Computational interpretation of metabolomics measurements: Steady-state metabolic network dynamics analysis

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

Volumn , Issue , 2011, Pages 387-392

  Cakmak, Ali ^a   Qi, Xinjian ^a   Cicek, A Ercument ^a   Özsoyoǧlu, Gultekin ^a  

^a Case Western Reserve University   (United States)

Author keywords

In Silico analysis; Metabolic network; Metabolomics; SMDA

Indexed keywords

BIOFLUIDS; COMPUTATIONAL INTERPRETATIONS; COMPUTATIONAL PERFORMANCE; EXPLORATORY SEARCH; IN-SILICO; METABOLIC MECHANISM; METABOLIC NETWORK; METABOLOMICS; SMDA;

DYNAMICS; MAMMALS; METABOLISM; METABOLITES;

BIOINFORMATICS;

EID: 84858959344     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2147805.2147856     Document Type: Conference Paper

References (10)

1. Yizhak, K. et al, Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model, Bioinformatics, Vol. 26, ISMB 2010, pp 1255-1260.
2. Price, N.D., Reed, J.L., Palsson, B.O., genome-scale models of microbial cells: Evaluating the consequences of constraints. Nature Reviews, Vol. 2, Nov. 2004, pp. 886-897. (Pubitemid 39567269)
3. Joyce, A.R., Palsson, B.O. Towards whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Progress in drug research, Vol. 64, 2007.
4. Oberhardt, M.A., Palsson, B.O., Papin, J.A. Applications of genome-scale metabolic reconstructions. Molecular Systems Biology, 5:320, 2009.
5. Schuster, S., Fell, D.A., Dandekar, T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnology Vol 18, March 2000, pp. 326-332. (Pubitemid 30159487)
6. SMDA tool, available at http://nashua.case.edu/pathwayssmda/web
7. PathCase family of applications, available at http://nashua.case.edu/ pathwaysweb
8. Supplement to this paper, available at http://nashua.case.edu/ pathwayssmda/smda.supplement.pdf
9. Cakmak A., Dsouza A., Hanson R. W., Ozsoyoglu Z. M. 2010. Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms. ACM Bioinformatics and Computational Biology Conference, Niagara Falls, NY.
10. Human Metabolome Database, available at http://www.hmdb.ca/biofluid- browse