VAPOR:变异自编码器与运输运营商在发展过程中脱了同时发生的生物过程
bioRxiv : the preprint server for biology
|November 18, 2024
概括
VAPOR是一种新的计算方法,通过分离不同的生物过程及其独特的时间尺度来解码发育过程中的复杂基因表达动态. 这种方法增强了从单细胞和空间转录基因数据中对细胞分化和成熟的理解.
科学领域:
- 计算生物学 计算生物学
- 发展生物学 发展生物学
- 基因组学就是基因组学.
背景情况:
- 单细胞和空间转录组学提供了对发育基因表达动态的见解.
- 现有的轨迹推断方法可以汇集在不同的时间尺度上发生的不同的生物过程.
- 一个单一的伪时间轴可以掩盖分化和成熟等同时发生的细胞过程的细微差别.
研究的目的:
- 引入VAPOR (运输运营商的变量自动编码器),一种新的计算方法.
- 在发育过程中解和分析不同的基因表达动态.
- 为多面时间尺度分析推断过程特定的伪时间.
主要方法:
- VAPOR使用一个变异自编码器来学习基因表达动态的潜在空间.
- 它将这种潜伏空间分解为多个子空间,每个子空间都受普通微分方程的支配.
- 过程特定的伪时间被推断为揭示不同的发育时间表.
主要成果:
- 在模拟数据集中,VAPOR成功地恢复了数据拓,并解了模拟数据集中的动态模式.
- 对人类大脑scRNA-seq数据的应用确定了关键的分化和成熟动态.
- 基准测试表明,与现有方法相比,VAPOR的性能优越.
- 对空间转录组学数据的VAPOR分析揭示了皮质层形成的"内外"模式.
结论:
- 在发育过程中,VAPOR有效地解开了复杂的基因表达动态.
- 该方法提供了特定过程的伪时间,为细胞进展提供了更细致的观点.
- VAPOR是开源的,适用于各种omics数据,包括表观基因组动态.
相关概念视频
Multi-input and Multi-variable systems
98
Cruise control systems in cars are designed as multi-input systems to maintain a driver's desired speed while compensating for external disturbances such as changes in terrain. The block diagram for a cruise control system typically includes two main inputs: the desired speed set by the driver and any external disturbances, such as the incline of the road. By adjusting the engine throttle, the system maintains the vehicle's speed as close to the desired value as possible.
In the absence...
In the absence...
98
Multicompartment Models: Overview
102
Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
102
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation
398
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...
398
Mechanistic Models: Compartment Models in Individual and Population Analysis
29
Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...
29
Neural Circuits
1.1K
Neural circuits and neuronal pools are two of the main structures found in the nervous system. Neural circuits are networks of neurons that work together to carry out a specific task or process. They consist of interconnected neurons and glial cells, which provide structural and metabolic support.
Neuronal pools are collections of nerve cells with similar functions and interact through chemical and electrical signals. These pools include both interneurons (the central neural circuit nodes that...
Neuronal pools are collections of nerve cells with similar functions and interact through chemical and electrical signals. These pools include both interneurons (the central neural circuit nodes that...
1.1K
Variability: Analysis
126
Measures of variability are statistical metrics that reveal the dispersion pattern within a dataset. They are pivotal in biostatistics, providing insights into the heterogeneity within health and biological data. Variability signifies the degree to which data points diverge from one another, helping researchers understand the potential range of values and associated uncertainty within the data.
The range is a simple measure of variability, indicating the difference between the highest and...
The range is a simple measure of variability, indicating the difference between the highest and...
126


