In silico models in oncology, neurology, and epidemiology: systems-level and multiscale perspectives [0.03%]
肿瘤学、神经病学和流行病学的计算机模型：系统级和多尺度视角
Matteo Italia,José Garcia Otero,Juan Jiménez-Sánchez et al.
Matteo Italia et al.
Computational medicine uses mathematical modelling, high-performance computing, and the availability of large-scale biomedical data to study multiscale complex diseases. This review synthesises recent developments in in silico oncology, neu...
Abhishek Sengupta,Vishal Singh,Muskan Syed et al.
Abhishek Sengupta et al.
Vitiligo is a multifaceted autoimmune skin disease characterized by the loss of epidermal melanocytes, yet its molecular basis remains poorly understood. To address the need for a specialized systems biology interface, we present VIRdb v3.0...
Molecular noise modulates transitions in the cell-fate differentiation landscape [0.03%]
分子噪声调节细胞分化命运景观中的转换事件
Yujing Liu,Adriana Zanca,Michael P H Stumpf et al.
Yujing Liu et al.
Waddington's epigenetic landscape has become one of biology's cornerstone metaphors, widely used both conceptually and computationally. Cell types are often associated with the qualitatively stable points or valleys of this landscape. In pr...
Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data [0.03%]
单细胞转录组学数据中基于信号通路的细胞间通讯可视化技术
Sidrah Maryam,Martin Manolov,Rafael Kramann et al.
Sidrah Maryam et al.
Single-nuclei transcriptomics enables investigating ligand-receptor mediated cell-cell communication between different cell-types. However, current tools do not allow for non-programmatic means to access this analysis. Additionally, most me...
Growth rate-dependent mutations and phenotypic switching facilitate rapid adaptation [0.03%]
依赖增长速率的突变和表型转换可促进快速适应性进化
Anton Grishechkin,Omer Karin
Anton Grishechkin
The mutation rates of many species are regulated in response to internal and external conditions. Studies in several model organisms have shown that mutation rates can be modulated by the organism's growth rate, particularly through stress-...
Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces [0.03%]
智能工具编排在机制模型原型设计中的应用：利用MCP服务器作为AI与生物接口进行快速假设验证
Marco Ruscone,Miguel Vazquez,Alfonso Valencia
Marco Ruscone
Constructing multicellular mechanistic models traditionally requires extensive time and computational expertise. We introduce intelligent tool orchestration via Model Context Protocol (MCP) servers, enabling Large Language Model (LLM) agent...
Determining parameter impact in systems biology models via sensitivity analysis: a comparative approach [0.03%]
基于敏感性分析鉴定系统生物学模型参数影响的比较方法
Kelsey I Gasior
Kelsey I Gasior
Mathematical modeling is a powerful tool to understand biological phenomena, predict behavior, and guide experiments. Model parameters represent experimentally derived rates, and it can be challenging to understand how parameters affect the...
Spatial analysis of malignant-immune cell interactions in the tumor microenvironment using topological data analysis [0.03%]
基于拓扑数据分析的肿瘤微环境中恶性免疫细胞交互作用的空间分析
Seol Ah Park,Davide Gurnari,Paweł Dłotko et al.
Seol Ah Park et al.
The spatial interactions between malignant and immune cells in the tumor microenvironment are important for tumor immunobiology and patient outcomes. However, analytical tools that can extract rigorous yet interpretable spatial features and...
Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns [0.03%]
小鼠黑色素瘤模型中ACT期间的纵向空间中性粒细胞谱分析揭示了独特的淋巴结浸润模式
Gemma van der Voort,Maike Effern,Michelle C R Yong et al.
Gemma van der Voort et al.
Reactive neutrophil infiltration can restrain CD8+ T cell expansion in lymph nodes during adoptive T cell therapy (ACT), yet its spatiotemporal regulation remains incompletely understood. Levaraging flow cytometry and multiplex immunofluore...
A powerful representation learning method for enhanced analysis of incomplete multi-omics data [0.03%]
一种强大的表示学习方法，可增强不完整多组学数据的分析效果
Jenna L Ballard,Zongyu Dai,Li Shen et al.
Jenna L Ballard et al.
Integrative analysis of multi-omics data provides a more comprehensive and nuanced view of a subject's biological state. However, high-dimensionality and ubiquitous modality missingness present significant analytical challenges. Existing me...