Integrating imaging and mathematical modeling to predict and optimize patient outcomes in oncology [0.03%]
整合影像与数学建模以预测并优化肿瘤学患者预后
Reshmi J S Patel,Ayesha Das,Aliya Anil et al.
Reshmi J S Patel et al.
Biology-based mathematical models calibrated to patient-specific imaging data can accurately predict and optimize therapeutic response for individual cancer patients. We present the framework, motivation, and examples of using imaging data ...
Hyperpathway: visualizing organization of pathway-molecule enriched interactions in omics studies via hyperbolic bipartite network embedding [0.03%]
基于双部分集网络嵌入的高维生物分子互作数据组织方式可视化超路径方法
Ilyes Abdelhamid,Ziheng Liao,Yuchi Liu et al.
Ilyes Abdelhamid et al.
Pathway enrichment analysis (PEA) of omics data identifies significant pathway-molecule associations, yet delivers results as tabular lists in which complex systems-biology insights remain inaccessible. Hyperpathway is an open-access networ...
Patient-specific modeling of G2/M cell cycle dynamics reveals prognostic dynamical regimes driven by copy number alterations [0.03%]
基于拷贝数变异的患者特异性G2/M细胞周期动力学模型揭示了预后的动态模式
Andrea Tonina,Alessandro Romanel
Andrea Tonina
Cell cycle dysregulation is a hallmark of cancer and a major source of tumor heterogeneity. While large-scale cancer genomics studies have characterized recurrent copy number alterations affecting cell cycle regulators, how these alteration...
Prediction variability in physiologically based pharmacokinetic modeling of tissue disposition under deep uncertainty [0.03%]
生理不确定性下的组织分布生理药动学模型预测变异性研究
Mustafa Farahat,D T Flaherty,Zachary R Fox et al.
Mustafa Farahat et al.
Physiologically based pharmacokinetic (PBPK) models are increasingly invoked in virtual screening workflows for therapeutics. These mechanistic models project pharmacokinetic (PK) outcomes from molecular properties, with data-driven models ...
Rangan Das,K Maheswari,Shaheen Siddiqui et al.
Rangan Das et al.
Agentic systems are proposed for clinical decision support, yet unrestricted tool access can undermine accountability and safety in precision oncology, where recommendations must be grounded in evolving guidelines, regulatory labels, and pa...
A fundamental trade-off among noise suppression, response sensitivity and speed in biological feedback networks [0.03%]
生物反馈网络中噪声抑制、响应灵敏度和速度的基本折衷方案
Ka Kit Kong,Feng Liu
Ka Kit Kong
Biological regulatory networks rely on feedback control to suppress intrinsic noise while remaining sensitive and responsive to external signals, yet whether these objectives can be achieved simultaneously remains unclear. Here, we show tha...
Improvement in model flexibility reveals signaling pathway in T cell responses to pulsatile stimuli [0.03%]
模型灵活性的提高揭示了T细胞对脉冲刺激反应的信号通路
Jun Allard
Jun Allard
Efforts to develop quantitative models must face a trade-off between interpretability and quantitative accuracy, which often disfavors interpretability. Here we adopt an operational definition of interpretability, specifically that a model ...
Systematic proteomic analysis of neuroimaging metrics identifies therapeutic targets for pituitary neuroendocrine [0.03%]
系统蛋白质组分析发现垂体神经内分泌肿瘤的影像学生物标志物及潜在治疗靶点
Xiao Wu,Haoyang Peng,Peng Wang et al.
Xiao Wu et al.
The relationship between proteomics and neuroimaging metrics (NIMs) is still not fully understood. By examining the specific proteins expressed in different NIMs, researchers can gain insights into how these NIMs contribute to pituitary neu...
Multiscale hyperbolic embedding reveals hierarchical structure in complex biological systems [0.03%]
多尺度双曲嵌入揭示复杂生物系统的层次结构
Mingchen Yao,Anoop Praturu,Tatyana O Sharpee
Mingchen Yao
The rapid expansion of biological and computational datasets demands scalable methods that support both visualization and quantitative interpretation. Hyperbolic embeddings are well-suited to represent hierarchical structure, but existing a...
Comparing kinetic versus stoichiometric priorities in hybrid models of CHO metabolism [0.03%]
CHO代谢杂交模型中动力学优先级与化学计量优先级的比较
Pratik Khare,Nelson Ndahiro,Stephanie Klaubert et al.
Pratik Khare et al.
Understanding Chinese hamster ovary (CHO) cell metabolism through mathematical models is essential for optimizing culture media and biomanufacturing processes. Stoichiometric models estimate intracellular fluxes under steady state, while ki...