Applications and trends in systems biology in biochemistry

FEBS Journal

Volumn 278, Issue 16, 2011, Pages 2767-2857

  Hübner, Katrin ^a   Sahle, Sven ^a   Kummer, Ursula ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

metabolism; modeling; quantitative experiments; signaling; simulation; systems biology

Indexed keywords

BIOCHEMISTRY; COMPUTER PROGRAM; EXPERIMENTAL STUDY; HUMAN; INFORMATION PROCESSING; MATHEMATICAL MODEL; METABOLISM; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; PUBLICATION; REVIEW; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ANIMALS; BIOCHEMISTRY; BIOTECHNOLOGY; HUMANS; SYSTEMS BIOLOGY;

EID: 79961027577     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2011.08217.x     Document Type: Review

References (53)

1. Kitano H, (2002) Systems biology: a brief overview. Science 295, 1662-1664. (Pubitemid 34202893)
2. Noble D, (2003) The future: putting Humpty-Dumpty together again. Biochem Soc Trans 31, 156-158. (Pubitemid 36241418)
3. Mesarović M, (1968) Systems Theory and Biology. Springer, New York, NY, pp. 59-87.
4. Heinrich R, &, Rapoport TA, (1973) Linear theory of enzymatic chains; its application for the analysis of the crossover theorem and of the glycolysis of human erythrocytes. Acta Biol Med Ger 31, 479-494.
5. Kacser H, &, Burns JA, (1973) The control of flux. Symp Soc Exp Biol 27, 65-104.
6. Savageau MA, (1969) Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 25, 365-369.
7. Clarke B, (1981) Complete set of steady states for the general stoichiometric dynamical system. J Chem Phys 75, 4970-4979.
8. Schuster S, (1994) On elementary fluxmodes in biochemical reaction systems at steady state. Journal of Biological Systems 2, 165-182.
9. Gillespie D, (1977) Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81, 2340-2361.
10. Csikasz-Nagy A, (2009) Computational systems biology of the cell cycle. Brief Bioinformatics 10, 424-434.
11. Hubbard KE, Robertson FC, Dalchau N, &, Webb AA, (2009) Systems analyses of circadian networks. Mol Biosyst 5, 1502-1511.
12. Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, &, Hucka M, (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34, D689-D691.
13. Wishart DS, (2007) Current progress in computational metabolomics. Brief Bioinformatics 8, 279-293. (Pubitemid 350142618)
14. Otero JM, &, Nielsen J, (2010) Industrial systems biology. Biotechnol Bioeng 105, 439-460.
15. Kholodenko BN, (2006) Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 7, 165-176.
16. Klipp E, &, Liebermeister W, (2006) Mathematical modeling of intracellular signaling pathways. BMC Neurosci 7 (Suppl 1), S10.
17. Gombert AK, &, Nielsen J, (2000) Mathematical modelling of metabolism. Curr Opin Biotechnol 11, 180-186. (Pubitemid 30182314)
18. Schuster S, Marhl M, &, Hofer T, (2002) Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling. Eur J Biochem 269, 1333-1355. (Pubitemid 34227075)
19. Helfert S, Estévez AM, Bakker B, Michels P, &, Clayton C, (2001) Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei. Biochem J 357, 117-125. (Pubitemid 32642909)
20. Albert MA, Haanstra JR, Hannaert V, Roy JV, Opperdoes FR, Bakker BM, &, Michels PAM, (2005) Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei. J Biol Chem 280, 28306-28315. (Pubitemid 41105727)
21. David H, Akesson M, &, Nielsen J, (2003) Reconstruction of the central carbon metabolism of Aspergillus niger. Eur J Biochem 270, 4243-4253. (Pubitemid 37340342)
22. Prathumpai W, Gabelgaard JB, Wanchanthuek P, de Vondervoort PJI, de Groot MJL, McIntyre M, &, Nielsen J, (2003) Metabolic control analysis of xylose catabolism in Aspergillus. Biotechnol Prog 19, 1136-1141. (Pubitemid 37007593)
23. de Groot MJL, Prathumpai W, Visser J, &, Ruijter GJG, (2005) Metabolic control analysis of Aspergillus niger L-arabinose catabolism. Biotechnol Prog 21, 1610-1616. (Pubitemid 41778983)
24. Andersen MR, Nielsen ML, &, Nielsen J, (2008) Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 4, 178. (Pubitemid 351441042)
25. Singh VK, &, Ghosh I, (2006) Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets. Theor Biol Med Model 3, 27.
26. Fang X, Wallqvist A, &, Reifman J, (2009) A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. BMC Syst Biol 3, 92.
27. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, &, Palsson BO, (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 184, 4582-4593. (Pubitemid 34832586)
28. Franke R, Müller M, Wundrack N, Gilles ED, Klamt S, Kähne T, &, Naumann M, (2008) Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. BMC Syst Biol 2, 4.
29. Hua Q, Yang C, &, Shimizu K, (2000) Metabolic control analysis for lysine synthesis using Corynebacterium glutamicum and experimental verification. J Biosci Bioeng 90, 184-192.
30. Rohwer JM, &, Botha FC, (2001) Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem J 358, 437-445. (Pubitemid 32826361)
31. Schäfer WE, Rohwer JM, &, Botha FC, (2004) A kinetic study of sugarcane sucrose synthase. Eur J Biochem 271, 3971-3977. (Pubitemid 39423095)
32. Uys L, Botha FC, Hofmeyr JHS, &, Rohwer JM, (2007) Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68, 2375-2392. (Pubitemid 47211193)
33. Letisse F, Chevallereau P, Simon JL, &, Lindley N, (2002) The influence of metabolic network structures and energy requirements on xanthan gum yields. J Biotechnol 99, 307-317. (Pubitemid 35223327)
34. Lobit P, Génard M, Wu BH, Soing P, &, Habib R, (2003) Modelling citrate metabolism in fruits: responses to growth and temperature. J Exp Bot 54, 2489-2501. (Pubitemid 37379261)
35. Brasen JC, Barington T, &, Olsen LF, (2010) On the mechanism of oscillations in neutrophils. Biophys Chem 148, 82-92.
36. Roman BB, Meyer RA, &, Wiseman RW, (2002) Phosphocreatine kinetics at the onset of contractions in skeletal muscle of MM creatine kinase knockout mice. Am J Physiol Cell Physiol 283, C1776-C1783. (Pubitemid 35340610)
37. 13C-NMR and modelling study of metabolic yield response to ethanol stress in a wild-type strain of Saccharomyces cerevisiae. FEBS Lett 564, 63-68. (Pubitemid 38490701)
38. Beard DA, (2006) Modeling of oxygen transport and cellular energetics explains observations on in vivo cardiac energy metabolism. PLoS Comput Biol 2, e107.
39. Andersen AZ, Carvalho AL, Neves AR, Santos H, Kummer U, &, Olsen LF, (2009) The metabolic pH response in Lactococcus lactis: an integrative experimental and modelling approach. Comput Biol Chem 33, 71-83. (Pubitemid 50285890)
40. Ozalp VC, Pedersen TR, Nielsen LJ, &, Olsen LF, (2010) Time-resolved measurements of intracellular ATP in the yeast Saccharomyces cerevisiae using a new type of nanobiosensor. J Biol Chem 285, 37579-37588.
41. Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, &, Snoep JL, (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267, 5313-5329.
42. Ermentrout G, (2002) Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students. SIAM, Philadelphia, PA.
43. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, &, Kummer U, (2006) COPASI-a COmplex PAthway SImulator. Bioinformatics 22, 3067-3074. (Pubitemid 44884083)
44. Mendes P, (1993) GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci 9, 563-571. (Pubitemid 23309017)
45. Macey R, &, Oster G
46. van Gend C, Conradie R, du Preez FB, &, Snoep JL, (2007) Data and model integration using JWS Online. In Silico Biol (Gedrukt) 7, 27-35. (Pubitemid 46864320)
47. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, &, Wang J, (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (Pubitemid 36336519)
48. Lloyd CM, Halstead MDB, &, Nielsen PF, (2004) CellML: its future, present and past. Prog Biophys Mol Biol 85, 433-450. (Pubitemid 38629921)
49. Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, &, Wanner BL, (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23, 1509-1515. (Pubitemid 41752928)
50. Lloyd CM, Lawson JR, Hunter PJ, &, Nielsen PF, (2008) The CellML Model Repository. Bioinformatics 24, 2122-2123.
51. Schellenberger J, Park JO, Conrad TM, &, Palsson B, (2010) BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11, 213.
52. Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, &, Novère NL, (2011) Minimum information about a simulation experiment (miase). PLoS Comput Biol 7, e1001122.
53. Klipp E, Liebermeister W, Helbig A, Kowald A, &, Schaber J, (2007) Systems biology standards-the community speaks. Nat Biotechnol 25, 390-391. (Pubitemid 46572833)