关于单细胞优化目标和权衡推断的协议
Da-Wei Lin1, Cara Teixeira2, Carolina Chung3
1Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, Ann Arbor, MI 48109, USA; Department of Statistics, University of Michigan, Ann Arbor, MI, USA.
STAR protocols
|March 6, 2026
概括
本研究介绍了单细胞优化目标和权衡推断 (SCOOTI) 框架,用于使用多组数据分析代谢权衡. SCOOTI集成了各种数据类型,以在不同条件下揭示细胞代谢优先级.
科学领域:
- 计算生物学 计算生物学
- 系统生物学 系统生物学
- 代谢工程是代谢工程.
背景情况:
- 了解细胞代谢对于生物研究至关重要.
- 将多omics数据与代谢模型的整合提供了更深入的见解.
- 现有的方法可能无法完全捕捉细胞特异性代谢目标和权衡.
研究的目的:
- 介绍一个安装和使用SCOOTI计算框架的协议.
- 为了证明SCOOTI如何推断生物系统中的代谢目标和权衡.
- 为解释不同细胞状态的代谢优先级提供一种方法.
主要方法:
- 集成大量和单细胞奥米克数据 (转录组学,蛋白质组学,代谢组学).
- 基因组规模代谢建模的应用.
- 使用SCOOTI来限制代谢模型和推断目标.
- 采用聚类,缩小维度和权衡分析进行解释.
主要成果:
- 成功安装和执行SCOOTI.的协议.
- 使用多omics数据推断代谢目标和权衡的演示.
- 分析和解释不同细胞状态或条件的代谢优先级的方法.
结论:
- SCOOTI为代谢系统分析提供了一个强大的计算框架.
- 该协议使研究人员能够利用多omics数据获得详细的代谢见解.
- 斯科蒂促进了对细胞代谢灵活性和适应性的理解.
相关概念视频
Determination of Multiple Dosing Parameters: Steady-State, Minimum and Maximum Concentrations
305
Gentamicin, an aminoglycoside antibiotic, is commonly administered via intermittent intravenous infusion to treat severe infections. An intermittent one-hour infusion of gentamicin, administered at eight-hour intervals, allows for precise control of plasma drug concentrations, minimizing toxicity while ensuring therapeutic efficacy. Pharmacokinetic principles govern the dynamics of plasma concentrations and can be mathematically described using specific equations.The plasma drug concentration...
305
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation
1.3K
This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
On...
1.3K
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
376
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
376


