Identification of small scale biochemical networks based on general type system perturbations

FEBS Journal

Volumn 272, Issue 9, 2005, Pages 2141-2151

  Schmidt, Henning ^a   Cho, Kwang Hyun ^b   Jacobsen, Elling W ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b Seoul National University   (South Korea)

Author keywords

Biochemical networks; Identification; Jacobian; Time series measurements

Indexed keywords

ARTICLE; BIOCHEMISTRY; COMPUTER MODEL; GENE INTERACTION; MATHEMATICAL ANALYSIS; METABOLITE; MOLECULAR GENETICS; PARAMETER; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEOMICS; REGRESSION ANALYSIS; STEADY STATE; TECHNOLOGY; TIME SERIES ANALYSIS;

CELL PHYSIOLOGY; GENE EXPRESSION REGULATION; LEAST-SQUARES ANALYSIS; MATHEMATICS; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY; SYSTEMS THEORY;

EID: 18444388867     PISSN: 1742464X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04605.x     Document Type: Article

References (15)

1. Kanehisa M & Goto S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30. http://www.genome.jp/kegg/.
2. Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV & Hoek JB (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci USA 99, 12841-12846.
3. Gardner T, di Bernardo D, Lorenz D & Collins J. (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102-105.
4. Sontag E, Kiyatkin A & Kholodenko B (2004) Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 20, 1877-1886.
5. Ross J (2003) New approaches to the deduction of complex reaction mechanisms. Acc Chem Res 36, 839-847.
6. Vance W, Arkin A & Ross J (2002) Determination of causal connectivities of species in reaction networks. Proc Natl Acad Sci USA 99, 5816-5821.
7. Torralba A, Yu K, Shen P, Oefner P & Ross J (2003) Experimental test of a method for determining causal connectivities of species in reactions. Proc Natl Acad Sci USA 100, 1494-1498.
8. Arkin A & Ross J (1995) Statistical construction of chemical reaction mechanisms from measured time-series. J Phys Chem 99, 970-979.
9. de la Fuente A, Brazhnik P & Mendes P (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet 18, 395-398.
10. Mihaliuk E, Skodt H, Hynne F, Sorensen PG & Showalter K (1999) Normal modes for chemical reactions from time series analysis. J Phys Chem 103, 8246-8251.
11. Crampin EJ, Schnell S & McSharry PE (2004) Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog Biophys Mol Biol 86, 77-112.
12. Siddhartha J & van Schuppen JH (2001) Modelling and control of cell reaction networks. PNA-R0116, CWI, Amsterdam.
13. Rugh W (1996) Linear System Theory. Prentice Hall, Upper Saddle River, NJ, USA.
14. Kay S (1993) Fundamentals of Statistical Signal Processing. Prentice Hall, Upper Saddle River, NJ, USA.
15. Ljung L (1999) System Identification - Theory for the User, 2nd edn. Prentice Hall, Upper Saddle River, NJ, USA.