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Current Opinion in Systems Biology最新文献

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ODE-based models of signaling networks in autophagy 基于 ODE 的自噬信号网络模型
IF 3.4
Current Opinion in Systems Biology Pub Date : 2024-12-01 Epub Date: 2024-05-31 DOI: 10.1016/j.coisb.2024.100519
Markus Galhuber , Kathrin Thedieck
{"title":"ODE-based models of signaling networks in autophagy","authors":"Markus Galhuber ,&nbsp;Kathrin Thedieck","doi":"10.1016/j.coisb.2024.100519","DOIUrl":"https://doi.org/10.1016/j.coisb.2024.100519","url":null,"abstract":"<div><p>Aberrant metabolism and nutrient processing are hallmarks of cancer. Autophagy is a catabolic process, clearing macromolecules and providing metabolite intermediates for anabolism. Autophagy safeguards healthy cells from tumorigenesis while mobilizing metabolites promoting tumor growth. Autophagy is controlled by the mTOR signaling network in conjunction with AMPK and ULK1. This kinase triad features highly intertwined feedback and feedforward mechanisms, complicating predictions on nutrient and drug response. ODE-based models offer a deterministic approach frequently used for the exploration of signaling dynamics. Recent ODE models of the mTOR-AMPK-ULK1 network revealed non-linear behaviors, bistable switches, and oscillatory patterns, shedding light on the robustness and adaptability of autophagy control. We highlight emerging perspectives on AMPK in mTORC1-ULK1 crosstalk and mechanisms for integration into future models.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"39 ","pages":"Article 100519"},"PeriodicalIF":3.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000155/pdfft?md5=532f93bc6d4222d42ab440c05bdddad3&pid=1-s2.0-S2452310024000155-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141594007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial Board Page 编委会页面
IF 3.4
Current Opinion in Systems Biology Pub Date : 2024-12-01 Epub Date: 2024-12-02 DOI: 10.1016/S2452-3100(24)00031-3
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(24)00031-3","DOIUrl":"10.1016/S2452-3100(24)00031-3","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"39 ","pages":"Article 100535"},"PeriodicalIF":3.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142759043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Large-scale knowledge graph representations of disease processes 疾病过程的大规模知识图谱表示
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-06-01 Epub Date: 2024-04-30 DOI: 10.1016/j.coisb.2024.100517
Matti Hoch , Shailendra Gupta , Olaf Wolkenhauer
{"title":"Large-scale knowledge graph representations of disease processes","authors":"Matti Hoch ,&nbsp;Shailendra Gupta ,&nbsp;Olaf Wolkenhauer","doi":"10.1016/j.coisb.2024.100517","DOIUrl":"https://doi.org/10.1016/j.coisb.2024.100517","url":null,"abstract":"<div><p>Today, a wide range of technologies and data types are available when studying disease-relevant processes. Therefore, a major challenge is integrating data from different technologies covering different levels of functional cellular organization. This motivates approaches that start with a bird's-eye perspective, initially considering as many molecules, cell types, and cellular functions as possible. Knowledge graphs (KGs) provide such a perspective through graphically structured representations of the functional connections between biological entities. However, linking KGs of disease processes with experimental or clinical data requires their curation in a large-scale, multi-level layout. The resulting heterogeneity leads to new challenges in KG curation, data integration, and analysis. Existing approaches for small-scale applications must be adapted or combined into multi-scale tools to analyze multi-omics data in KGs. This short review reflects upon the large-scale KG approach to studying disease processes. We do not review all modeling approaches but focus on a personal perspective on.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"38 ","pages":"Article 100517"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000131/pdfft?md5=612c0970fb95e722075e70945bafea7f&pid=1-s2.0-S2452310024000131-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140817028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial Board Page 编辑委员会页面
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-06-01 Epub Date: 2024-06-06 DOI: 10.1016/S2452-3100(24)00022-2
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(24)00022-2","DOIUrl":"https://doi.org/10.1016/S2452-3100(24)00022-2","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"38 ","pages":"Article 100526"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000222/pdfft?md5=716e77e36be5ebe62ada61f5a261ff2e&pid=1-s2.0-S2452310024000222-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141264011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational systems biology of cellular processes in the human lymph node 人体淋巴结细胞过程的计算系统生物学
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-06-01 Epub Date: 2024-05-07 DOI: 10.1016/j.coisb.2024.100518
Sonja Scharf , Jörg Ackermann , Patrick Wurzel , Martin-Leo Hansmann , Ina Koch
{"title":"Computational systems biology of cellular processes in the human lymph node","authors":"Sonja Scharf ,&nbsp;Jörg Ackermann ,&nbsp;Patrick Wurzel ,&nbsp;Martin-Leo Hansmann ,&nbsp;Ina Koch","doi":"10.1016/j.coisb.2024.100518","DOIUrl":"10.1016/j.coisb.2024.100518","url":null,"abstract":"<div><p>The human immune system is determined by the functionality of the human lymph node. With the use of high-throughput techniques in clinical diagnostics, a large number of data is currently collected. The new data on the spatiotemporal organization of cells offer new possibilities to build a mathematical model of the human lymph node - a <em>virtual lymph node</em>. The virtual lymph node can be applied to simulate drug responses and may be used in clinical diagnosis. Here, we review mathematical models of the human lymph node from the viewpoint of cellular processes. Starting with classical methods, such as systems of differential equations, we discuss the values of different levels of abstraction and methods in the range of artificial intelligence techniques formalism.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"38 ","pages":"Article 100518"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000143/pdfft?md5=66c9fec4f5325a388d754ce533b52cf6&pid=1-s2.0-S2452310024000143-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141031573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enzymes, auxiliaries, and cells for the recycling and upcycling of polyethylene terephthalate 用于聚对苯二甲酸乙二酯（PET）回收和再循环的酶、助剂和细胞
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-06-01 Epub Date: 2024-03-19 DOI: 10.1016/j.coisb.2024.100515
Thanakrit Wongsatit , Thanate Srimora , Cholpisit Kiattisewee , Chayasith Uttamapinant
{"title":"Enzymes, auxiliaries, and cells for the recycling and upcycling of polyethylene terephthalate","authors":"Thanakrit Wongsatit ,&nbsp;Thanate Srimora ,&nbsp;Cholpisit Kiattisewee ,&nbsp;Chayasith Uttamapinant","doi":"10.1016/j.coisb.2024.100515","DOIUrl":"10.1016/j.coisb.2024.100515","url":null,"abstract":"<div><p>Biological recycling and valorization of plastics are promising approaches to solve global plastic waste accumulation. Out of diverse plastic materials, polyethylene terephthalate (PET) is one of the most abundant polymers with rapid development in both biodegradation and product upcycling. In this perspective, we review recent discoveries and engineering of PET-degrading enzymes together with plausible auxiliary pathways, and provide insights on how to construct better parts through systematic bioengineering (metagenome mining, protein design, and directed evolution). Then, we discuss the potential of microbial-based PET degradation and upcycling in either a single host or consortia, as well as bottom-up and top-down methods of microbial consortia engineering using novel synthetic biology tools for enhanced PET circularization.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"38 ","pages":"Article 100515"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140275700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quantitatively mapping immune control during influenza 定量绘制流感期间的免疫控制图
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-06-01 Epub Date: 2024-03-20 DOI: 10.1016/j.coisb.2024.100516
Jordan J.A. Weaver, Amber M. Smith
{"title":"Quantitatively mapping immune control during influenza","authors":"Jordan J.A. Weaver,&nbsp;Amber M. Smith","doi":"10.1016/j.coisb.2024.100516","DOIUrl":"https://doi.org/10.1016/j.coisb.2024.100516","url":null,"abstract":"<div><p>Host immune responses play a pivotal role in defending against influenza viruses. The activation of various immune components, such as interferon, macrophages, and CD8<sup>+</sup> T cells, works to limit viral spread while maintaining lung integrity. Recent mathematical modeling studies have investigated these responses, describing their regulation, efficacy, and movement within the lung. Here, we discuss these studies and their emphasis on identifying nonlinearities and multifaceted roles of different cell phenotypes that could be responsible for spatially heterogeneous infection patterns.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"38 ","pages":"Article 100516"},"PeriodicalIF":3.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S245231002400012X/pdfft?md5=32f7c5e3112251b43a5b24b1786085b1&pid=1-s2.0-S245231002400012X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140543536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthetic interventions in epigenome: Unraveling chromatin's potential for therapeutic applications 表观基因组的合成干预：揭示染色质的治疗应用潜力
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-01-03 DOI: 10.1016/j.coisb.2023.100504
Junyoung Kim , Jonghyun Kim , Minhee Park
{"title":"Synthetic interventions in epigenome: Unraveling chromatin's potential for therapeutic applications","authors":"Junyoung Kim ,&nbsp;Jonghyun Kim ,&nbsp;Minhee Park","doi":"10.1016/j.coisb.2023.100504","DOIUrl":"10.1016/j.coisb.2023.100504","url":null,"abstract":"<div><p>The epigenome, comprising DNA and histone modifications alongside intricate chromatin structures, has emerged as pivotal players in disease development. These factors offer promising opportunities for therapeutic interventions, expanding the avenues traditionally explored within genetic elements. Eukaryotic chromatin exhibits an impressive capacity for computation and information storage, fueled by the dynamic interplay of factors that modify the physicochemical states of chromatin. With its unique attributes, chromatin emerges as a compelling candidate for synthetic intervention and therapeutic reprogramming. In this review, we explore pioneering initiatives aimed at synthetically manipulating the epigenome, a relatively uncharted domain with transformative potential for both diagnostics and treatments.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100504"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310023000616/pdfft?md5=d2fd90b0ed0b99197e5a1965c2be3e3b&pid=1-s2.0-S2452310023000616-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139455078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial Board Page 编辑委员会页面
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-03-15 DOI: 10.1016/S2452-3100(24)00007-6
{"title":"Editorial Board Page","authors":"","doi":"10.1016/S2452-3100(24)00007-6","DOIUrl":"https://doi.org/10.1016/S2452-3100(24)00007-6","url":null,"abstract":"","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100511"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000076/pdfft?md5=dcd349d4abd3cf377c47076cacf2c924&pid=1-s2.0-S2452310024000076-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140138531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Shaping the future of precision oncology: Integrating circadian medicine and mathematical models for personalized cancer treatment 塑造精准肿瘤学的未来：整合昼夜节律医学和数学模型，实现个性化癌症治疗
IF 3.7
Current Opinion in Systems Biology Pub Date : 2024-03-01 Epub Date: 2024-02-29 DOI: 10.1016/j.coisb.2024.100506
Janina Hesse , Nina Nelson , Angela Relógio
{"title":"Shaping the future of precision oncology: Integrating circadian medicine and mathematical models for personalized cancer treatment","authors":"Janina Hesse ,&nbsp;Nina Nelson ,&nbsp;Angela Relógio","doi":"10.1016/j.coisb.2024.100506","DOIUrl":"https://doi.org/10.1016/j.coisb.2024.100506","url":null,"abstract":"<div><p>The growing numbers of cancer cases represent a medical and societal burden worldwide. More than half of all cancer patients are treated with chemotherapy. Yet, chemotherapeutic drugs kill not only cancer cells, but also healthy tissue, causing massive adverse side effects. Recent research on circadian medicine suggests that side-effects can be reduced, and treatment efficacy increased, by considering the biological clock of patients. Integrating circadian profiles of molecular clock markers in personalized mathematical models can simulate individual circadian dynamics of drug uptake, drug action and cellular response to chemotherapy. This requires advanced computational tools that balance prediction quality with overfitting. Personalized mathematical models will eventually lead to an optimal alignment of treatment timing with the inner circadian clock of the patient, reducing side effects, increasing efficacy and enhancing patient well-being.</p></div>","PeriodicalId":37400,"journal":{"name":"Current Opinion in Systems Biology","volume":"37 ","pages":"Article 100506"},"PeriodicalIF":3.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2452310024000027/pdfft?md5=ca1548e10b73e11752c874903a1363a1&pid=1-s2.0-S2452310024000027-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139992381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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