Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.
复制标题
DOI：
10.1186/s13059-021-02289-z
复制
发表时间：
2021-02-18
期刊：
影响因子：
12.3
通讯作者：
Segrè D
中科院分区：
文献类型：
--
作者：
Bernstein DB;Sulheim S;Almaas E;Segrè D
基因组规模代谢模型的重建和分析构成了一种强大的系统生物学方法，其应用范围从基本了解基因-表型图谱到解决生物医学和环境问题。然而，从这些模型中获得的生物学洞察力受到多种不同不确定性来源的限制，这些来源往往很难量化。在这里，我们审查了不确定性的主要来源，并概述了为表现和解决这些不确定性而制定的现有方法。通过概率方法和集合建模对这些不确定性进行统一的形式表征，将有助于朝着一致的重建管道、改进的数据集成算法和更准确的预测能力评估趋同。网上版载有补充材料，可在10.1186/s13059-021-02289-z查阅。
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity. The online version contains supplementary material available at 10.1186/s13059-021-02289-z.
登录
查看更多内容
影响因子：
3.6
作者：
Aurich, Maike K.;Paglia, Giuseppe;Rolfsson, Ottar;Hrafnsdottir, Sigrun;Magnusdottir, Manuela;Stefaniak, Magdalena M.;Palsson, Bernhard O.;Fleming, Ronan M. T.;Thiele, Ines
通讯作者：
Thiele, Ines
影响因子：
--
作者：
Chen J;Gomez JA;Höffner K;Phalak P;Barton PI;Henson MA
通讯作者：
Henson MA
影响因子：
4.3
作者：
Aite, Meaziane;Chevallier, Marie;Siegel, Anne
通讯作者：
Siegel, Anne
影响因子：
4.3
作者：
Bordel, Sergio;Agren, Rasmus;Nielsen, Jens
通讯作者：
Nielsen, Jens
影响因子：
3.5
作者：
Beck, Ashley E.;Hunt, Kristopher A.;Carlson, Ross P.
通讯作者：
Carlson, Ross P.