Analyzing metabolite measurements for automated prediction of underlying biological mechanisms

2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010

Volumn , Issue , 2010, Pages 137-146

  Cakmak, Ali ^a   Dsouza, Arun ^b   Hanson, Richard W ^a   Ozsoyoglu, Meral ^a  

^a Case Western Reserve University   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED REASONING; AUTOMATICALLY GENERATED; BIOFLUIDS; BIOLOGICAL MECHANISMS; CONSISTENCY ANALYSIS; CONSISTENCY CHECKING; CONTROL SUBJECT; FLUX RATIO; HYPOTHESIS GENERATION; MANUAL ANALYSIS; MEASURE CONCENTRATION; METABOLIC ACTION; METABOLIC NETWORK; METABOLITE ANALYSIS; METABOLITE CHANGES; METABOLITE CONCENTRATIONS; METABOLOMICS; METABOLOMICS DATA; PROTEIN TURNOVERS; RUNNING TIME;

AUTOMATA THEORY; BIOINFORMATICS; BIOMOLECULES; CONCENTRATION (PROCESS); METABOLITES;

METABOLISM;

EID: 77958037791     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1854776.1854799     Document Type: Conference Paper

References (36)

1. Daviss, B. 2005. Growing pains for metabolomics. The Scientist, 19[8]:25-28.
2. Wikipedia Entry (Metabolomics), http://en.wikipedia.org/wiki/Metabolite. (Retrieved on May 13, 2008)
3. Oliver, SG et al. 1998. Systematic Functional Analysis of the Yeast genome. Trends BioTechnol., Vol. 16, 1998, pp. 373-378.
4. Harrigan, GG., and Goodacre, R. (Eds). 2003. Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis. Kluwer Academic Publishers, Boston, USA.
5. Fell, D.A. (1997). Understanding the control of metabolism. (Portland Press, London, UK).
6. Schilling, C.H., Schuster, S., Palsson, B.O., Heinrich, R. (1999). Metabolic Pathway Analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog., 15, 296-303.
7. Stephanopoulas, G., Aristidou, A., Nielsen, J.H. (1998). Metabolic Engineering: principles and methodologies. (Academic Press, Maryland Hts, MO).
8. Trinh, C.T., Wlaschin, A., Srienc, F. (2009). Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism, Appl. Microbiol. Biotech., 81, 813-826.
9. Hoppe, A. et al. 2007. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst Biol. 1:23.
10. Schuster, S., Higetag, S. (1994). On elementary flux modes in biochemical reaction systems at steady state", J. Biol. Syst., 2, 165-182.
11. Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N.et al. (2006). COPASI - a COmplex PAthway Simulator, Bioinformatics 22, 3067-74.
12. Pfeiffer, T., Sánchez-valdenebro, I., Nuño, J.C. et al. (1999). METATOOL: for studying metabolic networks, Bioinformatics, 15: 251-257.
13. Urbanczik, R. (2006). SNA-A toolbox for the stoichiometric analysis of metabolic networks. BMC Bioinformatics, 7: 129.
14. Klamt, S., Stelling J, Ginkel, M., Gilles, E.D. (2003). FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics, 19, 261-269.
15. Schwartz, J.M., Gaugain, C., Nacher, J.C., De Daruvar, A., Kanehisa, M. (2007b). Observing metabolic functions at the genome scale. Genome Biol, 8, R213.
16. Wlaschin, A.P., Trinh, C.T., Carlson, R., Srienc, F. (2006). The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies, Metabolic Eng., 8, 338-352.
17. Urbanczik, R., Wagner, C. (2005). An improved algorithm for stoichiometric network analysis: theory and applications. Bioinformatics, 21, 1203-1210.
18. Cakmak, A., Ozsoyoglu, G., Hanson, RW. Querying Metabolism under Different Physiological Constraints. Journal of Bioinformatics and Computational Biology, 8:(2) pp. 247-293, April 2010.
19. [19]Klamt, S., Stelling, J. (2003). Two approaches for metabolic pathway analysis? Trends in Biotech., 21, 2, 64-69.
20. Glykys, D.J., Banta, S. (2009). Metabolic Control Analysis of an enzymatic biofuel cell. Biotechnology and Bioengineering. 102 (6), 1625-1635.
21. Kuipers, B.J. 1993. Reasoning with Qualitative Models. Artificial Intelligence 59, 125-132.
22. rd edn. Academic Press, 287-300.
23. Forbus, K.D. 1984. Qualitative Process Theory. Artificial Intelligence 24. 85-168.
24. Karp, P.D. 1993a. Design Methods for Scientific Hypothesis Formation and Their Application to Molecular Biology. Machine Learning, 12, 89-116.
25. Wishart, DS. 2007. Current progress in computational metabolomics. Briefings in Bioinformatics (8) 5: 279-293.
26. Devlin, TM. 2006. Textbook of Biochemistry with Clinical Correlations, Sixth Edition. Hoboken, NJ, John Wiley & Sons.
27. Salway, JG. 1999. Metabolism at a Glance, 2nd Edition. Blackwell Science.
28. Cakmak, A., Dsouza, A., Hanson, R.W., Ozsoyoglu, M., Ozsoyoglu, G. A Web-Based Data Source for Metabolomics. ISCIS, 2009. Available online at: http://dblab.case.edu/PathwaysMetabolomics/Web/
29. Cakmak, A. et al. (2010). Analyzing Metabolite Measurements for Automated Prediction of Underlying Biological Mechanisms. Technical Report. Dept. of EECS, CWRU, Cleveland, OH.
30. Wishart, DS et al. (2008). HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research, doi:10.1093/nar/gkn810, October 25, 2008.
31. Cakmak, A. et al. (2010). Automated Metabolomics Data Interpretation: A Case Study on Non-Alcoholic Fatty Liver Disease. Technical Report. Dept. of EECS, CWRU, Cleveland, OH.
32. Kanehisa M et al. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34 (Database issue):D354-7.
33. Joshi-Tope G et al. 2005. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33 (Database issue):D428-32.
34. Caspi, R et al. 2006. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 34 (Database issue):D511-16.
35. Elliott, B., Kirac, M., Cakmak, A. et al. 2008. PathCase Pathways Database System. Bioinformatics 24(21): 2526-2533, November 2008.
36. Lawton, K.A., Berger, A., Mitchell, M. et al. (2008). Analysis of the adult human plasma metabolome. Pharmacogenomics Apr;9(4):383-9.