PLoS Computational Biology最新文献_第6页

A Bayesian model of distance perception from ocular convergence. 眼会聚距离感知的贝叶斯模型。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-10-03 eCollection Date: 2025-10-01 DOI: 10.1371/journal.pcbi.1013506

Peter Scarfe, Paul B Hibbard

引用次数: 0

RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation. rnatransator：将蛋白质条件RNA设计建模为序列到序列的自然语言翻译。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-10-03 eCollection Date: 2025-10-01 DOI: 10.1371/journal.pcbi.1013541

Sobhan Shukueian Tabrizi, Sina Barazandeh, Helyasadat Hashemi Aghdam, A Ercument Cicek

{"title":"RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation.","authors":"Sobhan Shukueian Tabrizi, Sina Barazandeh, Helyasadat Hashemi Aghdam, A Ercument Cicek","doi":"10.1371/journal.pcbi.1013541","DOIUrl":"10.1371/journal.pcbi.1013541","url":null,"abstract":"Protein-RNA interactions are essential in gene regulation, splicing, RNA stability, and translation, making RNA a promising therapeutic agent for targeting proteins, including those considered undruggable. However, designing RNA sequences that selectively bind to proteins remains a significant challenge due to the vast sequence space and limitations of current experimental and computational methods. Traditional approaches rely on in vitro selection techniques or computational models that require post-generation optimization, restricting their applicability to well-characterized proteins. We introduce RNAtranslator, a generative language model that formulates protein-conditional RNA design as a sequence-to-sequence natural language translation problem for the first time. By learning a joint representation of RNA and protein interactions from large-scale datasets, RNAtranslator directly generates binding RNA sequences for any given protein target without the need for additional optimization. Our results demonstrate that RNAtranslator produces RNA sequences with natural-like properties, high novelty, and enhanced binding affinity compared to existing methods. This approach enables efficient RNA design for a wide range of proteins and even proteins with no RNA-interaction data available, paving the way for new RNA-based therapeutics and synthetic biology applications.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"21 10","pages":"e1013541"},"PeriodicalIF":3.6,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12510665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225617","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

Correction: Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning. 修正：层次强化运动学习的成功高效/失败安全策略。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-30 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013537

引用次数: 0

Harmony-based data integration for distributed single-cell multi-omics data. 基于和谐的分布式单细胞多组学数据集成。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-30 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013526

Ruizhi Yuan, Ziqi Rong, Haoran Hu, Tianhao Liu, Shiyue Tao, Wei Chen, Lu Tang

引用次数: 0

Optimization of echinococcosis control measures based on system dynamics. 基于系统动力学的棘球蚴病控制措施优化。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-30 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013186

Jinrui Ma, Xingyu Liu, Zengwen He, Haohao Zhang, Yonghui Ma, Ziqiu Fan, Xuehui Zhao, Ji Zhi, Qing Cao, Huiwen Xue, Huitian Gou

{"title":"Optimization of echinococcosis control measures based on system dynamics.","authors":"Jinrui Ma, Xingyu Liu, Zengwen He, Haohao Zhang, Yonghui Ma, Ziqiu Fan, Xuehui Zhao, Ji Zhi, Qing Cao, Huiwen Xue, Huitian Gou","doi":"10.1371/journal.pcbi.1013186","DOIUrl":"10.1371/journal.pcbi.1013186","url":null,"abstract":"This study aimed to provide strategies to optimize the prevention and control measures of echinococcosis in Gansu Province. Based on the transmission mechanism of echinococcosis, a System Dynamics (SD) model of echinococcosis in Gansu Province was established using Vensim software. Through this model, parameters such as vaccination coverage, domestic dog deworming coverage, slaughter management level, and health education level were adjusted to predict the changing trends in the number of human cases and infected sheep. The results showed that the number of human cases was most sensitive to the adjustment of health education level, followed by changes to vaccination coverage. The number of infected sheep was most sensitive to the adjustment of vaccination coverage, followed by the adjustment of slaughter management level. Based on these simulation results, the prevention and control measures for echinococcosis in Gansu Province were further optimized. The results showed that if the health education level and the vaccination coverage were increased by 50% and 40%, respectively, based on the current prevention and control levels, the number of human cases would approach zero by approximately 2026. When the vaccination coverage and slaughter management level increased by 60% and 45%, respectively, based on current prevention and control levels, the number of infected sheep would approach zero by approximately 2027. This study applied the SD method to the prevention and control of echinococcosis for the first time, and the results can provide key decision-making recommendations to optimize the prevention and control measures of echinococcosis in Gansu province.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"21 9","pages":"e1013186"},"PeriodicalIF":3.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12483238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200750","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 computational framework for the investigation of phosphoinositide regulation. 研究磷酸肌苷调控的计算框架。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-30 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013477

Hilaire Yam Fung Cheung, Chukiat Tantiwong, Dipali Kale, Jonathan M Gibbins, Steve P Watson, Johan W M Heemskerk, Albert Sickmann, Robert Ahrends, Joanne L Dunster

{"title":"A computational framework for the investigation of phosphoinositide regulation.","authors":"Hilaire Yam Fung Cheung, Chukiat Tantiwong, Dipali Kale, Jonathan M Gibbins, Steve P Watson, Johan W M Heemskerk, Albert Sickmann, Robert Ahrends, Joanne L Dunster","doi":"10.1371/journal.pcbi.1013477","DOIUrl":"10.1371/journal.pcbi.1013477","url":null,"abstract":"Phosphoinositides are a group of interconvertible lipids that are located in the membrane of eukaryotic cells. They turnover via complex network of reactions (called the phosphoinositide pathway) that respond rapidly to regulate many aspects of a cell's response to their environment. Given their low-abundance they are difficult to characterise experimentally. Here we utilise a new experimental method to generate an unusually large dataset that characterises the time-dependent changes in five membrane bound phospoinositides and a soluble inositide in platelet, downstream of its GPVI receptor, where we know the phosphoinositide pathway is particularly active. To shed light on regulatotory steps that are often opaque to experimentation we use this data within a mathematical and computational framework. We construct and assess eleven mathematical models that represent competing interpretations of the dominant mechanisms that regulate the pathway. We find that while four of the models can generate the available data only one model, that incorporates an additional pool of PtdIns, is consistent with the data and is able to successfully predict the effects of an inhibitor. We publish all models openly in a form that is easily usable and adaptable for other researchers to use alongside our or their own data. We studied how changes in the shape and magnitude of events that stimulate the phosphoinositide pathway affect its dynamics. Despite these perturbations, the abundance of Phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) remained stable, consistent with findings reported in the literature.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"21 9","pages":"e1013477"},"PeriodicalIF":3.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12510658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200668","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 graph neural network-based spatial multi-omics data integration method for deciphering spatial domains. 一种基于图神经网络的空间多组学数据集成方法。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-30 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013546

Congqiang Gao, Chenghui Yang, Lihua Zhang

引用次数: 0

Early visual signatures and benefits of intra-saccadic motion streaks. 眼内运动条纹的早期视觉特征和益处。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-29 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013544

Richard Schweitzer, Thomas Seel, Jörg Raisch, Martin Rolfs

引用次数: 0

Generalizing population RT-qPCR cycle threshold values-informed estimation of epidemiological dynamics: Impact of surveillance practices and pathogen variability. 推广人群RT-qPCR周期阈值-流行病学动态的知情估计：监测实践和病原体变异性的影响。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-29 DOI: 10.1371/journal.pcbi.1013527

Yun Lin, James A Hay, Yu Meng, Benjamin J Cowling, Bingyi Yang

{"title":"Generalizing population RT-qPCR cycle threshold values-informed estimation of epidemiological dynamics: Impact of surveillance practices and pathogen variability.","authors":"Yun Lin, James A Hay, Yu Meng, Benjamin J Cowling, Bingyi Yang","doi":"10.1371/journal.pcbi.1013527","DOIUrl":"https://doi.org/10.1371/journal.pcbi.1013527","url":null,"abstract":"Population-level viral load distributions, measured by RT-qPCR or qPCR cycle threshold (Ct) values from surveillance testing, can be used to estimate the time-varying reproductive number ([Formula: see text]) in real-time during COVID-19 outbreaks. However, it remains unclear whether this approach can be broadly applied to other pathogens, sources of virologic test data, or surveillance strategies beyond those specifically implemented during the COVID-19 pandemic in Hong Kong. We systematically evaluated the accuracy of Ct-based [Formula: see text] estimates using simulated epidemics under different surveillance testing systems and pathogen viral kinetics. Using area under the ROC curve (AUC) to assess accuracy in detecting epidemic growth or decline, we found that case ascertainment rates minimally impacted estimation accuracy, except when detection was heavily biased towards severe patients (AUC: 0.64, 95% CIs: 0.59 - 0.71) or during prolonged waves with stable [Formula: see text] near one (AUC: 0.54, 0.48 - 0.64), compared to stable detection patterns over time (AUC 0.76, 0.66 - 0.82). By comparing model accuracies across different viral shedding patterns and by parameterizing our model using data from six respiratory pathogens, we found that model performance largely depends on a monotonic viral shedding trajectory following case detection. A pathogen that lacks such shedding pattern - for example, those with a viral peak after onset - exhibited lower accuracy (AUC: 0.58, 0.49 - 0.65). Overall, our findings demonstrate that Ct-based [Formula: see text] estimation methods are generally accurate across diverse surveillance conditions and pathogen shedding patterns, supporting their practical use as a supplementary tool for timely transmission monitoring while highlighting limitations that warrant further consideration.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"21 9","pages":"e1013527"},"PeriodicalIF":3.6,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145192533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management. 耦合浮游生物和霍乱动力学：洞察爆发预测和实际疾病管理。

IF 3.6 2区生物学

PLoS Computational Biology Pub Date : 2025-09-29 eCollection Date: 2025-09-01 DOI: 10.1371/journal.pcbi.1013523

Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Jon Pitchford, Joydev Chattopadhyay

{"title":"Coupling plankton and cholera dynamics: Insights into outbreak prediction and practical disease management.","authors":"Biplab Maity, Swarnendu Banerjee, Abhishek Senapati, Jon Pitchford, Joydev Chattopadhyay","doi":"10.1371/journal.pcbi.1013523","DOIUrl":"10.1371/journal.pcbi.1013523","url":null,"abstract":"Despite extensive control efforts over the centuries, cholera remains a globally significant health issue. Seasonal emergence of cholera cases has been reported, particularly in the Bengal delta region, which is often synchronized with plankton blooms. This phenomenon has been widely attributed to the commensal interaction between Vibrio cholerae and zooplankton in aquatic environments. The role of plankton dynamics in cholera epidemiology has been acknowledged but remains poorly understood, and consequently, its importance in effective policymaking is largely overlooked. To this end, we propose and analyze a novel compartment-based transmission model that integrates phytoplankton-zooplankton interactions into a human-bacteria cholera framework. Our study shows that, beyond the reproduction number, the relative contribution of bacterial versus zooplankton-mediated transmission plays a crucial role in shaping epidemic progression and severity. In presence of zooplankton-mediated transmission, an outbreak with a delayed and lower peak may still result in a larger overall outbreak size. Additionally, contrary to common intuition, even for a large and early outbreak, the epidemic overshoot may intensify due to the maintenance of lower-level infections during the post-peak phase. Furthermore, our analysis reveals that the timing of filtration-like interventions can be strategically guided by ecological indicators, such as phytoplankton blooms. Our study underscores the importance of incorporating ecological aspects in epidemiological research to better predict and manage disease outbreaks.","PeriodicalId":20241,"journal":{"name":"PLoS Computational Biology","volume":"21 9","pages":"e1013523"},"PeriodicalIF":3.6,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12507262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145192488","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