메뉴 건너뛰기




Volumn 34, Issue 9, 2013, Pages 508-526

Toward an integrated software platform for systems pharmacology

Author keywords

integrated software platform; systems biology; systems pharmacology

Indexed keywords

ARTICLE; BIOLOGY; COMPUTATIONAL FLUID DYNAMICS; COMPUTER MODEL; COMPUTER PROGRAM; COST EFFECTIVENESS ANALYSIS; INFORMATION PROCESSING; INTELLIGENCE; METABOLIC REGULATION; PHARMACOLOGY; PHASE SPACE ANALYSIS; SENSITIVITY ANALYSIS; SIMULATION; SYSTEMS BIOLOGY; SYSTEMS PHARMACOLOGY;

EID: 84890553923     PISSN: 01422782     EISSN: 1099081X     Source Type: Journal    
DOI: 10.1002/bdd.1875     Document Type: Article
Times cited : (20)

References (92)
  • 1
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano H,. Systems biology: a brief overview. Science 2002; 295: 1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 2
    • 0037079054 scopus 로고    scopus 로고
    • Computational systems biology
    • Kitano H,. Computational systems biology. Nature 2002; 420: 206-210.
    • (2002) Nature , vol.420 , pp. 206-210
    • Kitano, H.1
  • 3
    • 0033716382 scopus 로고    scopus 로고
    • Perspectives on systems biology
    • Kitano H,. Perspectives on systems biology. Future Generat Comput Syst 2000; 18: 199-216.
    • (2000) Future Generat Comput Syst , vol.18 , pp. 199-216
    • Kitano, H.1
  • 4
    • 0035775725 scopus 로고    scopus 로고
    • A new approach to decoding life: Systems biology
    • doi: 10.1146/annurev.genom.2.1.343
    • Ideker T, Galitski T, Hood L,. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2001; 2: 343-372. doi: 10.1146/annurev. genom.2.1.343.
    • (2001) Annu Rev Genomics Hum Genet , vol.2 , pp. 343-372
    • Ideker, T.1    Galitski, T.2    Hood, L.3
  • 6
    • 52949139763 scopus 로고    scopus 로고
    • Big data: Open-source format needed to aid wiki collaboration
    • doi: 10.1038/455461c
    • Lee TL,. Big data: open-source format needed to aid wiki collaboration. Nature 2008; 455: 461. doi: 10.1038/455461c.
    • (2008) Nature , vol.455 , pp. 461
    • Lee, T.L.1
  • 7
    • 78651341450 scopus 로고    scopus 로고
    • The 2011 nucleic acids research database issue and the online molecular biology database collection
    • doi: 10.1093/nar/gkq1243
    • Galperin MY, Cochrane GR,. The 2011 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Res 2011; 39: D1-D6. doi: 10.1093/nar/gkq1243.
    • (2011) Nucleic Acids Res , vol.39
    • Galperin, M.Y.1    Cochrane, G.R.2
  • 9
    • 63349098742 scopus 로고    scopus 로고
    • Linked data and provenance in biological data webs
    • doi: 10.1093/bib/bbn044
    • Zhao J, Miles A, Klyne G, Shotton D,. Linked data and provenance in biological data webs. Brief Bioinform 2009; 10: 139-152. doi: 10.1093/bib/bbn044.
    • (2009) Brief Bioinform , vol.10 , pp. 139-152
    • Zhao, J.1    Miles, A.2    Klyne, G.3    Shotton, D.4
  • 10
  • 11
    • 33751252571 scopus 로고    scopus 로고
    • Saving big pharma from drowning in the data pool
    • doi: 10.1016/j.drudis.2006.10.002
    • Brown F,. Saving big pharma from drowning in the data pool. Drug Discov Today 2006; 11: 1043-1045. doi: 10.1016/j.drudis.2006.10.002.
    • (2006) Drug Discov Today , vol.11 , pp. 1043-1045
    • Brown, F.1
  • 12
    • 0036462146 scopus 로고    scopus 로고
    • A computational biology database digest: Data, data analysis, and data management
    • Bry F, Kröger P,. A computational biology database digest: data, data analysis, and data management. Distrib Parallel Databases 2003; 13: 7-42.
    • (2003) Distrib Parallel Databases , vol.13 , pp. 7-42
    • Bry, F.1    Kröger, P.2
  • 13
    • 23944436932 scopus 로고    scopus 로고
    • Bioinformatics and data management support for environmental genomics
    • doi: 10.1371/journal.pbio.0030297
    • Field D, Tiwari B, Snape J,. Bioinformatics and data management support for environmental genomics. PLoS Biol 2005; 3: e297. doi: 10.1371/journal.pbio. 0030297.
    • (2005) PLoS Biol , vol.3
    • Field, D.1    Tiwari, B.2    Snape, J.3
  • 14
    • 70350786636 scopus 로고    scopus 로고
    • Management of information in distributed biomedical collaboratories
    • doi: 10.1007/978-1-59745-524-4-1
    • Keator DB,. Management of information in distributed biomedical collaboratories. Methods Mol Biol 2009; 569: 123. doi: 10.1007/978-1-59745-524- 4-1.
    • (2009) Methods Mol Biol , vol.569 , pp. 123
    • Keator, D.B.1
  • 15
    • 33746218196 scopus 로고    scopus 로고
    • Standards for systems biology
    • doi: 10.1038/nrg1922
    • Brazma A, Krestyaninova M, Sarkans U,. Standards for systems biology. Nat Rev Genet 2006; 7: 593-605. doi: 10.1038/nrg1922.
    • (2006) Nat Rev Genet , vol.7 , pp. 593-605
    • Brazma, A.1    Krestyaninova, M.2    Sarkans, U.3
  • 16
    • 10244255212 scopus 로고    scopus 로고
    • Taverna: A tool for the composition and enactment of bioinformatics workflows
    • doi: 10.1093/bioinformatics/bth361
    • Oinn T, Addis M, Ferris J, et al,. Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004; 20: 3045-3054. doi: 10.1093/bioinformatics/bth361.
    • (2004) Bioinformatics , vol.20 , pp. 3045-3054
    • Oinn, T.1    Addis, M.2    Ferris, J.3
  • 17
    • 33747824847 scopus 로고    scopus 로고
    • CaGrid: Design and implementation of the core architecture of the cancer biomedical informatics grid
    • doi: 10.1093/bioinformatics/btl272
    • Saltz J, Oster S, Hastings S, et al,. caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid. Bioinformatics 2006; 22: 1910-1916. doi: 10.1093/bioinformatics/btl272.
    • (2006) Bioinformatics , vol.22 , pp. 1910-1916
    • Saltz, J.1    Oster, S.2    Hastings, S.3
  • 18
    • 33750809488 scopus 로고    scopus 로고
    • Bio-STEER: A semantic web workflow tool for grid computing in the life sciences
    • Lee S, Wang TD, Hashmi N, Cummings MP,. Bio-STEER: a semantic web workflow tool for grid computing in the life sciences. Future Generations Computer Systems 2007; 23 (3): 497-509.
    • (2007) Future Generations Computer Systems , vol.23 , Issue.3 , pp. 497-509
    • Lee, S.1    Wang, T.D.2    Hashmi, N.3    Cummings, M.P.4
  • 19
    • 77649252269 scopus 로고    scopus 로고
    • Visualization of omics data for systems biology
    • doi: 10.1038/nmeth.1436
    • Gehlenborg N, O'Donoghue SI, Baliga NS, et al,. Visualization of omics data for systems biology. Nat Methods 2010; 7: S56-S68. doi: 10.1038/nmeth.1436.
    • (2010) Nat Methods , vol.7
    • Gehlenborg, N.1    O'Donoghue, S.I.2    Baliga, N.S.3
  • 20
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • doi: 10.1101/gr.092759.109
    • Krzywinski M, Schein J, Birol I, et al,. Circos: an information aesthetic for comparative genomics. Genome Res 2009; 19: 1639-1645. doi: 10.1101/gr.092759.109.
    • (2009) Genome Res , vol.19 , pp. 1639-1645
    • Krzywinski, M.1    Schein, J.2    Birol, I.3
  • 21
    • 79952202448 scopus 로고    scopus 로고
    • Cytoscape: Software for visualization and analysis of biological networks
    • doi: 10.1007/978-1-60761-987-1-18
    • Kohl M, Wiese S, Warscheid B,. Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 2011; 696: 291-303. doi: 10.1007/978-1-60761-987-1-18.
    • (2011) Methods Mol Biol , vol.696 , pp. 291-303
    • Kohl, M.1    Wiese, S.2    Warscheid, B.3
  • 22
    • 64049085062 scopus 로고    scopus 로고
    • A network view of disease and compound screening
    • doi: 10.1038/nrd2826
    • Schadt EE, Friend SH, Shaywitz DA,. A network view of disease and compound screening. Nat Rev Drug Discov 2009; 8: 286-295. doi: 10.1038/nrd2826.
    • (2009) Nat Rev Drug Discov , vol.8 , pp. 286-295
    • Schadt, E.E.1    Friend, S.H.2    Shaywitz, D.A.3
  • 23
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • doi: 10.1038/415530a
    • van't Veer LJ, Dal H, van der Vijver MJ, et al,. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002; 415: 530-536. doi: 10.1038/415530a.
    • (2002) Nature , vol.415 , pp. 530-536
    • Van'T Veer, L.J.1    Dal, H.2    Van Der Vijver, M.J.3
  • 24
    • 55449120805 scopus 로고    scopus 로고
    • Genetic mapping in human disease
    • doi: 10.1126/science.1156409
    • Altshuler D, Daly MJ, Lander ES,. Genetic mapping in human disease. Science 2008; 322: 881-888. doi: 10.1126/science.1156409.
    • (2008) Science , vol.322 , pp. 881-888
    • Altshuler, D.1    Daly, M.J.2    Lander, E.S.3
  • 25
    • 33751011889 scopus 로고    scopus 로고
    • HTRA1 promoter polymorphism in wet age-related macular degeneration
    • doi: 10.1126/science.1133807
    • Dewan A, Liu M, Hartman S, et al,. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 2006; 314: 989-992. doi: 10.1126/science.1133807.
    • (2006) Science , vol.314 , pp. 989-992
    • Dewan, A.1    Liu, M.2    Hartman, S.3
  • 26
    • 33751004690 scopus 로고    scopus 로고
    • A variant of the HTRA1 gene increases susceptibility to agerelated macular degeneration
    • doi: 10.1126/science.1133811
    • Yang Z, Camp NJ, Sun H, et al,. A variant of the HTRA1 gene increases susceptibility to agerelated macular degeneration. Science 2006; 314: 992-993. doi: 10.1126/science.1133811.
    • (2006) Science , vol.314 , pp. 992-993
    • Yang, Z.1    Camp, N.J.2    Sun, H.3
  • 27
    • 20144386111 scopus 로고    scopus 로고
    • Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function
    • doi: 10.1038/ng1518
    • Chesler EJ, Lu L, Shou S, et al,. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 2005; 37: 233-242. doi: 10.1038/ng1518.
    • (2005) Nat Genet , vol.37 , pp. 233-242
    • Chesler, E.J.1    Lu, L.2    Shou, S.3
  • 28
    • 8844244726 scopus 로고    scopus 로고
    • Genetic inheritance of gene expression in human cell lines
    • doi: 10.1086/426461
    • Monks SA, Leonardson A, Zhu H, et al,. Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 2004; 75: 1094-1105. doi: 10.1086/426461.
    • (2004) Am J Hum Genet , vol.75 , pp. 1094-1105
    • Monks, S.A.1    Leonardson, A.2    Zhu, H.3
  • 29
    • 4043128071 scopus 로고    scopus 로고
    • Genetic analysis of genome-wide variation in human gene expression
    • doi: 10.1038/nature02797
    • Morley M, Molony CM, Weber TM, et al,. Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430: 743-747. doi: 10.1038/nature02797.
    • (2004) Nature , vol.430 , pp. 743-747
    • Morley, M.1    Molony, C.M.2    Weber, T.M.3
  • 30
    • 3242806720 scopus 로고    scopus 로고
    • An integrative genomics approach to the reconstruction of gene networks in segregating populations
    • doi: 10.1159/000078209
    • Zhu J, Lum PY, Lamb J, et al,. An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenetic Genome Res 2004; 105: 363-374. doi: 10.1159/000078209.
    • (2004) Cytogenetic Genome Res , vol.105 , pp. 363-374
    • Zhu, J.1    Lum, P.Y.2    Lamb, J.3
  • 31
    • 34247556038 scopus 로고    scopus 로고
    • Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations
    • doi: 10.1371/journal.pcbi.0030069
    • Zhu J, Wiener MC, Zhang C, et al,. Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLoS Comput Biol 2007; 3: e69. doi: 10.1371/journal.pcbi.0030069.
    • (2007) PLoS Comput Biol , vol.3
    • Zhu, J.1    Wiener, M.C.2    Zhang, C.3
  • 32
    • 45149106353 scopus 로고    scopus 로고
    • Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
    • doi: 10.1038/ng.167
    • Zhu J, Zhang B, Smith EN, et al,. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 2008; 40: 854-861. doi: 10.1038/ng.167.
    • (2008) Nat Genet , vol.40 , pp. 854-861
    • Zhu, J.1    Zhang, B.2    Smith, E.N.3
  • 33
    • 33947305781 scopus 로고    scopus 로고
    • ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
    • doi: 10.1186/1471-2105-7-S1-S7
    • Margolin AA, Nemenman I, Basso K, et al,. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006; 7 (Suppl 1): S7. doi: 10.1186/1471-2105-7-S1-S7.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 1
    • Margolin, A.A.1    Nemenman, I.2    Basso, K.3
  • 34
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • e8. doi: 10.1371/journal.pbio.0050008
    • Faith JJ, Hayete B, Thaden JT, et al,. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 2007: 5: e8. doi: 10.1371/journal.pbio.0050008.
    • (2007) PLoS Biol , vol.5
    • Faith, J.J.1    Hayete, B.2    Thaden, J.T.3
  • 35
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • doi: 10.1038/ng881
    • Shen-Orr SS, Milo R, Mangan S, Alon U,. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002; 31: 64-68. doi: 10.1038/ng881.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 36
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • doi: 10.1038/nrg2102
    • Alon U,. Network motifs: theory and experimental approaches. Nature Rev Genet 2007; 8: 450-461. doi: 10.1038/nrg2102.
    • (2007) Nature Rev Genet , vol.8 , pp. 450-461
    • Alon, U.1
  • 38
    • 70449370314 scopus 로고    scopus 로고
    • The transcription unit architecture of the Escherichia coli genome
    • doi: 10.1038/nbt.1582
    • Cho BK, Zengler K, Qiu Y, et al,. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 2009; 27: 1043-1049. doi: 10.1038/nbt.1582.
    • (2009) Nat Biotechnol , vol.27 , pp. 1043-1049
    • Cho, B.K.1    Zengler, K.2    Qiu, Y.3
  • 39
    • 70449380939 scopus 로고    scopus 로고
    • Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. Coli
    • e7526. doi: 10.1371/journal.pone.0007526
    • Mendoza-Vargas A, Olvera L, Olvera M, et al,. Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 2009; 4: e7526. doi: 10.1371/journal.pone.0007526.
    • (2009) PLoS One , vol.4
    • Mendoza-Vargas, A.1    Olvera, L.2    Olvera, M.3
  • 40
    • 63449134229 scopus 로고    scopus 로고
    • DISTILLER: A data integration framework to reveal condition dependency of complex regulons in Escherichia coli
    • R27. doi: 10.1186/gb-2009-10-3-r27
    • Lemmens K, De Bie T, Dhollander T, et al,. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol 2009; 10: R27. doi: 10.1186/gb-2009-10-3-r27.
    • (2009) Genome Biol , vol.10
    • Lemmens, K.1    De Bie, T.2    Dhollander, T.3
  • 41
    • 79953685181 scopus 로고    scopus 로고
    • Building Watson: An overview of the DeepQA project
    • Ferrucci D, Brown E, Chu-Carroll J, et al,. Building Watson: an overview of the DeepQA project. AI Magazine 2010; 31: 59-79.
    • (2010) AI Magazine , vol.31 , pp. 59-79
    • Ferrucci, D.1    Brown, E.2    Chu-Carroll, J.3
  • 42
    • 33745463739 scopus 로고    scopus 로고
    • A comprehensive map of the toll-like receptor signaling network
    • 2006.0015. doi:msb4100057 [pii] 10.1038/msb4100057 [doi]
    • Oda K, Kitano H,. A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2006; 2: 2006.0015. doi:msb4100057 [pii] 10.1038/msb4100057 [doi].
    • (2006) Mol Syst Biol , vol.2
    • Oda, K.1    Kitano, H.2
  • 43
    • 33746889808 scopus 로고    scopus 로고
    • A comprehensive pathway map of epidermal growth factor receptor signaling
    • 2005 0010. doi:msb4100014 [pii] 10.1038/msb4100014 [doi]
    • Oda K, Matsuoka Y, Funahashi A, Kitano H,. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 2005; 1: 2005 0010. doi:msb4100014 [pii] 10.1038/msb4100014 [doi].
    • (2005) Mol Syst Biol , vol.1
    • Oda, K.1    Matsuoka, Y.2    Funahashi, A.3    Kitano, H.4
  • 44
    • 78650647490 scopus 로고    scopus 로고
    • A comprehensive map of the mTOR signaling network
    • doi:msb2010108 [pii] 10.1038/msb.2010.108
    • Caron E, Ghosh S, Matsuoka Y, et al,. A comprehensive map of the mTOR signaling network. Mol Syst Biol 2010; 6: 453. doi:msb2010108 [pii] 10.1038/msb.2010.108.
    • (2010) Mol Syst Biol , vol.6 , pp. 453
    • Caron, E.1    Ghosh, S.2    Matsuoka, Y.3
  • 45
    • 77957274480 scopus 로고    scopus 로고
    • A comprehensive molecular interaction map of the budding yeast cell cycle
    • doi:msb201073 [pii] 10.1038/msb.2010.73
    • Kaizu K, Ghosh S, Matsuoka Y, et al,. A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol 2010; 6: 415, doi:msb201073 [pii] 10.1038/msb.2010.73.
    • (2010) Mol Syst Biol , vol.6 , pp. 415
    • Kaizu, K.1    Ghosh, S.2    Matsuoka, Y.3
  • 46
    • 68749099453 scopus 로고    scopus 로고
    • Pathway databases and tools for their exploitation: Benefits, current limitations and challenges
    • doi:msb200947 [pii] 10.1038/msb.2009.47
    • Bauer-Mehren A, Furlong LI, Sanz F,. Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 2009; 5: 290. doi:msb200947 [pii] 10.1038/msb.2009.47.
    • (2009) Mol Syst Biol , vol.5 , pp. 290
    • Bauer-Mehren, A.1    Furlong, L.I.2    Sanz, F.3
  • 47
    • 10644250404 scopus 로고    scopus 로고
    • Evolving a lingua franca and associated software infrastructure for computational systems biology: The Systems Biology Markup Language (SBML) project
    • Hucka M, Finney A, Bornskin BJ, et al,. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Systems Biol (Stevenage) 2004; 1: 41-53.
    • (2004) Systems Biol (Stevenage) , vol.1 , pp. 41-53
    • Hucka, M.1    Finney, A.2    Bornskin, B.J.3
  • 48
    • 68449103579 scopus 로고    scopus 로고
    • The systems biology graphical notation
    • doi: 10.1038/nbt.1558
    • Le Novere N, Hucke M, Mi H, et al,. The systems biology graphical notation. Nat Biotechnol 2009; 27: 735-741. doi: 10.1038/nbt.1558.
    • (2009) Nat Biotechnol , vol.27 , pp. 735-741
    • Le Novere, N.1    Hucke, M.2    Mi, H.3
  • 49
    • 28644433993 scopus 로고    scopus 로고
    • Minimum information requested in the annotation of biochemical models (MIRIAM)
    • doi: 10.1038/nbt1156
    • Le Novere N, Finney A, Hucka M, et al,. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 2005; 23: 1509-1515. doi: 10.1038/nbt1156.
    • (2005) Nat Biotechnol , vol.23 , pp. 1509-1515
    • Le Novere, N.1    Finney, A.2    Hucka, M.3
  • 50
    • 23444439817 scopus 로고    scopus 로고
    • Using process diagrams for the graphical representation of biological networks
    • doi: 10.1038/nbt1111
    • Kitano H, Funahashi A, Matsuoka Y, Oda K,. Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 2005; 23: 961-966. doi: 10.1038/nbt1111.
    • (2005) Nat Biotechnol , vol.23 , pp. 961-966
    • Kitano, H.1    Funahashi, A.2    Matsuoka, Y.3    Oda, K.4
  • 52
    • 65649138437 scopus 로고    scopus 로고
    • Computational modeling of biochemical networks using COPASI
    • doi: 10.1007/978-1-59745-525-1-2
    • Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U,. Computational modeling of biochemical networks using COPASI. Methods Mol Biol 2009; 500: 17-59. doi: 10.1007/978-1-59745-525-1-2.
    • (2009) Methods Mol Biol , vol.500 , pp. 17-59
    • Mendes, P.1    Hoops, S.2    Sahle, S.3    Gauges, R.4    Dada, J.5    Kummer, U.6
  • 53
    • 33745631242 scopus 로고    scopus 로고
    • The SBML ODE Solver Library: A native API for symbolic and fast numerical analysis of reaction networks
    • doi: 10.1093/bioinformatics/btl086
    • Machne R, Finney A, Muller S, Lu J, Widder S, Flamm C,. The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 2006; 22: 1406-1407. doi: 10.1093/ bioinformatics/btl086.
    • (2006) Bioinformatics , vol.22 , pp. 1406-1407
    • Machne, R.1    Finney, A.2    Muller, S.3    Lu, J.4    Widder, S.5    Flamm, C.6
  • 54
    • 67349284339 scopus 로고    scopus 로고
    • Irreversibility of mitotic exit is the consequence of systems-level feedback
    • doi: 10.1038/nature07984
    • Lopez-Aviles S, Kapuy O, Novak B, Uhlmann F,. Irreversibility of mitotic exit is the consequence of systems-level feedback. Nature 2009; 459: 592-595. doi: 10.1038/nature07984.
    • (2009) Nature , vol.459 , pp. 592-595
    • Lopez-Aviles, S.1    Kapuy, O.2    Novak, B.3    Uhlmann, F.4
  • 55
    • 69849115198 scopus 로고    scopus 로고
    • Therapeutically targeting ErbB3: A key node in ligand-induced activation of the ErbB receptor-PI3K axis
    • ra31. doi: 10.1126/scisignal.2000352
    • Schoeberl B, Pace EA, Fitzgerald JB, et al,. Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis. Sci Signal 2009; 2: ra31. doi: 10.1126/scisignal.2000352.
    • (2009) Sci Signal , vol.2
    • Schoeberl, B.1    Pace, E.A.2    Fitzgerald, J.B.3
  • 56
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • McAdams HH, Arkin A,. Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A 1997; 94: 814-819.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , pp. 814-819
    • McAdams, H.H.1    Arkin, A.2
  • 58
    • 0027716813 scopus 로고
    • Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos
    • Novak B, Tyson JJ,. Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. J Cell Sci 1993; 106 (Pt 4): 1153-1168.
    • (1993) J Cell Sci , vol.106 , Issue.PART 4 , pp. 1153-1168
    • Novak, B.1    Tyson, J.J.2
  • 60
    • 77950216941 scopus 로고    scopus 로고
    • An ErbB3 antibody, MM-121, is active in cancers with ligand-dependent activation
    • doi: 10.1158/0008-5472.CAN-09-3145
    • Schoeberl B, Faber AC, Li D, et al,. An ErbB3 antibody, MM-121, is active in cancers with ligand-dependent activation. Cancer Res 2010; 70: 2485-2494. doi: 10.1158/0008-5472.CAN-09-3145.
    • (2010) Cancer Res , vol.70 , pp. 2485-2494
    • Schoeberl, B.1    Faber, A.C.2    Li, D.3
  • 61
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
    • Arkin A, Ross J, McAdams HH,. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 1998; 149: 1633-1648.
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 62
    • 20744434856 scopus 로고    scopus 로고
    • AgentCell: A digital single-cell assay for bacterial chemotaxis
    • doi: 10.1093/bioinformatics/bti391
    • Emonet T, Macal CM, North MJ, Wickersham CE, Cluzel P,. AgentCell: a digital single-cell assay for bacterial chemotaxis. Bioinformatics 2005; 21: 2714-2721. doi: 10.1093/bioinformatics/bti391.
    • (2005) Bioinformatics , vol.21 , pp. 2714-2721
    • Emonet, T.1    Macal, C.M.2    North, M.J.3    Wickersham, C.E.4    Cluzel, P.5
  • 63
    • 81355143152 scopus 로고    scopus 로고
    • Quantitative modeling of biochemical networks
    • Hofestadt R, Thelen S,. Quantitative modeling of biochemical networks. Stud Health Technol Inform 2011; 162: 3-16.
    • (2011) Stud Health Technol Inform , vol.162 , pp. 3-16
    • Hofestadt, R.1    Thelen, S.2
  • 64
    • 79955570036 scopus 로고    scopus 로고
    • Minimum Information about a Simulation Experiment (MIASE)
    • e1001122, doi: 10.1371/journal.pcbi.1001122
    • Waltemath D, Adams R, Beard DA, et al,. Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol 2011; 7: e1001122, doi: 10.1371/journal.pcbi.1001122.
    • (2011) PLoS Comput Biol , vol.7
    • Waltemath, D.1    Adams, R.2    Beard, D.A.3
  • 67
    • 0032485842 scopus 로고    scopus 로고
    • How will bioinformatics influence metabolic engineering?
    • Edwards JS, Palsson BO,. How will bioinformatics influence metabolic engineering? Biotechnol Bioengineer 1998; 58: 162-169.
    • (1998) Biotechnol Bioengineer , vol.58 , pp. 162-169
    • Edwards, J.S.1    Palsson, B.O.2
  • 68
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • doi: 10.1038/84379
    • Edwards JS, Ibarra RU, Palsson BO,. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 2001; 19: 125-130. doi: 10.1038/84379.
    • (2001) Nat Biotechnol , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 69
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman SA,. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 1969; 22: 437-467.
    • (1969) J Theor Biol , vol.22 , pp. 437-467
    • Kauffman, S.A.1
  • 70
    • 75249087912 scopus 로고    scopus 로고
    • SimBoolNet - A Cytoscape plugin for dynamic simulation of signaling networks
    • doi: 10.1093/bioinformatics/btp617
    • Zheng J, Zhang D, Przkycki PF, Zielinski R, Capala J, Prztycka TM,. SimBoolNet-a Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics 2010; 26: 141-142. doi: 10.1093/bioinformatics/btp617.
    • (2010) Bioinformatics , vol.26 , pp. 141-142
    • Zheng, J.1    Zhang, D.2    Przkycki, P.F.3    Zielinski, R.4    Capala, J.5    Prztycka, T.M.6
  • 71
    • 18344396568 scopus 로고    scopus 로고
    • Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    • doi: 10.1038/ng1201-365
    • Brazma A, Hingamp P, Quackenbush J, et al,. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001; 29: 365-371. doi: 10.1038/ng1201-365.
    • (2001) Nat Genet , vol.29 , pp. 365-371
    • Brazma, A.1    Hingamp, P.2    Quackenbush, J.3
  • 72
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • Hucka M, Finney A, Sauro HM, et al,. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003; 19: 524-531.
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3
  • 73
    • 77956664073 scopus 로고    scopus 로고
    • The BioPAX community standard for pathway data sharing
    • doi: 10.1038/nbt.1666
    • Demir E, Cary MP, Paley S, et al,. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010; 28: 935-942. doi: 10.1038/nbt.1666.
    • (2010) Nat Biotechnol , vol.28 , pp. 935-942
    • Demir, E.1    Cary, M.P.2    Paley, S.3
  • 74
    • 68449103579 scopus 로고    scopus 로고
    • The systems biology graphical notation
    • doi:nbt.1558 [pii] 10.1038/nbt.1558 [doi]
    • Le Novere N, Hucka M, Mi H, et al,. The systems biology graphical notation. Nat Biotechnol 2009; 27: 735-741. doi:nbt.1558 [pii] 10.1038/nbt.1558 [doi].
    • (2009) Nat Biotechnol , vol.27 , pp. 735-741
    • Le Novere, N.1    Hucka, M.2    Mi, H.3
  • 75
    • 70349581595 scopus 로고    scopus 로고
    • PANTHER pathway: An ontology-based pathway database coupled with data analysis tools
    • doi: 10.1007/978-1-60761-175-2-7
    • Mi H, Thomas P,. PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol 2009; 563: 123-140. doi: 10.1007/978-1-60761-175-2-7.
    • (2009) Methods Mol Biol , vol.563 , pp. 123-140
    • Mi, H.1    Thomas, P.2
  • 76
    • 77954195270 scopus 로고    scopus 로고
    • PathText: A text mining integrator for biological pathway visualizations
    • doi: 10.1093/bioinformatics/btq221
    • Kemper B, Matsuzaki T, Matsuoka Y, et al,. PathText: a text mining integrator for biological pathway visualizations. Bioinformatics 2010; 26: i374-i381. doi: 10.1093/bioinformatics/btq221.
    • (2010) Bioinformatics , vol.26
    • Kemper, B.1    Matsuzaki, T.2    Matsuoka, Y.3
  • 78
    • 48349105261 scopus 로고    scopus 로고
    • WikiPathways: Pathway editing for the people
    • e184. doi:08-PLBI-CP-0724 [pii] 10.1371/journal.pbio.0060184
    • Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C,. WikiPathways: pathway editing for the people. PLoS Biol 2008; 6: e184. doi:08-PLBI-CP-0724 [pii] 10.1371/journal.pbio.0060184.
    • (2008) PLoS Biol , vol.6
    • Pico, A.R.1    Kelder, T.2    Van Iersel, M.P.3    Hanspers, K.4    Conklin, B.R.5    Evelo, C.6
  • 79
    • 23144449917 scopus 로고    scopus 로고
    • LitMiner and WikiGene: Identifying problem-related key players of gene regulation using publication abstracts
    • doi: 10.1093/nar/gki417
    • Maier H, Dohr S, Grote K, et al,. LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts. Nucleic Acids Res 2005; 33: W779-782. doi: 10.1093/nar/gki417.
    • (2005) Nucleic Acids Res , vol.33
    • Maier, H.1    Dohr, S.2    Grote, K.3
  • 80
    • 77952794294 scopus 로고    scopus 로고
    • Payao: A community platform for SBML pathway model curation
    • doi:btq143 [pii] 10.1093/bioinformatics/btq143
    • Matsuoka Y, Ghosh S, Kikuchi N, Kitano H,. Payao: a community platform for SBML pathway model curation. Bioinformatics 2010; 26: 1381-1383. doi:btq143 [pii] 10.1093/bioinformatics/btq143.
    • (2010) Bioinformatics , vol.26 , pp. 1381-1383
    • Matsuoka, Y.1    Ghosh, S.2    Kikuchi, N.3    Kitano, H.4
  • 81
    • 79956099883 scopus 로고    scopus 로고
    • Social engineering for virtual 'big science' in systems biology
    • doi: 10.1038/nchembio.574
    • Kitano H, Ghosh S, Matsuoka Y,. Social engineering for virtual 'big science' in systems biology. Nat Chem Biol 2011; 7: 323-326. doi: 10.1038/nchembio.574.
    • (2011) Nat Chem Biol , vol.7 , pp. 323-326
    • Kitano, H.1    Ghosh, S.2    Matsuoka, Y.3
  • 82
    • 84888011244 scopus 로고    scopus 로고
    • Network-based approaches in drug discovery and early development
    • doi: 10.1038/clpt.2013.176
    • Harrold MJ, Ramanathan M, Mager ED,. Network-based approaches in drug discovery and early development. Clin Pharmacol Ther 2013. doi: 10.1038/clpt.2013.176.
    • (2013) Clin Pharmacol Ther
    • Harrold, M.J.1    Ramanathan, M.2    Mager, E.D.3
  • 83
    • 70350690962 scopus 로고    scopus 로고
    • Systems pharmacology and genome medicine: A future perspective
    • doi: 10.1186/gm11
    • Wist DA, Berger IS, Iyengar R,. Systems pharmacology and genome medicine: a future perspective. Genome Med 2009; 1: 11. doi: 10.1186/gm11.
    • (2009) Genome Med , vol.1 , pp. 11
    • Wist, D.A.1    Berger, I.S.2    Iyengar, R.3
  • 84
    • 79957936421 scopus 로고    scopus 로고
    • Role of systems pharmacology in understanding drug adverse events
    • doi: 10.1002/wsbm.114
    • Berger SI, Iyengar R,. Role of systems pharmacology in understanding drug adverse events. Wiley Interdiscip Rev Syst Biol Med 2011; 3 (2): 129-135. doi: 10.1002/wsbm.114.
    • (2011) Wiley Interdiscip Rev Syst Biol Med , vol.3 , Issue.2 , pp. 129-135
    • Berger, S.I.1    Iyengar, R.2
  • 85
    • 84855906454 scopus 로고    scopus 로고
    • Systems pharmacology: Network analysis to identify multiscale mechanisms of drug action
    • doi: 10.1146/annurev-pharmtox-010611-134520
    • Zhao S, Iyengar R,. Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu Rev Pharmacol Toxicol 2012; 52: 505-521. doi: 10.1146/annurev-pharmtox-010611-134520.
    • (2012) Annu Rev Pharmacol Toxicol , vol.52 , pp. 505-521
    • Zhao, S.1    Iyengar, R.2
  • 86
    • 84883409705 scopus 로고    scopus 로고
    • Basic concepts in physiologically based pharmacokinetic modeling in drug discovery and development
    • e63. doi: 10.1038/psp.2013.41
    • Jones H, Rowland-Yeo K,. Basic concepts in physiologically based pharmacokinetic modeling in drug discovery and development. CPT Pharmacometrics Syst Pharmacol 2013; 2: e63. doi: 10.1038/psp.2013.41.
    • (2013) CPT Pharmacometrics Syst Pharmacol , vol.2
    • Jones, H.1    Rowland-Yeo, K.2
  • 88
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
    • doi: 10.1016/j.pharmthera.2013.01.016
    • Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R,. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013; 138 (3): 333-408. doi: 10.1016/j.pharmthera.2013.01.016.
    • (2013) Pharmacol Ther , vol.138 , Issue.3 , pp. 333-408
    • Csermely, P.1    Korcsmáros, T.2    Kiss, H.J.3    London, G.4    Nussinov, R.5
  • 89
    • 84890561012 scopus 로고    scopus 로고
    • Models that take drugs
    • 11 June
    • Models that take drugs. The Economist report, 11 June 2005.
    • (2005) The Economist Report
  • 90
    • 4444343665 scopus 로고    scopus 로고
    • Assessing the Impact of Predictive Biosimulation on Drug Discovery and Development
    • Michelson S,. Assessing the Impact of Predictive Biosimulation on Drug Discovery and Development. Journal of Bioinformatics and Computational Chemistry 2003; 1 (1): 169-177.
    • (2003) Journal of Bioinformatics and Computational Chemistry , vol.1 , Issue.1 , pp. 169-177
    • Michelson, S.1
  • 91
    • 84890551505 scopus 로고    scopus 로고
    • Merrimack Pharmaceuticals Initiates Enrollment In A Phase 1 Study Of MM-121, An ErbB3 Antagonist. Medical News Today, 12 August 2008
    • Merrimack Pharmaceuticals Initiates Enrollment In A Phase 1 Study Of MM-121, An ErbB3 Antagonist. Medical News Today, 12 August 2008.
  • 92
    • 84881151372 scopus 로고    scopus 로고
    • NIH Support for the emergence of quantitative and systems pharmacology
    • e37. doi: 10.1038/psp.2013.13
    • Rogers M, Lyster P, Okita R,. NIH Support for the emergence of quantitative and systems pharmacology. CPT Pharmacometrics Syst Pharmacol 2013; 2: e37. doi: 10.1038/psp.2013.13.
    • (2013) CPT Pharmacometrics Syst Pharmacol , vol.2
    • Rogers, M.1    Lyster, P.2    Okita, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.