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相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Background and Environment Affect Phenotype02:27

Background and Environment Affect Phenotype

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Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
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Epistasis Analysis01:09

Epistasis Analysis

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Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
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Incomplete Dominance01:43

Incomplete Dominance

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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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Genetic Drift03:33

Genetic Drift

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Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.
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相关实验视频

Updated: Jun 27, 2025

Author Spotlight: Generating Neuronal Phenotypic Profiles - A Protocol to Culture and Image Human Midbrain Dopaminergic Neurons
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基因型-表型景观计算基于第一个原则和深度学习.

Yuexing Liu1, Yao Luo2, Xin Lu1

  • 1Guangzhou Laboratory, Guangzhou, Guangdong Province 510005, China.

Briefings in bioinformatics
|May 3, 2024
PubMed
概括

我们开发了一个新的表型嵌入定理,将基因型映射到适应性,从而能够准确预测病毒进化和免疫逃生突变. 这种计算生物学方法创建了基因型-表型景观.

关键词:
这就是SARS-CoV-2病毒.深度学习是一种深度学习.基因型-适应性景观.免疫系统的逃脱是免疫逃脱.可以解释的解释性.相对基本复制数 (R0) 的相对基本复制数.

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科学领域:

  • 理论和计算生物学理论和计算生物学
  • 进化生物学 进化生物学
  • 遗传学 是一个遗传学.

背景情况:

  • 将基因型映射到表型和适应性对于理解进化至关重要,但仍然是一个重大挑战.
  • 现有的方法在弥合基因型适应性差距方面缺乏定量精度.

研究的目的:

  • 引入表型嵌入 (P-E) 定理作为一种新的框架,用于定量地将基因型与表型联系起来.
  • 建立一个可计算的基础,以建立一个将基因型和表型相关联的一般第一原则.
  • 开发一种用于模拟病毒演变和预测免疫逃生突变的计算模型.

主要方法:

  • 使用编码器-解码器深度学习框架开发了表型嵌入 (P-E) 定理.
  • 提出了基因型-表型相关性的第一个一般原则.
  • 创建了一个基于Co-attention的变压器模型,用于基因型-适应性映射.
  • 应用了P-E定理来计算SARS-CoV-2的基本复制数 (R0).

主要成果:

  • 精确模拟病毒的中性进化和预测免疫逃生突变.
  • 病毒免疫逃脱与病毒健康有数量联系.
  • 成功地从第一原则中推导出SARS-CoV-2的基本复制数 (R0).
  • 构建了一个基因型-适应性景观.

结论:

  • P-E定理为构建基因型-表型景观提供了一个一般的,可解释的方法.
  • 这项工作为理论和计算生物学建立了新的范式.
  • 开发的模型准确地预测了病毒演变和免疫逃脱,这对公共卫生和疫苗开发有影响.