PBIP:一种深度学习框架,用于预测菌根-细菌相互作用在菌株水平
Lijia Ma1, Peng Gao1, Gufeng Liu1
1College of Computer Science and Software Engineering, Shenzhen University, No. 3688 Nanhai Avenue, Nanshan District, Shenzhen 518060, Guangdong, China.
Briefings in bioinformatics
|December 10, 2025
概括
我们开发了PBIP,这是一个深度学习框架,用于在菌株水平上预测菌-细菌相互作用 (PBIs). 这种方法通过准确识别特定的菌-细菌关系来增强菌疗法,克服现有方法的局限性.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 菌体治疗是一种有前途的抗微生物策略,菌体与细菌相互作用 (PBI) 的预测是关键.
- 目前用于PBI预测的计算方法缺乏菌株级特异性和深度序列特征分析.
- 这限制了菌体治疗的临床应用和发现新菌体与细菌之间的关系.
研究的目的:
- 开发一种新的深度学习框架,PBIP,用于精确的菌株水平菌体-细菌相互作用预测.
- 通过结合深层嵌入表示和菌株特定数据来解决现有方法的局限性.
- 通过改进PBI预测来增强菌体治疗的潜力.
主要方法:
- 应变水平的PBI数据是从*Klebsiella pneumoniae*临床隔离物中生成的.
- 一个预训练的统一表示模型从菌体和细菌蛋白序列中产生了深层嵌入.
- 合成少数人过量抽样技术平衡了数据集.
- 一个深度神经网络 (CNN,Bi-GRU,注意力) 设计用于特征提取和PBI预测.
主要成果:
- 与最先进的方法相比,PBIP在菌株水平PBI预测方面表现优异.
- 该框架有效地从序列数据中捕获复杂的生物模式.
- 深度嵌入和先进的神经网络架构显著提高了预测准确性.
结论:
- PBIP提供了一种强大的新工具,用于菌株级PBI预测,推进菌体治疗研究.
- 该框架分析深层序列特征的能力为发现特定的菌体-细菌相互作用开辟了新的途径.
- 这项工作有助于优化菌体治疗中的治疗策略.
相关概念视频
01:26DNA Bacteriophages
726
Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
726
01:30Lytic Cycle of Bacteriophages
77.2K
Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
77.2K
00:43Lysogenic Cycle of Bacteriophages
67.2K
In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
67.2K
01:16Viral Replication: Lysogenic Cycle
1.2K
The lysogenic cycle is a crucial viral replication strategy that allows bacteriophages to persist within host cells without immediately destroying them. This process is primarily observed in temperate phages, such as bacteriophage lambda (λ), which infects Escherichia coli. The cycle allows the viral genome to persist across bacterial generations while keeping host cells viable.Integration of the Viral GenomeUpon infection, bacteriophage lambda attaches to the bacterial surface and injects...
1.2K