Metabolic network analysis integrated with transcript verification for sequenced genomes

Nature Methods

Volumn 6, Issue 8, 2009, Pages 589-592

  Manichaikul, Ani ^a   Ghamsari, Lila ^b   Hom, Erik F Y ^c   Lin, Chenwei ^b   Murray, Ryan R ^b   Chang, Roger L ^d   Balaji, S ^b   Hao, Tong ^b   Shen, Yun ^b   Chavali, Arvind K ^a   Thiele, Ines ^d,e   Yang, Xinping ^b   Fan, Changyu ^b   Mello, Elizabeth ^b   Hill, David E ^b   Vidal, Marc ^b   Salehi Ashtiani, Kourosh ^b   Papin, Jason A ^a  

^a University of Virginia   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^e UNIVERSITY OF ICELAND   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

6 PHOSPHOFRUCTOKINASE; CARBOXYLYASE; DEXTRO LACTATE DEHYDROGENASE; LACTATE DEHYDROGENASE; LACTATE DEHYDROGENASE (CYTOCHROME); LONG CHAIN FATTY ACID COENZYME A LIGASE; OLIGO 1,6 GLUCOSIDASE; OXALATE DECARBOXYLASE; PYRUVATE SYNTHASE; SUCCINATE DEHYDROGENASE; SUCCINYL COENZYME A LIGASE; UBIQUINOL CYTOCHROME C REDUCTASE; UNCLASSIFIED DRUG;

ARTICLE; CHLAMYDOMONAS REINHARDTII; CONTROLLED STUDY; GENE AMPLIFICATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC CODE; GENETIC TRANSCRIPTION; METABOLIC ENGINEERING; NONHUMAN; OPEN READING FRAME; PLANT GENETICS; PLANT GENOME; PRIORITY JOURNAL; PROTEIN METABOLISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; CHLAMYDOMONAS REINHARDTII; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ENZYMES; GENETIC ENGINEERING; GENOME, PROTOZOAN; MODELS, GENETIC; PROTOZOAN PROTEINS; TRANSCRIPTION, GENETIC;

CHLAMYDOMONAS REINHARDTII;

EID: 68349108021     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1348     Document Type: Article

References (27)

1. Feist, A.M., Herrgård, M.J., Thiele, I., Reed, J.L. & Palsson, B. Nat. Rev. Microbiol. 7, 129-143 (2009).
2. Reboul, J. et al. Nat. Genet. 27, 332-336 (2001).
3. Jones, S.J.M. Annu. Rev. Genomics Hum. Genet. 7, 315-338 (2006).
4. Frishman, D. Chem. Rev. 107, 3448-3466 (2007).
5. Boyle, N.R. & Morgan, J.A. BMC Syst. Biol. 3, 4 (2009).
6. Apweiler, R. et al. Nucleic Acids Res. 32, D115-D119 (2004).
7. Lu, Z. et al. Bioinformatics 20, 547-556 (2004).
8. Zhang, Z. & Wood, W.I. Bioinformatics 19, 307-308 (2003).
9. Walhout, A.J. et al. Methods Enzymol. 328, 575-592 (2000).
10. Reed, J.L., Vo, T.D., Schilling, C.H. & Palsson, B.O. Genome Biol. 4, R54 (2003).
11. Kucho, K. et al. J. Bacteriol. 187, 2190-2199 (2005).
12. Shendure, J. & Ji, H. Nat. Biotechnol. 26, 1135-1145 (2008).
13. Herrgård, M.J., Covert, M.W. & Palsson, B. Curr. Opin. Biotechnol. 15, 70-77 (2004).
14. Papin, J.A., Hunter, T., Palsson, B.O. & Subramaniam, S. Nat. Rev. Mol. Cell Biol. 6, 99-111 (2005).
15. Belknap, W.R. & Togasaki, R.K. Proc. Natl. Acad. Sci. USA 78 2310-2314 (1981).
16. Klein, U., Chen, C. & Gibbs, M. Plant Physiol. 72, 488-491 (1983).
17. Clemetson, J.M., Boschetti, A. & Clemetson, K.J. J. Biol. Chem. 267, 19773-19779 (1992).
18. Lemaire, S.D. et al. Proc. Natl. Acad. Sci. USA 101, 7475-7480 (2004).
19. Gfeller, R.P. & Gibbs, M. Plant Physiol. 75, 212-218 (1984).
20. Price, N.D., Famili, I., Beard, D.A. & Palsson, B.O. Biophys. J. 83, 2879-2882 (2002).
21. Becker, S.A. et al. Nat. Protocols 2, 727-738 (2007).
22. Lee, J.M., Gianchandani, E.P. & Papin, J.A. Brief. Bioinform. 7 140-150 (2006).
23. Mahadevan, R. & Schilling, C.H. Metab. Eng. 5, 264-276 (2003).
24. Merchant, S.S. et al. Science 318, 245-250 (2007).
25. Rual, J.F., Hill, D.E. & Vidal, M. Curr. Opin. Chem. Biol. 8 20-25 (2004).
26. Notredame, C., Higgins, D.G. & Heringa, J. J. Mol. Biol. 302 205-217 (2000).
27. Edgar, R.C. Nucleic Acids Res. 32, 1792-1797 (2004).