• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

相似文献

1
Do genome-scale models need exact solvers or clearer standards?基因组规模模型需要精确求解器还是更清晰的标准？
Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157.
2
Reply to "Do genome-scale models need exact solvers or clearer standards?".对《基因组规模模型需要精确求解器还是更清晰的标准？》的回复
Mol Syst Biol. 2015 Oct 14;11(10):830. doi: 10.15252/msb.20156548.
3
A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities.用于生物体和群落基因组规模代谢建模的优化求解器基准。
mSystems. 2024 Feb 20;9(2):e0083323. doi: 10.1128/msystems.00833-23. Epub 2024 Jan 22.
4
Genome-scale estimate of the metabolic turnover of E. coli from the energy balance analysis.通过能量平衡分析对大肠杆菌代谢周转率进行全基因组规模估计。
Phys Biol. 2016 Jan 29;13(1):016003. doi: 10.1088/1478-3975/13/1/016003.
5
Quantitative analysis of numerical solvers for oscillatory biomolecular system models.振荡生物分子系统模型数值求解器的定量分析
BMC Bioinformatics. 2008 May 28;9 Suppl 6(Suppl 6):S17. doi: 10.1186/1471-2105-9-S6-S17.
6
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models.ETFL 公式允许在符合热力学的代谢和表达模型中进行多组学整合。
Nat Commun. 2020 Jan 13;11(1):30. doi: 10.1038/s41467-019-13818-7.
7
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics.酿酒酵母基于表达约束和反应热力学整合的基因组代谢模型
Nat Commun. 2021 Aug 9;12(1):4790. doi: 10.1038/s41467-021-25158-6.
8
Mathematical solutions in internal dose assessment: A comparison of Python-based differential equation solvers in biokinetic modeling.体内剂量评估中的数学解：生物动力学建模中基于 Python 的微分方程求解器的比较。
J Radiol Prot. 2023 Oct 30;43(4):041507. doi: 10.1088/1361-6498/ad0409.
9
Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.对基因组尺度代谢模型解空间的热力学约束进行定量评估。
Biophys J. 2013 Jul 16;105(2):512-22. doi: 10.1016/j.bpj.2013.06.011.
10
Design and application of genome-scale reconstructed metabolic models.基因组规模重建代谢模型的设计与应用。
Methods Mol Biol. 2008;416:409-31. doi: 10.1007/978-1-59745-321-9_29.

引用本文的文献

1
The transition from genomics to phenomics in personalized population health.从个体化人群健康的基因组学到表型组学的转变。
Nat Rev Genet. 2024 Apr;25(4):286-302. doi: 10.1038/s41576-023-00674-x. Epub 2023 Dec 13.
2
Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism?红青霉全基因组代谢网络的调和与进化——特殊代谢物如何？
PLoS One. 2023 Aug 30;18(8):e0289757. doi: 10.1371/journal.pone.0289757. eCollection 2023.
3
Standards, dissemination, and best practices in systems biology.系统生物学中的标准、传播和最佳实践。
Curr Opin Biotechnol. 2023 Jun;81:102922. doi: 10.1016/j.copbio.2023.102922. Epub 2023 Mar 31.
4
Phenotype-specific estimation of metabolic fluxes using gene expression data.利用基因表达数据进行代谢通量的表型特异性估计。
iScience. 2023 Feb 15;26(3):106201. doi: 10.1016/j.isci.2023.106201. eCollection 2023 Mar 17.
5
Guidelines for extracting biologically relevant context-specific metabolic models using gene expression data.使用基因表达数据提取具有生物学相关性的特定代谢模型的指南。
Metab Eng. 2023 Jan;75:181-191. doi: 10.1016/j.ymben.2022.12.003. Epub 2022 Dec 22.
6
High-Quality Genome-Scale Reconstruction of ATCC 13032.ATCC 13032的高质量基因组规模重建
Front Microbiol. 2021 Nov 15;12:750206. doi: 10.3389/fmicb.2021.750206. eCollection 2021.
7
ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data.使用基因组尺度代谢模型和差异转录组数据预测代谢通量变化。
PLoS Comput Biol. 2021 Nov 10;17(11):e1009589. doi: 10.1371/journal.pcbi.1009589. eCollection 2021 Nov.
8
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.评估不同酵母物种的基因组规模代谢模型的可访问性、可用性和互操作性。
FEMS Yeast Res. 2021 Mar 4;21(1). doi: 10.1093/femsyr/foab002.
9
Metabolic flux configuration determination using information entropy.基于信息熵的代谢通量分布测定
PLoS One. 2020 Dec 4;15(12):e0243067. doi: 10.1371/journal.pone.0243067. eCollection 2020.
10
SBML Level 3: an extensible format for the exchange and reuse of biological models.SBML 级别 3：一种用于生物模型交换和重用的可扩展格式。
Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110.

本文引用的文献

1
Critical assessment of genome-scale metabolic networks: the need for a unified standard.基因组规模代谢网络的批判性评估：统一标准的必要性。
Brief Bioinform. 2015 Nov;16(6):1057-68. doi: 10.1093/bib/bbv003. Epub 2015 Feb 28.
2
Improving collaboration by standardization efforts in systems biology.通过系统生物学中的标准化工作来提高协作。
Front Bioeng Biotechnol. 2014 Dec 8;2:61. doi: 10.3389/fbioe.2014.00061. eCollection 2014.
3
An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models.一个用于代谢网络模型的一致且可重复结构分析的精确算法工具箱。
Nat Commun. 2014 Oct 7;5:4893. doi: 10.1038/ncomms5893.
4
Constraint-based models predict metabolic and associated cellular functions.基于约束的模型预测代谢和相关的细胞功能。
Nat Rev Genet. 2014 Feb;15(2):107-20. doi: 10.1038/nrg3643. Epub 2014 Jan 16.
5
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.大肠杆菌基因组规模代谢网络重建的基础和应用。
Mol Syst Biol. 2013;9:661. doi: 10.1038/msb.2013.18.
6
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.基于约束的模型对细胞代谢进行定量预测：COBRA Toolbox v2.0。
Nat Protoc. 2011 Aug 4;6(9):1290-307. doi: 10.1038/nprot.2011.308.
7
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.古生菌产甲烷菌嗜乙酸甲烷八叠球菌的代谢重建。
BMC Syst Biol. 2011 Feb 15;5:28. doi: 10.1186/1752-0509-5-28.
8
Elimination of thermodynamically infeasible loops in steady-state metabolic models.消除稳态代谢模型中的热力学不可行环。
Biophys J. 2011 Feb 2;100(3):544-553. doi: 10.1016/j.bpj.2010.12.3707.
9
What is flux balance analysis?通量平衡分析是什么？
Nat Biotechnol. 2010 Mar;28(3):245-8. doi: 10.1038/nbt.1614.
10
Systems metabolic engineering of Escherichia coli for L-threonine production.用于生产L-苏氨酸的大肠杆菌系统代谢工程
Mol Syst Biol. 2007;3:149. doi: 10.1038/msb4100196. Epub 2007 Dec 4.

Do genome-scale models need exact solvers or clearer standards?

作者信息

Ebrahim Ali, Almaas Eivind, Bauer Eugen, Bordbar Aarash, Burgard Anthony P, Chang Roger L, Dräger Andreas, Famili Iman, Feist Adam M, Fleming Ronan Mt, Fong Stephen S, Hatzimanikatis Vassily, Herrgård Markus J, Holder Allen, Hucka Michael, Hyduke Daniel, Jamshidi Neema, Lee Sang Yup, Le Novère Nicolas, Lerman Joshua A, Lewis Nathan E, Ma Ding, Mahadevan Radhakrishnan, Maranas Costas, Nagarajan Harish, Navid Ali, Nielsen Jens, Nielsen Lars K, Nogales Juan, Noronha Alberto, Pal Csaba, Palsson Bernhard O, Papin Jason A, Patil Kiran R, Price Nathan D, Reed Jennifer L, Saunders Michael, Senger Ryan S, Sonnenschein Nikolaus, Sun Yuekai, Thiele Ines

机构信息

Department of Bioengineering, University of California, San Diego, CA, USA.

Department of Biotechnology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.

出版信息

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157.

DOI:10.15252/msb.20156157
PMID:26467284
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4631202/
Abstract
摘要