메뉴 건너뛰기




Volumn 7, Issue , 2013, Pages

Probabilistic strain optimization under constraint uncertainty

Author keywords

Chance constrained optimization; Enzyme activity modification; Flux capacity; Uncertainty

Indexed keywords

ENZYME;

EID: 84875383513     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-29     Document Type: Article
Times cited : (5)

References (37)
  • 1
    • 0036244992 scopus 로고    scopus 로고
    • Efficient transfection method for primary cells
    • 10.1089/107632702753725003, 12031113
    • Hamm A, Krott N, Breibach I, Blindt R, Bosserhoff A. Efficient transfection method for primary cells. Tissue Eng 2002, 8(2):235-245. 10.1089/107632702753725003, 12031113.
    • (2002) Tissue Eng , vol.8 , Issue.2 , pp. 235-245
    • Hamm, A.1    Krott, N.2    Breibach, I.3    Blindt, R.4    Bosserhoff, A.5
  • 2
    • 52449135231 scopus 로고    scopus 로고
    • Transfection efficiency and toxicity of polyethylenimine in differentiated Calu-3 and nondifferentiated COS-1 cell cultures
    • 10.1208/ps040313, 2751351, 12423061
    • Florea B, Meaney C, Junginger H, Borchard G. Transfection efficiency and toxicity of polyethylenimine in differentiated Calu-3 and nondifferentiated COS-1 cell cultures. AAPS PharmSci 2002, 4(3):E12. 10.1208/ps040313, 2751351, 12423061.
    • (2002) AAPS PharmSci , vol.4 , Issue.3
    • Florea, B.1    Meaney, C.2    Junginger, H.3    Borchard, G.4
  • 3
    • 29544436058 scopus 로고    scopus 로고
    • An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
    • 10.1016/j.ymben.2005.08.003, 16199194
    • Pharkya P, Maranas CD. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 2006, 8(1):1-13. 10.1016/j.ymben.2005.08.003, 16199194.
    • (2006) Metab Eng , vol.8 , Issue.1 , pp. 1-13
    • Pharkya, P.1    Maranas, C.D.2
  • 4
    • 0242487787 scopus 로고    scopus 로고
    • Optknock, A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • 10.1002/bit.10803, 14595777
    • Burgard AP, Pharkya P, Maranas CD. Optknock, A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84(6):647-657. 10.1002/bit.10803, 14595777.
    • (2003) Biotechnol Bioeng , vol.84 , Issue.6 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 6
    • 78649344448 scopus 로고    scopus 로고
    • Solving chance-constrained stochastic programs via sampling and integer programming
    • Anonymous INFORMS
    • Ahmed S, Shapiro A. Solving chance-constrained stochastic programs via sampling and integer programming. Tutorials in Operations Research 2008, 261-269. Anonymous INFORMS.
    • (2008) Tutorials in Operations Research , pp. 261-269
    • Ahmed, S.1    Shapiro, A.2
  • 7
    • 0002395681 scopus 로고
    • Chance-constrained programming
    • Charnes A, Cooper WW. Chance-constrained programming. Management Science 1959, 6(1):73-79.
    • (1959) Management Science , vol.6 , Issue.1 , pp. 73-79
    • Charnes, A.1    Cooper, W.W.2
  • 9
    • 0002478485 scopus 로고
    • Chance Constrained Programming Models for Risk-Based Economic and Policy Analysis of Soil Conservation
    • Zhu M, Taylor DB, Sarin SC, Kramer R. Chance Constrained Programming Models for Risk-Based Economic and Policy Analysis of Soil Conservation. Agric Resour Econ Rev 1994, 23(1).
    • (1994) Agric Resour Econ Rev , vol.23 , Issue.1
    • Zhu, M.1    Taylor, D.B.2    Sarin, S.C.3    Kramer, R.4
  • 10
    • 0022440903 scopus 로고
    • Groundwater management by chance-constrained model
    • Yeou-Koung Tung AM. Groundwater management by chance-constrained model. J Water Resour Plann Manage 1986, 112:1.
    • (1986) J Water Resour Plann Manage , vol.112 , pp. 1
    • Yeou-Koung Tung, A.M.1
  • 11
    • 84865676820 scopus 로고    scopus 로고
    • Chance Constrained Programming and Its Applications to Energy Management, Stochastic Optimization
    • Anonymous InTech,
    • Ackooij W, Zorgati R, Henrion R, Möller A. Chance Constrained Programming and Its Applications to Energy Management, Stochastic Optimization. 2011, Anonymous InTech, http://cdn.intechweb.org/pdfs/13877.pdf.
    • (2011)
    • Ackooij, W.1    Zorgati, R.2    Henrion, R.3    Möller, A.4
  • 12
    • 0031142344 scopus 로고    scopus 로고
    • Optimal molecular design under property prediction uncertainty
    • Maranas CD. Optimal molecular design under property prediction uncertainty. AIChE J 1997, 43(5):1250-1264.
    • (1997) AIChE J , vol.43 , Issue.5 , pp. 1250-1264
    • Maranas, C.D.1
  • 13
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • 10.1186/1471-2105-6-308, 1327682, 16375763
    • Patil K, Rocha I, Forster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005, 6(1):308. 10.1186/1471-2105-6-308, 1327682, 16375763.
    • (2005) BMC Bioinformatics , vol.6 , Issue.1 , pp. 308
    • Patil, K.1    Rocha, I.2    Forster, J.3    Nielsen, J.4
  • 14
    • 77952585143 scopus 로고    scopus 로고
    • CASOP, a computational approach for strain optimization aiming at high productivity
    • 10.1016/j.jbiotec.2010.03.006, 20303369
    • Hädicke O, Klamt S. CASOP, a computational approach for strain optimization aiming at high productivity. J Biotechnol 2010, 147(2):88-101. 10.1016/j.jbiotec.2010.03.006, 20303369.
    • (2010) J Biotechnol , vol.147 , Issue.2 , pp. 88-101
    • Hädicke, O.1    Klamt, S.2
  • 15
    • 74549189949 scopus 로고    scopus 로고
    • Flux design, in silico design of cell factories based on correlation of pathway fluxes to desired properties
    • 10.1186/1752-0509-3-120, 2808316, 20035624
    • Melzer G, Esfandabadi M, Franco-Lara E, Wittmann C. Flux design, in silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol 2009, 3(1):120. 10.1186/1752-0509-3-120, 2808316, 20035624.
    • (2009) BMC Syst Biol , vol.3 , Issue.1 , pp. 120
    • Melzer, G.1    Esfandabadi, M.2    Franco-Lara, E.3    Wittmann, C.4
  • 16
    • 84855419801 scopus 로고    scopus 로고
    • Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production
    • 10.1016/j.ymben.2011.11.002, 22115737
    • Driouch H, Melzer G, Wittmann C. Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production. Metab Eng 2012, 14(1):47-58. 10.1016/j.ymben.2011.11.002, 22115737.
    • (2012) Metab Eng , vol.14 , Issue.1 , pp. 47-58
    • Driouch, H.1    Melzer, G.2    Wittmann, C.3
  • 20
    • 58149277477 scopus 로고    scopus 로고
    • Probability fold change, A robust computational approach for identifying differentially expressed gene lists
    • 10.1016/j.cmpb.2008.07.013, 18842321
    • Deng X, Xu J, Hui J, Wang C. Probability fold change, A robust computational approach for identifying differentially expressed gene lists. Comput Methods Programs Biomed 2009, 93(2):124-139. 10.1016/j.cmpb.2008.07.013, 18842321.
    • (2009) Comput Methods Programs Biomed , vol.93 , Issue.2 , pp. 124-139
    • Deng, X.1    Xu, J.2    Hui, J.3    Wang, C.4
  • 21
    • 33748760643 scopus 로고    scopus 로고
    • The expression of genes related to adipocyte differentiation in pigs
    • Wang HC, Ko YH, Mersmann HJ, Chen CL, Ding ST. The expression of genes related to adipocyte differentiation in pigs. J Anim Sci 2006, 84(5):1059-1066.
    • (2006) J Anim Sci , vol.84 , Issue.5 , pp. 1059-1066
    • Wang, H.C.1    Ko, Y.H.2    Mersmann, H.J.3    Chen, C.L.4    Ding, S.T.5
  • 22
    • 34548546603 scopus 로고    scopus 로고
    • Integration of enzyme activities into metabolic flux distributions by elementary mode analysis
    • 10.1186/1752-0509-1-31, 1973080, 17640350
    • Kurata H, Zhao Q, Okuda R, Shimizu K. Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst Biol 2007, 1(1):31. 10.1186/1752-0509-1-31, 1973080, 17640350.
    • (2007) BMC Syst Biol , vol.1 , Issue.1 , pp. 31
    • Kurata, H.1    Zhao, Q.2    Okuda, R.3    Shimizu, K.4
  • 23
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks, a promising tool for pathway analysis and metabolic engineering
    • 10.1016/S0167-7799(98)01290-6, 10087604
    • Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks, a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 1999, 17(2):53-60. 10.1016/S0167-7799(98)01290-6, 10087604.
    • (1999) Trends Biotechnol , vol.17 , Issue.2 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 24
    • 0028108519 scopus 로고
    • Metabolic flux balancing, basic concepts. Scientific and practical Use
    • Varma A, Palsson BO. Metabolic flux balancing, basic concepts. Scientific and practical Use. Nat Biotech 1994, 12(10):994-998.
    • (1994) Nat Biotech , vol.12 , Issue.10 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 25
    • 78650525718 scopus 로고    scopus 로고
    • Dynamic model of CHO cell metabolism
    • 10.1016/j.ymben.2010.09.003, 20933095
    • Nolan RP, Lee K. Dynamic model of CHO cell metabolism. Metab Eng 2011, 13(1):108-124. 10.1016/j.ymben.2010.09.003, 20933095.
    • (2011) Metab Eng , vol.13 , Issue.1 , pp. 108-124
    • Nolan, R.P.1    Lee, K.2
  • 26
    • 34447562749 scopus 로고    scopus 로고
    • Flux profile and modularity analysis of time-dependent metabolic changes of de novo adipocyte formation
    • 10.1152/ajpendo.00670.2006, 17284573
    • Si Y, Yoon J, Lee K. Flux profile and modularity analysis of time-dependent metabolic changes of de novo adipocyte formation. American Journal of Physiology - Endocrinology And Metabolism 2007, 292(6):E1637-E1646. 10.1152/ajpendo.00670.2006, 17284573.
    • (2007) American Journal of Physiology - Endocrinology And Metabolism , vol.292 , Issue.6
    • Si, Y.1    Yoon, J.2    Lee, K.3
  • 27
    • 70449531464 scopus 로고    scopus 로고
    • Impact of perturbed pyruvate metabolism on adipocyte triglyceride accumulation
    • 10.1016/j.ymben.2009.08.001, 2783285, 19683593
    • Si Y, Shi H, Lee K. Impact of perturbed pyruvate metabolism on adipocyte triglyceride accumulation. Metab Eng 2009, 11(6):382-390. 10.1016/j.ymben.2009.08.001, 2783285, 19683593.
    • (2009) Metab Eng , vol.11 , Issue.6 , pp. 382-390
    • Si, Y.1    Shi, H.2    Lee, K.3
  • 28
    • 84855594266 scopus 로고    scopus 로고
    • Engineering Mammalian Cells for Recombinant Monoclonal Antibody Production
    • Davies SL, James DC. Engineering Mammalian Cells for Recombinant Monoclonal Antibody Production. 2009, 6:153-173. http://link.springer.com/chapter/10.1007%2F978-90-481-2245-5_8?LI=true.
    • (2009) , vol.6 , pp. 153-173
    • Davies, S.L.1    James, D.C.2
  • 29
    • 0348044478 scopus 로고    scopus 로고
    • Proteome analysis of antibody-expressing CHO cells in response to hyperosmotic pressure
    • 10.1021/bp034093a, 14656149
    • Lee MS, Kim KW, Kim YH, Lee GM. Proteome analysis of antibody-expressing CHO cells in response to hyperosmotic pressure. Biotechnol Prog 2003, 19(6):1734-1741. 10.1021/bp034093a, 14656149.
    • (2003) Biotechnol Prog , vol.19 , Issue.6 , pp. 1734-1741
    • Lee, M.S.1    Kim, K.W.2    Kim, Y.H.3    Lee, G.M.4
  • 30
    • 48749110651 scopus 로고    scopus 로고
    • Lipid droplets, a classic organelle with new outfits
    • 10.1007/s00418-008-0449-0, 2491702, 18546013
    • Fujimoto T, Ohsaki Y, Cheng J, Suzuki M, Shinohara Y. Lipid droplets, a classic organelle with new outfits. Histochemistry and Cell Biology 2008, 130(2):263-279. 10.1007/s00418-008-0449-0, 2491702, 18546013.
    • (2008) Histochemistry and Cell Biology , vol.130 , Issue.2 , pp. 263-279
    • Fujimoto, T.1    Ohsaki, Y.2    Cheng, J.3    Suzuki, M.4    Shinohara, Y.5
  • 31
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • 10.1093/bioinformatics/btn401, 18676417
    • Terzer M, Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24(19):2229-2235. 10.1093/bioinformatics/btn401, 18676417.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 32
    • 77449092780 scopus 로고    scopus 로고
    • Differential effect of saturated and unsaturated free fatty acids on the generation of Monocyte adhesion and chemotactic factors by adipocytes
    • 10.2337/db09-0925, 2809975, 19934003
    • Han CY, Kargi AY, Omer M, Chan CK, Wabitsch M, O'Brien KD, Wight TN, Chait A. Differential effect of saturated and unsaturated free fatty acids on the generation of Monocyte adhesion and chemotactic factors by adipocytes. Diabetes 2010, 59(2):386-396. http://diabetes.diabetesjournals.org/content/59/2/386.long, 10.2337/db09-0925, 2809975, 19934003.
    • (2010) Diabetes , vol.59 , Issue.2 , pp. 386-396
    • Han, C.Y.1    Kargi, A.Y.2    Omer, M.3    Chan, C.K.4    Wabitsch, M.5    O'Brien, K.D.6    Wight, T.N.7    Chait, A.8
  • 36
    • 79952149701 scopus 로고    scopus 로고
    • Mixed glucose and lactate uptake by Corynebacterium glutamicum through metabolic engineering
    • 10.1002/biot.201000307, 21370474
    • Neuner A, Heinzle E. Mixed glucose and lactate uptake by Corynebacterium glutamicum through metabolic engineering. Biotechnology Journal 2011, 6(3):318-329. 10.1002/biot.201000307, 21370474.
    • (2011) Biotechnology Journal , vol.6 , Issue.3 , pp. 318-329
    • Neuner, A.1    Heinzle, E.2
  • 37
    • 58149307906 scopus 로고    scopus 로고
    • Natural computation meta-heuristics for the in silico optimization of microbial strains
    • 10.1186/1471-2105-9-499, 2612012, 19038030
    • Rocha M, Maia P, Mendes R, Pinto J, Ferreira E, Nielsen J, Patil K, Rocha I. Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 2008, 9(1):499. 10.1186/1471-2105-9-499, 2612012, 19038030.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 499
    • Rocha, M.1    Maia, P.2    Mendes, R.3    Pinto, J.4    Ferreira, E.5    Nielsen, J.6    Patil, K.7    Rocha, I.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.