NPJ Systems Biology and Applications最新文献_第4页

Dynamical systems theory as an organizing principle for single-cell biology. 动力系统理论作为单细胞生物学的组织原理。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-08-01 DOI: 10.1038/s41540-025-00565-3

Samia Islam, Sudin Bhattacharya

引用次数: 0

Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production. 条件通用微分方程捕捉c肽生产中的种群动态和个体间变化。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-31 DOI: 10.1038/s41540-025-00570-6

Max de Rooij, Natal A W van Riel, Shauna D O'Donovan

{"title":"Conditional universal differential equations capture population dynamics and interindividual variation in c-peptide production.","authors":"Max de Rooij, Natal A W van Riel, Shauna D O'Donovan","doi":"10.1038/s41540-025-00570-6","DOIUrl":"10.1038/s41540-025-00570-6","url":null,"abstract":"Universal differential equations (UDEs) are an emerging approach in biomedical systems biology, integrating physiology-driven mathematical models with machine learning for data-driven model discovery in areas where knowledge of the underlying physiology is limited. However, current approaches to training UDEs do not directly accommodate heterogeneity in the underlying data. As a data-driven approach, UDEs are also vulnerable to overfitting and consequently cannot sufficiently generalize to heterogeneous populations. We propose a conditional UDE (cUDE) where we assume that the structure and weights of the embedded neural network are common across individuals, and introduce a conditioning parameter that is allowed to vary between individuals. In this way, the cUDE architecture can accommodate inter-individual variation in data while learning a generalizable network representation. We demonstrate the effectiveness of the cUDE as an extension of the UDE framework by training a cUDE model of c-peptide production. We show that our cUDE model can accurately describe postprandial c-peptide levels in individuals with normal glucose tolerance, impaired glucose tolerance, and type 2 diabetes mellitus. Furthermore, we show that the conditional parameter captures relevant inter-individual variation. Subsequently, we use symbolic regression to derive a generalizable analytical expression for c-peptide production.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"84"},"PeriodicalIF":3.5,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12313987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modeling the metabolic response of A2780 ovarian cancer cells to gold-based cytotoxic drugs. 模拟卵巢癌A2780细胞对含金细胞毒性药物的代谢反应。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-28 DOI: 10.1038/s41540-025-00535-9

Walter Vieri, Veronica Ghini, Paola Turano, Lara Massai, Luigi Messori, Marco Fondi

引用次数: 0

Unraveling regulatory feedback mechanisms in adult neurogenesis through mathematical modelling. 通过数学模型揭示成人神经发生中的调节反馈机制。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-26 DOI: 10.1038/s41540-025-00563-5

Diana-Patricia Danciu, Filip Z Klawe, Alexey Kazarnikov, Laura Femmer, Ekaterina Kostina, Ana Martin-Villalba, Anna Marciniak-Czochra

{"title":"Unraveling regulatory feedback mechanisms in adult neurogenesis through mathematical modelling.","authors":"Diana-Patricia Danciu, Filip Z Klawe, Alexey Kazarnikov, Laura Femmer, Ekaterina Kostina, Ana Martin-Villalba, Anna Marciniak-Czochra","doi":"10.1038/s41540-025-00563-5","DOIUrl":"10.1038/s41540-025-00563-5","url":null,"abstract":"Adult neurogenesis is defined as the process by which new neurons are produced from neural stem cells in the adult brain. A comprehensive understanding of the mechanisms that regulate this process is essential for the development of effective interventions aimed at decelerating the decline of adult neurogenesis associated with ageing. Mathematical models provide a valuable tool for studying the dynamics of neural stem cells and their lineage, and have revealed alterations in these processes during the ageing process. The present study draws upon experimental data to explore how these processes are modulated by investigating regulatory feedback mechanisms among neural populations through the lens of nonlinear differential equations models. Our observations indicate that the time evolution of the neural lineage is predominantly regulated by neural stem cells, with more differentiated neural populations exerting a comparatively weaker influence. Furthermore, we shed light on the manner in which different subpopulations govern these regulations and gain insights into the impact of specific perturbations on the system.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"82"},"PeriodicalIF":3.5,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Complex-mediated evasion: modeling defense against antimicrobial peptides with application to human-pathogenic fungus Candida albicans. 复合物介导的逃避：模拟抗微生物肽的防御与应用于人类致病真菌白色念珠菌。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-22 DOI: 10.1038/s41540-025-00559-1

Yann Bachelot, Anastasia Solomatina, Marc Thilo Figge

{"title":"Complex-mediated evasion: modeling defense against antimicrobial peptides with application to human-pathogenic fungus Candida albicans.","authors":"Yann Bachelot, Anastasia Solomatina, Marc Thilo Figge","doi":"10.1038/s41540-025-00559-1","DOIUrl":"10.1038/s41540-025-00559-1","url":null,"abstract":"Understanding the complex interplay between host and pathogen during infection is critical for developing diagnostics and improving therapeutic interventions. Among the diverse arsenal employed by the host, antimicrobial peptides (AMP) play a key role in the defense against pathogens. We propose an immune evasion mechanism termed \"Complex-mediated evasion\" (CME), that allows pathogens to protect themselves against AMP and investigate it through mathematical modeling and computer simulations. To achieve CME, we hypothesize that the pathogen secretes defense molecules that bind AMP. When bound within the complex, AMP are unable to harm the pathogen. Due to molecular gradients, complexes may diffuse away from the pathogen, enhancing the protective effect of the mechanism by decreasing the concentration of AMP in the vicinity of the pathogen. We establish a mathematical model to (i) explore the sensitivity of the mechanism to various parameters and (ii) simulate the immune evasion of the human-pathogenic fungus Candida albicans.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"81"},"PeriodicalIF":3.5,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A systems biology approach to understand temporal evolution of silver nanoparticle toxicity. 用系统生物学的方法来理解银纳米颗粒毒性的时间演化。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-19 DOI: 10.1038/s41540-025-00561-7

Seung-Geun Park, Eunseo Lee, Hyun-Yi Kim, Tae Hyun Yoon

{"title":"A systems biology approach to understand temporal evolution of silver nanoparticle toxicity.","authors":"Seung-Geun Park, Eunseo Lee, Hyun-Yi Kim, Tae Hyun Yoon","doi":"10.1038/s41540-025-00561-7","DOIUrl":"10.1038/s41540-025-00561-7","url":null,"abstract":"Silver nanoparticles (AgNPs) are widely used in industrial and biomedical applications, however, their toxicity mechanisms at the molecular level are not completely understood. To address this gap, we investigate the temporal dynamics of gene expression in human lung epithelial cells exposed to AgNPs, integrating transcriptomic analysis, gene ontology (GO) enrichment, protein-protein interaction (PPI) networks, and dynamic simulations. GO analysis highlights early activation of ribosomal biogenesis and stress pathways, transitioning DNA repair and cell cycle regulation at later stages. PPI networks identify ribosomal proteins and DNA damage regulators as key hub genes. Dynamic simulations modeled gene expression changes over 48 hours, uncovering sequential activation of stress response genes, followed by DNA repair attempts and apoptotic signaling as cellular damage persisted. Through modeling the interplay between molecular responses and cell viability, the simulations provided a predictive temporal framework for advancing nanotoxicology research, providing insights into AgNPs-induced molecular disturbances, contributing to safety assessments.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"80"},"PeriodicalIF":3.5,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12274429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy. 脑网络的几何表征可以预测颞叶癫痫的手术结果。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-16 DOI: 10.1038/s41540-025-00562-6

Martin Guillemaud, Alice Longhena, Louis Cousyn, Valerio Frazzini, Bertrand Mathon, Vincent Navarro, Mario Chavez

{"title":"Geometric representations of brain networks can predict the surgery outcome in temporal lobe epilepsy.","authors":"Martin Guillemaud, Alice Longhena, Louis Cousyn, Valerio Frazzini, Bertrand Mathon, Vincent Navarro, Mario Chavez","doi":"10.1038/s41540-025-00562-6","DOIUrl":"10.1038/s41540-025-00562-6","url":null,"abstract":"Epilepsy surgery, particularly for temporal lobe epilepsy (TLE), remains a vital treatment option for patients with drug-resistant seizures. However, accurately predicting surgical outcomes remains a significant challenge. This study introduces a novel biomarker derived from brain connectivity, analyzed using non-Euclidean network geometry, to predict the surgery outcome in TLE. Using structural and diffusion magnetic resonance imaging (MRI) data from 51 patients, we examined differences in structural connectivity networks associated with surgical outcomes. Our approach uniquely utilized hyperbolic embeddings of pre- and post-surgery brain networks, successfully distinguishing patients with favorable outcomes from those with poor outcomes. Notably, the method identified regions in the contralateral hemisphere relative to the epileptogenic zone, whose connectivity patterns emerged as a potential biomarker for favorable surgical outcomes. The prediction model achieves an area under the curve (AUC) of 0.87 and a balanced accuracy of 0.81. These results underscore the predictive capability of our model and its effectiveness in individual outcome forecasting based on structural network changes. Our findings highlight the value of non-Euclidean representation of brain networks in gaining deeper insights into connectivity alterations in epilepsy and advancing personalized prediction of surgical outcomes in TLE.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"79"},"PeriodicalIF":3.5,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12267629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The effect of stochastic noise on antibiotic resistance in intestinal flora. 随机噪声对肠道菌群抗生素耐药性的影响。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-15 DOI: 10.1038/s41540-025-00548-4

Aofei Hu, Ling Yang, Jie Yan

{"title":"The effect of stochastic noise on antibiotic resistance in intestinal flora.","authors":"Aofei Hu, Ling Yang, Jie Yan","doi":"10.1038/s41540-025-00548-4","DOIUrl":"10.1038/s41540-025-00548-4","url":null,"abstract":"Antibiotic treatment is widely used for gastrointestinal diseases, often leading to drug resistance. However, the underlying mechanisms of drug resistance remain unclear. Mathematical modeling provides a powerful tool to explore the dynamics of antibiotic resistance, yet few models have considered the effect of biological noise, which originates from microscopic interactions between bacteria. In this study, we constructed a stochastic model based on the chemical master equations to investigate how stochastic noise influences the development of antibiotic resistance. Our simulations demonstrated that antibiotic resistance developed stepwise: while effective antibiotic treatments maintained the host's total pathogen numbers at healthy levels, the compositional balance shifted significantly through progressive increases in resistant pathogen proportions. Stochastic noise further amplified this shift and accelerated resistance by exacerbating post-treatment changes in the sensitive-to-resistant pathogen ratio. Finally, we found that the presence of coupling between different microbial communities can delay the onset of resistance and might even prevent its development. These results highlight noise's critical role in resistance development and suggest enhancing microbial interactions as a potential mitigation strategy.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"77"},"PeriodicalIF":3.5,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12264058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of resource packaging on the adaptative and pleiotropic consequences of evolution. 资源包装对进化的适应性和多效性的影响。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-15 DOI: 10.1038/s41540-025-00558-2

Neetika Ahlawat, Pavithra Venkataraman, Raman Gulab Brajesh, Supreet Saini

{"title":"Effects of resource packaging on the adaptative and pleiotropic consequences of evolution.","authors":"Neetika Ahlawat, Pavithra Venkataraman, Raman Gulab Brajesh, Supreet Saini","doi":"10.1038/s41540-025-00558-2","DOIUrl":"10.1038/s41540-025-00558-2","url":null,"abstract":"Adaptation to an environment is enabled by the accumulation of beneficial mutations. How do adaptive trajectories and pleiotropic effects of adaptation change in response to \"subtle\" changes in the environment? Since there exists no molecular framework to quantify \"subtle\" environmental change, designing experiments to answer this question has been challenging. In this work, we address this question by studying the effects of evolution in environments which differ solely in the way sugars are presented to a bacterial population. Specifically, we focus on glucose and galactose, which can be supplied to an E. coli population as a mixture of glucose and galactose, lactose, or melibiose. We evolve six replicate populations of E coli for 300 generations in these three chemically correlated or \"synonymous\" environments, and show that the adaptive responses of these populations are not similar. When tested for pleiotropic effects of fitness in a range of non-synonymous environments, our results show that despite uncorrelated adaptive changes, the nature of pleiotropic effects is largely predictable based on the fitness of the ancestor in the non-home environments. Overall, our results highlight how subtle changes in the environment can alter adaptation, but despite sequence-level variations, pleiotropy is qualitatively predictable.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":"11 1","pages":"78"},"PeriodicalIF":3.5,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12264277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. 作者更正：系统医学疾病地图：社区驱动的疾病机制的全面代表。

IF 3.5 2区生物学

NPJ Systems Biology and Applications Pub Date : 2025-07-12 DOI: 10.1038/s41540-025-00554-6

Alexander Mazein, Marek Ostaszewski, Inna Kuperstein, Steven Watterson, Nicolas Le Novère, Diane Lefaudeux, Bertrand De Meulder, Johann Pellet, Irina Balaur, Mansoor Saqi, Maria Manuela Nogueira, Feng Q HeFeng, Andrew Parton, Nathanaël Lemonnier, Piotr Gawron, Stephan Gebel, Pierre Hainaut, Markus Ollert, Ugur Dogrusoz, Emmanuel Barillot, Andrei Zinovyev, Reinhard Schneider, Rudi Balling, Charles Auffray

引用次数: 0