WholeCellKB: Model organism databases for comprehensive whole-cell models

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Karr, Jonathan R ^a   Sanghvi, Jayodita C ^b   Macklin, Derek N ^b   Arora, Abhishek ^b   Covert, Markus W ^b  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA BASE; GENE FUNCTION; GENE STRUCTURE; INTERMETHOD COMPARISON; MYCOPLASMA GENITALIUM; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN FUNCTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; WHOLECELLKB DATABASE; WHOLECELLKB-MG DATABASE;

BACTERIAL PROTEINS; CHROMOSOMES, BACTERIAL; DATABASES, GENETIC; GENES, BACTERIAL; INTERNET; MODELS, BIOLOGICAL; MYCOPLASMA GENITALIUM; RNA, BACTERIAL; SOFTWARE; USER-COMPUTER INTERFACE;

MYCOPLASMA GENITALIUM; POSIBACTERIA;

EID: 84876554105     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1108     Document Type: Article

References (28)

1. Karr, J.R., Sanghvi, J.C., Macklin, D.N., Jacobs, J.M., Gutschow, M.V., Bolival, B., Assad-Garcia, N., Glass, J.I. and Covert, M.W. (2012) A whole-cell computational model predicts phenotype from genotype. Cell, 150, 389-401.
2. Morowitz, H.J., Tourtellotte, M.E., Guild, W.R., Castro, E. and Woese, C. (1962) The chemical composition and submicroscopic morphology of Mycoplasma gallisepticum, Avian PPLO 5969. J. Mol. Biol., 4, 93-103.
3. Solabia. (2011) Biotechnology Products, Retrieved from http://www.solabia.com/ (14 March 2011, date last accessed).
4. Davidsen, T., Beck, E., Ganapathy, A., Montgomery, R., Zafar, N., Yang, Q., Madupu, R., Goetz, P., Galinsky, K., White, O. et al. (2010) The comprehensive microbial resource. Nucleic Acids Res., 38, D340-D345.
5. Güell, M., van Noort, V., Yus, E., Chen, W.H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kühner, S. et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science, 326, 1268-1271.
6. Weiner, J. 3rd, Herrmann, R. and Browning, G.F. (2000) Transcription in Mycoplasma pneumoniae. Nucleic Acids Res., 2, 241-249.
7. Weiner, J. 3rd, Zimmerman, C.U., Göhlmann, H.W. and Herrmann, R. (2003) Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures. Nucleic Acids Res., 37, 6306-6320.
8. Bernstein, J.A., Khodursky, A.B., Lin, P.H., Lin-Chao, S. and Cohen, S.N. (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl Acad. Sci. USA, 22, 235-244.
9. Glass, J.I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M.R., Maruf, M., Hutchison, C.A. 3rd, Smith, H.O. and Venter, J.C. (2006) Essential genes of a minimal bacterium. Proc. Natl Acad. Sci. USA, 77, 1175-1181.
10. Sierro, N., Makita, Y., de Hoon, M. and Nakai, K. (2008) DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res., 5, e8664.
11. Peil, L. (2009) Ribosome assembly factors in Escherichia coli, Master Thesis. Tartu University.
12. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 14, D554-D556.
13. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. and Bairoch, A. (2005) Protein identification and analysis tools on the ExPASy server. In: Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. and Bairoch, A. (eds), The Proteomics Protocols Handbook. Humana Press, Totowa, NJ, pp. 571-607.
14. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2011) GenBank. Nucleic Acids Res., 39, D32-D37.
15. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res., 40, D109-D114.
16. The UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
17. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Federhen, S. et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 38, D5-D16.
18. Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T. et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res., 39, D583-D590.
19. Suthers, P.F., Dasika, M.S., Kumar, V.S., Denisov, G., Glass, J.I. and Maranas, C.D. (2009) A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput. Biol., 26, 4694-4708.
20. Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V. and Palsson, B.Ø. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 28, 15-33.
21. Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Söhngen, C., Stelzer, M., Thiele, J. and Schomburg, D. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res., 39, D670-D676.
22. Wittig, U., Kania, R., Golebiewski, M., Rey, M., Shi, L., Jong, L., Algaa, E., Weidemann, A., Sauer-Danzwith, H., Mir, S. et al. (2012) SABIO-RK - database for biochemical reaction kinetics. Nucleic Acids Res., 40, D790-D796.
23. Sundararaj, S., Guo, A., Habibi-Nazhad, B., Rouani, M., Stothard, P., Ellison, M. and Wishart, D.S. (2004) The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res., 32, D293-D295.
24. Bolton, E., Wang, Y., Thiessen, P.A. and Bryant, S.H. (2008) PubChem: integrated platform of small molecules and biological activities. In: Bolton, E., Wang, Y., Thiessen, P.A. and Bryant, S.H. (eds), Annual Reports in Computational Chemistry. American Chemical Society, Washington, DC, pp. 217-241.
25. Bennett, B.D., Kimball, E.H., Gao, M., Osterhout, R., Van Dien, S.J. and Rabinowitz, J.D. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol., 5, 593-599.
26. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
27. Karp, P.D., Paley, S.M., Krummenacker, M., Latendresse, M., Dale, J.M., Lee, T.J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L. et al. (2010) Pathway tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform., 11, 40-79.
28. Schellenberger, J., Park, J.O., Conrad, T.M. and Palsson, B.Ø. (2010) BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics, 11, 213.