Skip to main content

2013 | OriginalPaper | Buchkapitel

11. Computational Systems Biology Approaches for Deciphering Traditional Chinese Medicine

verfasst von : Shao Li, Le Lu

Erschienen in: Basics of Bioinformatics

Verlag: Springer Berlin Heidelberg

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

Traditional Chinese medicine (TCM) is a system with its own rich tradition over 3,000 years. Compared to Western medicine (WM), TCM is holistic with emphasis on regulating the integrity of the human body. However, understanding TCM in the context of “system” and TCM modernization both remain to be problematic. Along with the “Omics” revolution, it comes the era of system biology (SB). After years of studies in the cross field of TCM and SB, we find that bioinformatics and computational systems biology (CSB) approaches may help for deciphering the scientific basis of TCM. And the previous difficulty in the direct combination of WM and TCM, two distinct medical systems, may also be overcome through the development of systems biology, which tends toward preventive, predictive, and personalized medicine [1].

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literatur
1.
Zurück zum Zitat Hood L, Heath JR, Phelps ME, Lin B (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306(5696):640–643CrossRef Hood L, Heath JR, Phelps ME, Lin B (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306(5696):640–643CrossRef
2.
Zurück zum Zitat Hiesinger PR, Hassan BA (2005) Genetics in the age of systems biology. Cell 123(7):1173–1174CrossRef Hiesinger PR, Hassan BA (2005) Genetics in the age of systems biology. Cell 123(7):1173–1174CrossRef
3.
Zurück zum Zitat Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci 102(43):15545–15550CrossRef Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci 102(43):15545–15550CrossRef
4.
Zurück zum Zitat Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA et al (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci 32(7):320–331CrossRef Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA et al (2007) Comparing classical pathways and modern networks: towards the development of an edge ontology. Trends Biochem Sci 32(7):320–331CrossRef
5.
Zurück zum Zitat Barabasi A-L, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5(2):101–113CrossRef Barabasi A-L, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5(2):101–113CrossRef
6.
Zurück zum Zitat Shatkay H, Feldman R (2003) Mining the biomedical literature in the genomic era: an overview. J Comput Biol 10(6):821–855CrossRef Shatkay H, Feldman R (2003) Mining the biomedical literature in the genomic era: an overview. J Comput Biol 10(6):821–855CrossRef
7.
Zurück zum Zitat Jenssen T-K, Laegreid A, Komorowski J, Hovig E (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28(1):21–28 Jenssen T-K, Laegreid A, Komorowski J, Hovig E (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28(1):21–28
8.
Zurück zum Zitat Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 7(2):119–129CrossRef Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 7(2):119–129CrossRef
9.
Zurück zum Zitat Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV et al (2005) A network-based analysis of systemic inflammation in humans. Nature 437(7061):1032–1037CrossRef Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV et al (2005) A network-based analysis of systemic inflammation in humans. Nature 437(7061):1032–1037CrossRef
10.
Zurück zum Zitat Stapley BG, Benoit G (2000) Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput 2000:529–540 Stapley BG, Benoit G (2000) Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput 2000:529–540
11.
Zurück zum Zitat Zhu S, Okuno Y, Tsujimoto G, Mamitsuka H (2005) A probabilistic model for mining implicit ‘chemical compound-gene’ relations from literature. Bioinformatics 21(Suppl 2):ii245–ii251CrossRef Zhu S, Okuno Y, Tsujimoto G, Mamitsuka H (2005) A probabilistic model for mining implicit ‘chemical compound-gene’ relations from literature. Bioinformatics 21(Suppl 2):ii245–ii251CrossRef
12.
Zurück zum Zitat Zhang C, Li S (2004) Modeling of neuro-endocrine-immune network via subject oriented literature mining. Proc BGRS 2:167–170 Zhang C, Li S (2004) Modeling of neuro-endocrine-immune network via subject oriented literature mining. Proc BGRS 2:167–170
13.
Zurück zum Zitat Someren EPV, Wessels LFA, Backer E, Reinders MJT (2002) Genetic network modeling. Pharmacogenomics 3(4):507–525CrossRef Someren EPV, Wessels LFA, Backer E, Reinders MJT (2002) Genetic network modeling. Pharmacogenomics 3(4):507–525CrossRef
14.
Zurück zum Zitat de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9(1):67–103CrossRef de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9(1):67–103CrossRef
15.
Zurück zum Zitat Liang S, Fuhrman S, Somogyi R (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998:18–29 Liang S, Fuhrman S, Somogyi R (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998:18–29
16.
Zurück zum Zitat Le Phillip P, Bahl A, Ungar LH (2004) Using prior knowledge to improve genetic network reconstruction from microarray data. In Silico Biol 4(3):335–353 Le Phillip P, Bahl A, Ungar LH (2004) Using prior knowledge to improve genetic network reconstruction from microarray data. In Silico Biol 4(3):335–353
17.
Zurück zum Zitat Kuffner R, Fundel K, Zimmer R (2005) Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics 21(Suppl 2):ii259–ii267CrossRef Kuffner R, Fundel K, Zimmer R (2005) Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics 21(Suppl 2):ii259–ii267CrossRef
18.
Zurück zum Zitat Wu L, Li S (2005) Combined literature mining and gene expression analysis for modeling neuro-endocrine-immune interactions. In: Advances in intelligent computing 2005. Springer, Heidelberg/Berlin, pp 31–40 Wu L, Li S (2005) Combined literature mining and gene expression analysis for modeling neuro-endocrine-immune interactions. In: Advances in intelligent computing 2005. Springer, Heidelberg/Berlin, pp 31–40
19.
Zurück zum Zitat Li S, Wu L, Zhang Z (2006) Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 22(17):2143–2150MathSciNetCrossRef Li S, Wu L, Zhang Z (2006) Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 22(17):2143–2150MathSciNetCrossRef
20.
Zurück zum Zitat Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC et al (2001) The Stanford microarray database. Nucleic Acids Res 29(1):152–155CrossRef Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC et al (2001) The Stanford microarray database. Nucleic Acids Res 29(1):152–155CrossRef
21.
Zurück zum Zitat D’Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16(8):707–726CrossRef D’Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16(8):707–726CrossRef
22.
Zurück zum Zitat Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29(4):482–486CrossRef Ge H, Liu Z, Church GM, Vidal M (2001) Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet 29(4):482–486CrossRef
23.
Zurück zum Zitat D’Haeseleer P, Wen X, Fuhrman S, Somogyi R (1999) Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput 1999:41–52 D’Haeseleer P, Wen X, Fuhrman S, Somogyi R (1999) Linear modeling of mRNA expression levels during CNS development and injury. Pac Symp Biocomput 1999:41–52
24.
Zurück zum Zitat Cary MP, Bader GD, Sander C (2005) Pathway information for systems biology. FEBS Lett 579(8):1815–1820CrossRef Cary MP, Bader GD, Sander C (2005) Pathway information for systems biology. FEBS Lett 579(8):1815–1820CrossRef
25.
Zurück zum Zitat Goto M, Kanehisa S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30CrossRef Goto M, Kanehisa S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30CrossRef
26.
Zurück zum Zitat Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787–3793CrossRef Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787–3793CrossRef
27.
Zurück zum Zitat Folkman J (1995) Angiogenesis in cancer, vascular, rheumatoid and other disease. Nat Med 1(1):27–30CrossRef Folkman J (1995) Angiogenesis in cancer, vascular, rheumatoid and other disease. Nat Med 1(1):27–30CrossRef
28.
Zurück zum Zitat Carmeliet P, Jain RK (2000) Angiogenesis in cancer and other diseases. Nature 407(6801):249–257CrossRef Carmeliet P, Jain RK (2000) Angiogenesis in cancer and other diseases. Nature 407(6801):249–257CrossRef
29.
Zurück zum Zitat Carmeliet P (2003) Angiogenesis in health and disease. Nat Med 9(6):653–660CrossRef Carmeliet P (2003) Angiogenesis in health and disease. Nat Med 9(6):653–660CrossRef
30.
Zurück zum Zitat Li S, Zhang ZQ, Wu LJ, Zhang XG, Li YD et al (2007) Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Syst Biol 1(1):51–60MathSciNetCrossRef Li S, Zhang ZQ, Wu LJ, Zhang XG, Li YD et al (2007) Understanding ZHENG in traditional Chinese medicine in the context of neuro-endocrine-immune network. IET Syst Biol 1(1):51–60MathSciNetCrossRef
31.
Zurück zum Zitat Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I et al (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14(3):292–299CrossRef Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I et al (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14(3):292–299CrossRef
32.
Zurück zum Zitat Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D et al (2002) Network motifs: simple building blocks of complex networks. Science 298(5594):824–827CrossRef Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D et al (2002) Network motifs: simple building blocks of complex networks. Science 298(5594):824–827CrossRef
33.
Zurück zum Zitat Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31(1):64–68CrossRef Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31(1):64–68CrossRef
34.
Zurück zum Zitat Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799–804CrossRef Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799–804CrossRef
35.
Zurück zum Zitat Qi YHG (2006) Modularity and dynamics of cellular networks. PLoS Comput Biol 2(12):e174CrossRef Qi YHG (2006) Modularity and dynamics of cellular networks. PLoS Comput Biol 2(12):e174CrossRef
36.
Zurück zum Zitat Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:47–52CrossRef Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:47–52CrossRef
37.
Zurück zum Zitat Oti M, Brunner HG (2007) The modular nature of genetic diseases. Clin Genet 71:1–11CrossRef Oti M, Brunner HG (2007) The modular nature of genetic diseases. Clin Genet 71:1–11CrossRef
38.
Zurück zum Zitat Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG et al (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25(3):309–316CrossRef Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG et al (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 25(3):309–316CrossRef
39.
Zurück zum Zitat Goh K-I, Cusick ME, Valle D, Childs B, Vidal M et al (2007) The human disease network. Proc Natl Acad Sci 104(21):8685–8690CrossRef Goh K-I, Cusick ME, Valle D, Childs B, Vidal M et al (2007) The human disease network. Proc Natl Acad Sci 104(21):8685–8690CrossRef
40.
Zurück zum Zitat Wu X, Zhang M, Li S (2007) Global inference of human phenotype-genotype associations by integrating interactome, phenome and diseasome. In: The 8th international conference on systems biology, Long Beach, 1–6 Oct 2007 Wu X, Zhang M, Li S (2007) Global inference of human phenotype-genotype associations by integrating interactome, phenome and diseasome. In: The 8th international conference on systems biology, Long Beach, 1–6 Oct 2007
41.
Zurück zum Zitat FDA (2006) Draft guidance for industry: complementary and alternative medicine products and their regulation by the Food and Drug Administration. FDA, Rockville FDA (2006) Draft guidance for industry: complementary and alternative medicine products and their regulation by the Food and Drug Administration. FDA, Rockville
42.
Zurück zum Zitat Gu CD (1956) The inner classic of the yellow emperor, essential questions (Huangdi Neijing, Suwen). People’s Medical Publishing House, Beijing, pp 186–191 Gu CD (1956) The inner classic of the yellow emperor, essential questions (Huangdi Neijing, Suwen). People’s Medical Publishing House, Beijing, pp 186–191
43.
Zurück zum Zitat Eisenberg DM, Davis RB, Ettner SL, Appel S, Wilkey S et al (1998) Trends in alternative medicine use in the United States, 1990–1997: results of a follow-up national survey. JAMA 280:1569–1575CrossRef Eisenberg DM, Davis RB, Ettner SL, Appel S, Wilkey S et al (1998) Trends in alternative medicine use in the United States, 1990–1997: results of a follow-up national survey. JAMA 280:1569–1575CrossRef
44.
Zurück zum Zitat Hunter T (1995) Protein kinases and phosphatases: The Yin and Yang of protein phosphorylation and signaling. Cell 80(2):225–236CrossRef Hunter T (1995) Protein kinases and phosphatases: The Yin and Yang of protein phosphorylation and signaling. Cell 80(2):225–236CrossRef
45.
Zurück zum Zitat Ou B, Huang D, Hampsch-Woodill M, Flanagan JA (2003) When east meets west: the relationship between yin-yang and antioxidation-oxidation. FASEB J 17(2):127–129CrossRef Ou B, Huang D, Hampsch-Woodill M, Flanagan JA (2003) When east meets west: the relationship between yin-yang and antioxidation-oxidation. FASEB J 17(2):127–129CrossRef
46.
Zurück zum Zitat Lu B, Pang PT, Woo NH (2005) The yin and yang of neurotrophin action. Nat Rev Neurosci 6(8):603–614CrossRef Lu B, Pang PT, Woo NH (2005) The yin and yang of neurotrophin action. Nat Rev Neurosci 6(8):603–614CrossRef
47.
Zurück zum Zitat Zhang J (2007) Yin and yang interplay of IFN-γ in inflammation and autoimmune disease. J Clin Invest 117(4):871–873CrossRef Zhang J (2007) Yin and yang interplay of IFN-γ in inflammation and autoimmune disease. J Clin Invest 117(4):871–873CrossRef
48.
Zurück zum Zitat Xue TRR (2003) Studying traditional Chinese medicine. Science 300(5620):740–741CrossRef Xue TRR (2003) Studying traditional Chinese medicine. Science 300(5620):740–741CrossRef
49.
Zurück zum Zitat Kitano H (ed) (2001) Foundations of systems biology. The MIT Press, Cambridge, MA Kitano H (ed) (2001) Foundations of systems biology. The MIT Press, Cambridge, MA
50.
Zurück zum Zitat Palsson B (2000) The challenges of in silico biology. Nat Biotechnol 18(11):1147–1150CrossRef Palsson B (2000) The challenges of in silico biology. Nat Biotechnol 18(11):1147–1150CrossRef
51.
Zurück zum Zitat Qiu J (2007) China plans to modernize traditional medicine. Nature 446(7136):590–591CrossRef Qiu J (2007) China plans to modernize traditional medicine. Nature 446(7136):590–591CrossRef
52.
Zurück zum Zitat Qiu J (2007) Traditional medicine: a culture in the balance. Nature 448(7150):126–128CrossRef Qiu J (2007) Traditional medicine: a culture in the balance. Nature 448(7150):126–128CrossRef
53.
Zurück zum Zitat State Administration of Traditional Chinese Medicine (SATCM) of The People’s Republic of China (ed) (1994) The criteria of diagnosis and therapeutic effect of diseases and ZHENGs in TCM. Nanjing University Press, Nanjing, p 29 State Administration of Traditional Chinese Medicine (SATCM) of The People’s Republic of China (ed) (1994) The criteria of diagnosis and therapeutic effect of diseases and ZHENGs in TCM. Nanjing University Press, Nanjing, p 29
54.
Zurück zum Zitat China State Bureau of Technical Supervision (ed) (1997) The clinic terminology of traditional Chinese medical diagnosis and treatment – ZHENG. Standard Press of China, Beijing, p 52 China State Bureau of Technical Supervision (ed) (1997) The clinic terminology of traditional Chinese medical diagnosis and treatment – ZHENG. Standard Press of China, Beijing, p 52
55.
Zurück zum Zitat Besedovsky H, Sorkin OE (1977) Network of immune-neuroendocrine interactions. Clin Exp Immunol 27:1–12 Besedovsky H, Sorkin OE (1977) Network of immune-neuroendocrine interactions. Clin Exp Immunol 27:1–12
56.
Zurück zum Zitat Roth J, LeRoith D, Shiloach J, Rosenzweig JL, Lesniak MA et al (1982) The evolutionary origins of hormones, neuro-transmitters, and other extracellular chemical messengers: implications for mammalian biology. N Engl J Med 306:523–527CrossRef Roth J, LeRoith D, Shiloach J, Rosenzweig JL, Lesniak MA et al (1982) The evolutionary origins of hormones, neuro-transmitters, and other extracellular chemical messengers: implications for mammalian biology. N Engl J Med 306:523–527CrossRef
57.
Zurück zum Zitat Zhuang Y, Li S, Li Y (2006) dbNEI: a specific database for neuro-endocrine-immune interactions. Neuroendocrinol Lett 27(1/2):53–59 Zhuang Y, Li S, Li Y (2006) dbNEI: a specific database for neuro-endocrine-immune interactions. Neuroendocrinol Lett 27(1/2):53–59
58.
Zurück zum Zitat Li S (2002) Advanced in TCM symptomatology of rheumatoid arthritis. J Tradit Chin Med 22:137–142 Li S (2002) Advanced in TCM symptomatology of rheumatoid arthritis. J Tradit Chin Med 22:137–142
59.
Zurück zum Zitat Hsu CH, Yu MC, Lee TC, Yang YS (2003) High eosinophil cationic protein level in asthmatic patients with “Heat”, Zheng. Am J Chin Med 31:277–283CrossRef Hsu CH, Yu MC, Lee TC, Yang YS (2003) High eosinophil cationic protein level in asthmatic patients with “Heat”, Zheng. Am J Chin Med 31:277–283CrossRef
60.
Zurück zum Zitat Zhang X, Ji B, Chen B, Xie Z (1999) Relationship of cytokines and cold-heat syndrome differentiation in patients of duodenal ulcer. Zhongguo Zhong Xi Yi Jie He Za Zhi 19:267–269 Zhang X, Ji B, Chen B, Xie Z (1999) Relationship of cytokines and cold-heat syndrome differentiation in patients of duodenal ulcer. Zhongguo Zhong Xi Yi Jie He Za Zhi 19:267–269
61.
Zurück zum Zitat Pennisi E (2005) How will big pictures emerge from a sea of biological data? Science 309:94CrossRef Pennisi E (2005) How will big pictures emerge from a sea of biological data? Science 309:94CrossRef
62.
Zurück zum Zitat Song C, Havlin S, Makse HA (2005) Self-similarity of complex networks. Nature 433:392–395CrossRef Song C, Havlin S, Makse HA (2005) Self-similarity of complex networks. Nature 433:392–395CrossRef
63.
Zurück zum Zitat Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406:378–382CrossRef Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406:378–382CrossRef
64.
Zurück zum Zitat Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407:651–654CrossRef Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407:651–654CrossRef
65.
Zurück zum Zitat Wilder RL (2002) Neuroimmunoendocrinology of the rheumatic diseases, past, present, and future. Ann N Y Acad Sci 966:13–19CrossRef Wilder RL (2002) Neuroimmunoendocrinology of the rheumatic diseases, past, present, and future. Ann N Y Acad Sci 966:13–19CrossRef
66.
Zurück zum Zitat Choy EH, Panayi SGS (2001) Cytokine pathways and joint inflammation in rheumatoid arthritis. N Engl J Med 344:907–916CrossRef Choy EH, Panayi SGS (2001) Cytokine pathways and joint inflammation in rheumatoid arthritis. N Engl J Med 344:907–916CrossRef
67.
Zurück zum Zitat Trentham DE, Townes AS, Kang AH (1977) Autoimmunity to type II collagen an experimental model of arthritis. J Exp Med 146(3):857–868CrossRef Trentham DE, Townes AS, Kang AH (1977) Autoimmunity to type II collagen an experimental model of arthritis. J Exp Med 146(3):857–868CrossRef
68.
Zurück zum Zitat Staines NA, Wooley PH (1994) Collagen arthritis – what can it teach us? Br J Rheumatol 33:798–807CrossRef Staines NA, Wooley PH (1994) Collagen arthritis – what can it teach us? Br J Rheumatol 33:798–807CrossRef
69.
Zurück zum Zitat Papin JA, Hunter T, Palsson BO, Subramaniam S (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6(2):99–111CrossRef Papin JA, Hunter T, Palsson BO, Subramaniam S (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6(2):99–111CrossRef
70.
Zurück zum Zitat Weng G, Bhalla US, Iyengar R (1999) Complexity in biological signaling systems. Science 284(5411):92–96CrossRef Weng G, Bhalla US, Iyengar R (1999) Complexity in biological signaling systems. Science 284(5411):92–96CrossRef
71.
Zurück zum Zitat Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US (2003) The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics 19(3):408–415CrossRef Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US (2003) The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics 19(3):408–415CrossRef
72.
Zurück zum Zitat Ge H, Walhout AJM, Vidal M (2003) Integrating ‘omic’ information: a bridge between genomics and systems biology. Trends Genet 19(10):551–560CrossRef Ge H, Walhout AJM, Vidal M (2003) Integrating ‘omic’ information: a bridge between genomics and systems biology. Trends Genet 19(10):551–560CrossRef
73.
Zurück zum Zitat Kang G-L, Li S, Zhang J-F (2007) Entropy-based model for interpreting life systems in traditional Chinese medicine. eCAM 5(3):273–279MathSciNet Kang G-L, Li S, Zhang J-F (2007) Entropy-based model for interpreting life systems in traditional Chinese medicine. eCAM 5(3):273–279MathSciNet
74.
Zurück zum Zitat Li S (2007) Framework and practice of network-based studies for Chinese herbal formula. J Chin Integr Med 5(5):489–493CrossRef Li S (2007) Framework and practice of network-based studies for Chinese herbal formula. J Chin Integr Med 5(5):489–493CrossRef
75.
Zurück zum Zitat Butcher EC, Berg EL, Kunkel EJ (2004) Systems biology in drug discovery. Nat Biotechnol 22(10):1253–1259CrossRef Butcher EC, Berg EL, Kunkel EJ (2004) Systems biology in drug discovery. Nat Biotechnol 22(10):1253–1259CrossRef
76.
Zurück zum Zitat Hood L, Perlmutter RM (2004) The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol 22(10):1215–1217CrossRef Hood L, Perlmutter RM (2004) The impact of systems approaches on biological problems in drug discovery. Nat Biotechnol 22(10):1215–1217CrossRef
77.
Zurück zum Zitat Butcher EC (2005) Can cell systems biology rescue drug discovery? Nat Rev Drug Discov 4:461–467CrossRef Butcher EC (2005) Can cell systems biology rescue drug discovery? Nat Rev Drug Discov 4:461–467CrossRef
78.
Zurück zum Zitat Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J (2006) Cancer: a systems biology disease. Biosystems 83(2–3):81–90CrossRef Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J (2006) Cancer: a systems biology disease. Biosystems 83(2–3):81–90CrossRef
79.
Zurück zum Zitat Kitano H (2004) Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer 4(3):227–235MathSciNetCrossRef Kitano H (2004) Cancer as a robust system: implications for anticancer therapy. Nat Rev Cancer 4(3):227–235MathSciNetCrossRef
80.
Zurück zum Zitat Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70CrossRef Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70CrossRef
81.
Zurück zum Zitat Keith CT, Borisy AA, Stockwell BR (2005) Multicomponent therapeutics for networked systems. Nat Rev Drug Discov 4(1):71–78 Keith CT, Borisy AA, Stockwell BR (2005) Multicomponent therapeutics for networked systems. Nat Rev Drug Discov 4(1):71–78
83.
Zurück zum Zitat Li GQ, Arnold K, Guo XB, Jian HX, Fu LC (1984) Randomised comparative study of mefloquine, qinghaosu, and pyrimethamine-sulfadoxine in patients with falciparum malaria. Lancet 2(8416):1360–1361CrossRef Li GQ, Arnold K, Guo XB, Jian HX, Fu LC (1984) Randomised comparative study of mefloquine, qinghaosu, and pyrimethamine-sulfadoxine in patients with falciparum malaria. Lancet 2(8416):1360–1361CrossRef
84.
Zurück zum Zitat Shen Z-X, Shi Z-Z, Fang J, Gu B-W, Li J-M et al (2004) Inaugural article: all-trans retinoic acid/As2O3 combination yields a high quality remission and survival in newly diagnosed acute promyelocytic leukemia. Proc Natl Acad Sci 101(15):5328–5335CrossRef Shen Z-X, Shi Z-Z, Fang J, Gu B-W, Li J-M et al (2004) Inaugural article: all-trans retinoic acid/As2O3 combination yields a high quality remission and survival in newly diagnosed acute promyelocytic leukemia. Proc Natl Acad Sci 101(15):5328–5335CrossRef
85.
Zurück zum Zitat Hoessel R, Leclerc S, Endicott JA, Nobel MEM, Lawrie A et al (1999) Indirubin, the active constituent of a Chinese antileukaemia medicine, inhibits cyclin-dependent kinases. Nat Cell Biol 1(1):60–67CrossRef Hoessel R, Leclerc S, Endicott JA, Nobel MEM, Lawrie A et al (1999) Indirubin, the active constituent of a Chinese antileukaemia medicine, inhibits cyclin-dependent kinases. Nat Cell Biol 1(1):60–67CrossRef
86.
Zurück zum Zitat Kong W, Wei J, Abidi P, Lin M, Inaba S et al (2004) Berberine is a novel cholesterol-lowering drug working through a unique mechanism distinct from statins. Nat Med 10(12):1344–1351CrossRef Kong W, Wei J, Abidi P, Lin M, Inaba S et al (2004) Berberine is a novel cholesterol-lowering drug working through a unique mechanism distinct from statins. Nat Med 10(12):1344–1351CrossRef
87.
Zurück zum Zitat Wang M, Lamers R-JAN, Korthout HAAJ, Nesselrooij JHJV, Witkamp RF et al (2005) Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology. Phytother Res 19(3):173–182CrossRef Wang M, Lamers R-JAN, Korthout HAAJ, Nesselrooij JHJV, Witkamp RF et al (2005) Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology. Phytother Res 19(3):173–182CrossRef
88.
Zurück zum Zitat Csermely P, Agoston V, Pongor S (2005) The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci 26(4):178–182CrossRef Csermely P, Agoston V, Pongor S (2005) The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci 26(4):178–182CrossRef
89.
Zurück zum Zitat Corson TW, Crews CM (2007) Molecular understanding and modern application of traditional medicines: triumphs and trials. Cell 130(5):769–774CrossRef Corson TW, Crews CM (2007) Molecular understanding and modern application of traditional medicines: triumphs and trials. Cell 130(5):769–774CrossRef
90.
Zurück zum Zitat Li S, Lu A-P, Wang Y-Y, Li Y-D (2003) Suppressive effects of a Chinese herbal medicine qing-luo-yin extract on the angiogenesis of collagen-induced arthritis in rats. Am J Chin Med 31:713–720CrossRef Li S, Lu A-P, Wang Y-Y, Li Y-D (2003) Suppressive effects of a Chinese herbal medicine qing-luo-yin extract on the angiogenesis of collagen-induced arthritis in rats. Am J Chin Med 31:713–720CrossRef
Metadaten
Titel
Computational Systems Biology Approaches for Deciphering Traditional Chinese Medicine
verfasst von
Shao Li
Le Lu
Copyright-Jahr
2013
Verlag
Springer Berlin Heidelberg
DOI
https://doi.org/10.1007/978-3-642-38951-1_11