    Rohn, H.2    Czauderna, T.3    Klukas, C.4    Hartmann, A.5    Schreiber, F.6
  • 55
    • 79960342167 scopus 로고    scopus 로고
    • Visualizing multi-omics data in metabolic networks with the software Omix: a case study
    • Droste P, Miebach S, Niedenführ S, Wiechert W, Nöh K. Visualizing multi-omics data in metabolic networks with the software Omix: a case study. Biosystems 2011, 105(2):154-161.
    • (2011) Biosystems , vol.105 , Issue.2 , pp. 154-161
    • Droste, P.1    Miebach, S.2    Niedenführ, S.3    Wiechert, W.4    Nöh, K.5
  • 59
    • 67849122322 scopus 로고    scopus 로고
    • VisANT 3.5: Multi-scale network visualization, analysis and inference based on the gene ontology
    • Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C. VisANT 3.5: Multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 2009, 37(Web Server issue):W115-W121.
    • (2009) Nucleic Acids Res , vol.37 , Issue.WEB SERVER ISSUE
    • Hu, Z.1    Hung, J.H.2    Wang, Y.3    Chang, Y.C.4    Huang, C.L.5    Huyck, M.6    DeLisi, C.7
  • 63
    • 83255189512 scopus 로고    scopus 로고
    • Advances in omics and bioinformatics tools for systems analyses of plant functions
    • Mochida K, Shinozaki K. Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiology 2011, 52(12):2017-2038.
    • (2011) Plant Cell Physiology , vol.52 , Issue.12 , pp. 2017-2038
    • Mochida, K.1    Shinozaki, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.