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Items: 1 to 20 of 56

1.

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.

Feng X, Xu Y, Chen Y, Tang YJ.

BMC Syst Biol. 2012 Aug 2;6:94.

2.

Software applications for flux balance analysis.

Lakshmanan M, Koh G, Chung BK, Lee DY.

Brief Bioinform. 2014 Jan;15(1):108-22. doi: 10.1093/bib/bbs069. Epub 2012 Nov 5. Review.

3.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.

Perez-Garcia O, Lear G, Singhal N.

Front Microbiol. 2016 May 18;7:673. doi: 10.3389/fmicb.2016.00673. eCollection 2016. Review.

4.

A survey of metabolic databases emphasizing the MetaCyc family.

Karp PD, Caspi R.

Arch Toxicol. 2011 Sep;85(9):1015-33. doi: 10.1007/s00204-011-0705-2. Epub 2011 Apr 27. Review.

5.

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

Toya Y, Shimizu H.

Biotechnol Adv. 2013 Nov;31(6):818-26. doi: 10.1016/j.biotechadv.2013.05.002. Epub 2013 May 13. Review.

PMID:
23680193
6.

Applications of genome-scale metabolic network model in metabolic engineering.

Kim B, Kim WJ, Kim DI, Lee SY.

J Ind Microbiol Biotechnol. 2015 Mar;42(3):339-48. doi: 10.1007/s10295-014-1554-9. Epub 2014 Dec 3. Review.

PMID:
25465049
7.

Computational tools for guided discovery and engineering of metabolic pathways.

Moura M, Broadbelt L, Tyo K.

Methods Mol Biol. 2013;985:123-47. doi: 10.1007/978-1-62703-299-5_8. Review.

PMID:
23417803
8.

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.

Kanehisa M, Sato Y, Morishima K.

J Mol Biol. 2016 Feb 22;428(4):726-31. doi: 10.1016/j.jmb.2015.11.006. Epub 2015 Nov 14. Review.

9.

Software applications toward quantitative metabolic flux analysis and modeling.

Dandekar T, Fieselmann A, Majeed S, Ahmed Z.

Brief Bioinform. 2014 Jan;15(1):91-107. doi: 10.1093/bib/bbs065. Epub 2012 Nov 9. Review.

10.

Analyzing methods for path mining with applications in metabolomics.

Tagore S, Chowdhury N, De RK.

Gene. 2014 Jan 25;534(2):125-38. doi: 10.1016/j.gene.2013.10.056. Epub 2013 Nov 12. Review.

PMID:
24230973
11.

Knowledge-Based Analysis of Protein Interaction Networks in Neurodegenerative Diseases.

Kanehisa M, Limviphuvadh V, Tanabe M.

In: Alzate O, editor. Neuroproteomics. Boca Raton (FL): CRC Press/Taylor & Francis; 2010. Chapter 9.

12.

Data-driven integration of genome-scale regulatory and metabolic network models.

Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND.

Front Microbiol. 2015 May 5;6:409. doi: 10.3389/fmicb.2015.00409. eCollection 2015. Review.

13.

Genome-scale modeling of human metabolism - a systems biology approach.

Mardinoglu A, Gatto F, Nielsen J.

Biotechnol J. 2013 Sep;8(9):985-96. doi: 10.1002/biot.201200275. Epub 2013 Apr 24. Review.

PMID:
23613448
14.

Software platforms to facilitate reconstructing genome-scale metabolic networks.

Hamilton JJ, Reed JL.

Environ Microbiol. 2014 Jan;16(1):49-59. doi: 10.1111/1462-2920.12312. Epub 2013 Nov 18. Review.

PMID:
24148076
15.

Shrinking the metabolic solution space using experimental datasets.

Reed JL.

PLoS Comput Biol. 2012;8(8):e1002662. doi: 10.1371/journal.pcbi.1002662. Epub 2012 Aug 30. Review.

16.

Reconstruction of genome-scale human metabolic models using omics data.

Ryu JY, Kim HU, Lee SY.

Integr Biol (Camb). 2015 Aug;7(8):859-68. doi: 10.1039/c5ib00002e. Review.

PMID:
25730289
17.

Genome-scale modeling for metabolic engineering.

Simeonidis E, Price ND.

J Ind Microbiol Biotechnol. 2015 Mar;42(3):327-38. doi: 10.1007/s10295-014-1576-3. Epub 2015 Jan 13. Review.

18.

Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.

Hwang KS, Kim HU, Charusanti P, Palsson BØ, Lee SY.

Biotechnol Adv. 2014 Mar-Apr;32(2):255-68. doi: 10.1016/j.biotechadv.2013.10.008. Epub 2013 Nov 2. Review.

PMID:
24189093
19.

Metabolic network modeling of microbial communities.

Biggs MB, Medlock GL, Kolling GL, Papin JA.

Wiley Interdiscip Rev Syst Biol Med. 2015 Sep-Oct;7(5):317-34. doi: 10.1002/wsbm.1308. Epub 2015 Jun 24. Review.

PMID:
26109480
20.

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models.

Vivek-Ananth RP, Samal A.

Biosystems. 2016 Sep;147:1-10. doi: 10.1016/j.biosystems.2016.06.001. Epub 2016 Jun 7. Review.

PMID:
27287878
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