ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network
文献类型：期刊论文
| 作者 | Xu, Zixiang1,2; Zheng, Ping1,2; Sun, Jibin1,2; Ma, Yanhe2 |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2013-12-11 |
| 卷号 | 8期号:12 |
| 英文摘要 | Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP) based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT) method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective. |
| WOS标题词 | Science & Technology |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | ESCHERICHIA-COLI ; KNOCKOUT STRATEGIES ; LINEAR BILEVEL ; RECONSTRUCTION ; FRAMEWORK ; MODELS ; SYSTEMS ; OVERPRODUCTION ; GSM/GPR |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000328730300002 |
| 源URL | [http://124.16.173.210/handle/834782/1264]  |
| 专题 | 天津工业生物技术研究所_系统与合成生物技术实验室 孙际宾_期刊论文 |
| 作者单位 | 1.Chinese Acad Sci, Key Lab Syst Microbial Biotechnol, Tianjin, Peoples R China 2.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin, Peoples R China |
| 推荐引用方式 GB/T 7714 | Xu, Zixiang,Zheng, Ping,Sun, Jibin,et al. ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network[J]. PLOS ONE,2013,8(12). |
| APA | Xu, Zixiang,Zheng, Ping,Sun, Jibin,&Ma, Yanhe.(2013).ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network.PLOS ONE,8(12). |
| MLA | Xu, Zixiang,et al."ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network".PLOS ONE 8.12(2013). |
入库方式： OAI收割
来源：天津工业生物技术研究所
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