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Computational modeling of single-cell mechanics and cytoskeletal mechanobiology. 单细胞力学和细胞骨架力学生物学的计算建模。
IF 7.9 Q1 Medicine Pub Date : 2018-03-01 Epub Date: 2017-11-30 DOI: 10.1002/wsbm.1407
Vijay Rajagopal, William R Holmes, Peter Vee Sin Lee

Cellular cytoskeletal mechanics plays a major role in many aspects of human health from organ development to wound healing, tissue homeostasis and cancer metastasis. We summarize the state-of-the-art techniques for mathematically modeling cellular stiffness and mechanics and the cytoskeletal components and factors that regulate them. We highlight key experiments that have assisted model parameterization and compare the advantages of different models that have been used to recapitulate these experiments. An overview of feed-forward mechanisms from signaling to cytoskeleton remodeling is provided, followed by a discussion of the rapidly growing niche of encapsulating feedback mechanisms from cytoskeletal and cell mechanics to signaling. We discuss broad areas of advancement that could accelerate research and understanding of cellular mechanobiology. A precise understanding of the molecular mechanisms that affect cell and tissue mechanics and function will underpin innovations in medical device technologies of the future. WIREs Syst Biol Med 2018, 10:e1407. doi: 10.1002/wsbm.1407 This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Cellular Models.

从器官发育到伤口愈合、组织稳态和癌症转移,细胞细胞骨架力学在人类健康的许多方面都发挥着重要作用。我们总结了对细胞硬度和力学以及细胞骨架成分和调控因素进行数学建模的最新技术。我们重点介绍了有助于模型参数化的关键实验,并比较了用于重现这些实验的不同模型的优势。我们概述了从信号传导到细胞骨架重塑的前馈机制,随后讨论了从细胞骨架和细胞力学到信号传导的反馈机制这一迅速发展的利基领域。我们讨论了可加速研究和理解细胞机械生物学的广泛进展领域。对影响细胞和组织力学与功能的分子机制的准确理解将成为未来医疗设备技术创新的基础。WIREs Syst Biol Med 2018, 10:e1407. doi: 10.1002/wsbm.1407 This article is categorized under:系统属性和过程模型 > 机制模型 生理学 > 健康和疾病中的哺乳动物生理学 系统属性和过程模型 > 细胞模型。
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引用次数: 0
Dynamic enhancer function in the chromatin context. 染色质中的动态增强子功能。
IF 7.9 Q1 Medicine Pub Date : 2018-01-01 Epub Date: 2017-05-22 DOI: 10.1002/wsbm.1390
Ido Goldstein, Gordon L Hager

Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding. More recently, fluorescent microscopy techniques, including fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single molecule tracking (SMT), reveal a highly dynamic binding behavior for these factors in live cells. Furthermore, a refined analysis of genomic footprinting suggests that many transcription factors leave minimal or no footprints in chromatin, even when present and active in a given cell type. In this study, we review the implications of these new approaches for an accurate understanding of enhancer function in real time. In vivo SMT, in particular, has recently evolved as a promising methodology to probe enhancer function in live cells. Integration of findings from the many approaches now employed in the study of enhancer function suggest a highly dynamic view for the action of enhancer activating factors, viewed on a time scale of milliseconds to seconds, rather than minutes to hours. WIREs Syst Biol Med 2018, 10:e1390. doi: 10.1002/wsbm.1390 This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Imaging.

增强子在高等真核细胞中起着关键的调节元件的作用。增强子功能的表征主要来自全基因组方法,包括染色质免疫沉淀(ChIP-seq)、DNA酶-I超敏反应(DNA酶-seq)、数字基因组足迹(DGF)和染色体构象捕获技术(3C、4C和Hi-C)。这些基于群体的测定平均了数百万细胞的信号,并产生了以静态和顺序结合为特征的增强子模型。最近,荧光显微镜技术,包括光漂白后的荧光回收、荧光相关光谱和单分子跟踪(SMT),揭示了这些因子在活细胞中的高度动态结合行为。此外,对基因组足迹的精细分析表明,即使在给定的细胞类型中存在并具有活性,许多转录因子也会在染色质中留下最小或没有足迹。在这项研究中,我们回顾了这些新方法对实时准确理解增强子功能的影响。特别是体内SMT,最近已经发展成为一种很有前途的方法来探测活细胞中的增强子功能。整合目前用于研究增强子功能的许多方法的发现,表明增强子激活因子的作用具有高度动态性,从毫秒到秒的时间尺度来看,而不是从分钟到小时。WIREs Syst Biol Med 2018,10:e1390。doi:10.1002/wsbm.1390本文分类在:分析和计算方法>计算方法实验室方法和技术>遗传/基因组方法实验室方法与技术>成像。
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引用次数: 20
Targeting epidermal growth factor receptor co-dependent signaling pathways in glioblastoma. 靶向胶质母细胞瘤中表皮生长因子受体共同依赖的信号通路。
IF 7.9 Q1 Medicine Pub Date : 2018-01-01 Epub Date: 2017-09-11 DOI: 10.1002/wsbm.1398
Feng Liu, Paul S Mischel

The epidermal growth factor receptor (EGFR) is a transmembrane receptor tyrosine kinase (RTK) that is critical for normal development and function. EGFR is also amplified or mutated in a variety of cancers including in nearly 60% of cases of the highly lethal brain cancer glioblastoma (GBM). EGFR amplification and mutation reprogram cellular metabolism and broadly alter gene transcription to drive tumor formation and progression, rendering EGFR as a compelling drug target. To date, brain tumor patients have yet to benefit from anti-EGFR therapy due in part to an inability to achieve sufficient intratumoral drug levels in the brain, cultivating adaptive mechanisms of resistance. Here, we review an alternative set of strategies for targeting EGFR-amplified GBMs, based on identifying and targeting tumor co-dependencies shaped both by aberrant EGFR signaling and the brain's unique biochemical environment. These approaches may include highly brain-penetrant drugs from non-cancer pipelines, expanding the pharmacopeia and providing promising new treatments. We review the molecular underpinnings of EGFR-activated co-dependencies in the brain and the promising new treatments based on this strategy. WIREs Syst Biol Med 2018, 10:e1398. doi: 10.1002/wsbm.1398 This article is categorized under: Biological Mechanisms > Cell Signaling Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine.

表皮生长因子受体(EGFR)是一种跨膜受体酪氨酸激酶(RTK),对正常发育和功能至关重要。EGFR在多种癌症中也会扩增或突变,包括近60%的高致死率脑癌胶质母细胞瘤(GBM)病例。EGFR扩增和突变重编程细胞代谢,广泛改变基因转录,驱动肿瘤的形成和进展,使EGFR成为一个引人注目的药物靶点。迄今为止,脑肿瘤患者尚未从抗egfr治疗中获益,部分原因是无法在大脑中达到足够的肿瘤内药物水平,从而培养耐药性的适应性机制。在这里,我们回顾了一组靶向EGFR扩增GBMs的替代策略,基于识别和靶向由异常EGFR信号和大脑独特生化环境形成的肿瘤共依赖性。这些方法可能包括来自非癌症管道的高脑渗透药物,扩大药典并提供有希望的新治疗方法。我们回顾了egfr在大脑中激活的共依赖性的分子基础以及基于这一策略的有希望的新治疗方法。中国生物医学工程学报,2018,32(1):444 - 444。doi: 10.1002 / wsbm.1398本文分类如下:生物机制>细胞信号实验室方法和技术>遗传/基因组方法转化、基因组和系统医学>转化医学。
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引用次数: 18
Metabolic interactions in cancer: cellular metabolism at the interface between the microenvironment, the cancer cell phenotype and the epigenetic landscape. 癌症中的代谢相互作用:微环境、癌细胞表型和表观遗传景观之间的细胞代谢界面。
IF 7.9 Q1 Medicine Pub Date : 2018-01-01 Epub Date: 2017-08-30 DOI: 10.1002/wsbm.1397
Gianmarco Rinaldi, Matteo Rossi, Sarah-Maria Fendt

Metabolism is tied into complex interactions with cell intrinsic and extrinsic processes that go beyond the conversion of nutrients into energy and biomass. Indeed, metabolism is a central cellular hub that interconnects and influences the microenvironment, the cellular phenotype, cell signaling, and the (epi)genetic landscape. While these interactions evolved to support survival and function of normal cells, they are hijacked by cancer cells to enable cancer maintenance and progression. Thus, a mechanistic and functional understanding of complex metabolic interactions provides a basis for the discovery of novel metabolic vulnerabilities in cancer. In this review, we will summarize and provide context for the to-date discovered complex metabolic interactions by discussing how the microenvironment as well as the cellular phenotype define cancer metabolism, and how metabolism shapes the epigenetic state of cancer cells. Many of the studies investigating the crosstalk of metabolism with cell intrinsic and extrinsic processes have used integrative data analysis approaches at the interface between computational and experimental cancer research, and we will highlight those throughout the review. In conclusion, identifying and understanding complex metabolic interactions is a basis for deciphering novel metabolic vulnerabilities of cancer cells. WIREs Syst Biol Med 2018, 10:e1397. doi: 10.1002/wsbm.1397 This article is categorized under: Biological Mechanisms > Metabolism Physiology > Mammalian Physiology in Health and Disease.

新陈代谢与细胞内在和外在过程的复杂相互作用有关,这些过程超出了将营养物质转化为能量和生物量的范围。事实上,代谢是一个中心细胞枢纽,它相互连接并影响微环境、细胞表型、细胞信号传导和(epi)遗传景观。虽然这些相互作用的进化是为了支持正常细胞的生存和功能,但它们被癌细胞劫持,使癌症得以维持和发展。因此,对复杂代谢相互作用的机制和功能的理解为发现癌症中新的代谢脆弱性提供了基础。在这篇综述中,我们将通过讨论微环境和细胞表型如何定义癌症代谢,以及代谢如何塑造癌细胞的表观遗传状态,来总结和提供迄今为止发现的复杂代谢相互作用的背景。许多研究研究了细胞内在和外在代谢过程的串扰,在计算和实验癌症研究的界面上使用了综合数据分析方法,我们将在整个综述中强调这些方法。总之,识别和理解复杂的代谢相互作用是破译癌细胞新代谢脆弱性的基础。中国生物医学工程学报,2018,32(1):444 - 444。doi: 10.1002 / wsbm.1397本文分类为:生物机制>代谢生理学>健康与疾病中的哺乳动物生理学。
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引用次数: 50
Stability analysis in spatial modeling of cell signaling. 细胞信号空间建模中的稳定性分析。
IF 7.9 Q1 Medicine Pub Date : 2018-01-01 Epub Date: 2017-08-08 DOI: 10.1002/wsbm.1395
Michael C Getz, Jasmine A Nirody, Padmini Rangamani

Advances in high-resolution microscopy and other techniques have emphasized the spatio-temporal nature of information transfer through signal transduction pathways. The compartmentalization of signaling molecules and the existence of microdomains are now widely acknowledged as key features in biochemical signaling. To complement experimental observations of spatio-temporal dynamics, mathematical modeling has emerged as a powerful tool. Using modeling, one can not only recapitulate experimentally observed dynamics of signaling molecules, but also gain an understanding of the underlying mechanisms in order to generate experimentally testable predictions. Reaction-diffusion systems are commonly used to this end; however, the analysis of coupled nonlinear systems of partial differential equations, generated by considering large reaction networks is often challenging. Here, we aim to provide an introductory tutorial for the application of reaction-diffusion models to the spatio-temporal dynamics of signaling pathways. In particular, we outline the steps for stability analysis of such models, with a focus on biochemical signal transduction. WIREs Syst Biol Med 2018, 10:e1395. doi: 10.1002/wsbm.1395 This article is categorized under: Biological Mechanisms > Cell Signaling Analytical and Computational Methods > Dynamical Methods Models of Systems Properties and Processes > Mechanistic Models.

高分辨率显微镜和其他技术的进步强调了通过信号转导途径传递信息的时空性质。信号分子的区隔化和微结构域的存在被广泛认为是生物化学信号传导的关键特征。为了补充时空动力学的实验观察,数学建模已经成为一种强大的工具。利用建模,人们不仅可以概括实验观察到的信号分子动力学,而且还可以了解潜在的机制,以便产生实验可测试的预测。反应-扩散系统通常用于此目的;然而,考虑大型反应网络产生的耦合非线性偏微分方程组的分析往往具有挑战性。在这里,我们的目的是为反应扩散模型在信号通路时空动力学中的应用提供一个入门教程。特别是,我们概述了这些模型的稳定性分析的步骤,重点是生化信号转导。中国生物医学工程学报,2018,32(1):444 - 444。doi: 10.1002 / wsbm.1395本文分类为:生物学机制>细胞信号传导分析与计算方法>系统特性与过程的动力学方法模型>机制模型。
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引用次数: 7
Crosstalk between transcription and metabolism: how much enzyme is enough for a cell? 转录和代谢之间的串扰:一个细胞需要多少酶?
IF 7.9 Q1 Medicine Pub Date : 2018-01-01 Epub Date: 2017-08-15 DOI: 10.1002/wsbm.1396
Stefano Donati, Timur Sander, Hannes Link

Cells employ various mechanisms for dynamic control of enzyme expression. An important mechanism is mutual feedback-or crosstalk-between transcription and metabolism. As recently suggested, enzyme levels are often much higher than absolutely needed to maintain metabolic flux. However, given the potential burden of high enzyme levels it seems likely that cells control enzyme expression to meet other cellular objectives. In this review, we discuss whether crosstalk between metabolism and transcription could inform cells about how much enzyme is optimal for various fitness aspects. Two major problems should be addressed in order to understand optimization of enzyme levels by crosstalk. First, mapping of metabolite-protein interactions will be crucial to obtain a better mechanistic understanding of crosstalk. Second, investigating cellular objectives that define optimal enzyme levels can reveal the functional relevance of crosstalk. We present recent studies that approach these problems, drawing from experimental transcript and metabolite data, and from theoretical network analyses. WIREs Syst Biol Med 2018, 10:e1396. doi: 10.1002/wsbm.1396 This article is categorized under: Biological Mechanisms > Metabolism Laboratory Methods and Technologies > Metabolomics Biological Mechanisms > Regulatory Biology.

细胞采用各种机制来动态控制酶的表达。一个重要的机制是转录和代谢之间的相互反馈或串扰。正如最近提出的那样,酶的水平往往远远高于维持代谢通量的绝对需要。然而,考虑到高酶水平的潜在负担,细胞控制酶表达以满足其他细胞目标似乎是可能的。在这篇综述中,我们讨论了代谢和转录之间的串扰是否可以告诉细胞多少酶对各种适应性方面是最佳的。为了理解通过串声优化酶水平,应该解决两个主要问题。首先,代谢物-蛋白质相互作用的图谱对于获得对串扰更好的机制理解至关重要。其次,研究确定最佳酶水平的细胞目标可以揭示串扰的功能相关性。我们提出了最近的研究接近这些问题,从实验转录和代谢物数据,并从理论网络分析。中国生物医学工程学报,2018,32(1):444 - 444。doi: 10.1002 / wsbm.1396本文分类如下:生物学机制>代谢实验室方法与技术>代谢组学生物学机制>调节生物学。
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引用次数: 29
Immunity to CRISPR Cas9 and Cas12a therapeutics. 对CRISPR Cas9和Cas12a疗法的免疫。
IF 7.9 Q1 Medicine Pub Date : 2018-01-01 Epub Date: 2017-10-30 DOI: 10.1002/wsbm.1408
Wei Leong Chew

Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself. These host defenses include inflammation via activation of innate immunity, antibody induction in humoral immunity, and cell death by T-cell-mediated cytotoxicity. If left unchecked, these immunological reactions can curtail therapeutic benefits and potentially lead to mortality. Ways to assay and reduce the immunogenicity of Cas9 and Cas12a proteins are therefore critical for ensuring patient safety and treatment efficacy, and for bringing us closer to realizing the vision of permanent genetic cures. WIREs Syst Biol Med 2018, 10:e1408. doi: 10.1002/wsbm.1408 This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine Translational, Genomic, and Systems Medicine > Therapeutic Methods.

基因组编辑疗法有望治疗人类疾病。随着最有前景的 CRISPR-Cas9 和 CRISPR-Cas12a (Cpf1) 模式进入临床试验阶段,向人类患者施用这些外来生物分子的相关风险日益突出。CRISPR-Cas9和CRISPR-Cas12a系统的临床前发现和基础基因治疗研究表明,宿主免疫系统会对施用的蛋白质和核酸、基因编辑细胞以及宿主本身产生不良反应。这些宿主防御措施包括通过激活先天性免疫引起的炎症、体液免疫中的抗体诱导以及 T 细胞介导的细胞毒性造成的细胞死亡。如果任其发展,这些免疫反应会影响治疗效果,并可能导致死亡。因此,检测和降低 Cas9 和 Cas12a 蛋白免疫原性的方法对于确保患者安全和治疗效果,以及让我们更接近实现永久性基因治疗的愿景至关重要。WIREs Syst Biol Med 2018, 10:e1408. doi: 10.1002/wsbm.1408 本文归类于:实验室方法和技术 > 基因/基因组方法 转化、基因组和系统医学 > 转化医学 转化、基因组和系统医学 > 治疗方法。
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引用次数: 97
Image-based computational fluid dynamics in the lung: virtual reality or new clinical practice? 基于图像的肺计算流体动力学:虚拟现实还是新的临床实践?
IF 7.9 Q1 Medicine Pub Date : 2017-11-01 Epub Date: 2017-06-13 DOI: 10.1002/wsbm.1392
Kelly S Burrowes, Jan De Backer, Haribalan Kumar

The development and implementation of personalized medicine is paramount to improving the efficiency and efficacy of patient care. In the respiratory system, function is largely dictated by the choreographed movement of air and blood to the gas exchange surface. The passage of air begins in the upper airways, either via the mouth or nose, and terminates at the alveolar interface, while blood flows from the heart to the alveoli and back again. Computational fluid dynamics (CFD) is a well-established tool for predicting fluid flows and pressure distributions within complex systems. Traditionally CFD has been used to aid in the effective or improved design of a system or device; however, it has become increasingly exploited in biological and medical-based applications further broadening the scope of this computational technique. In this review, we discuss the advancement in application of CFD to the respiratory system and the contributions CFD is currently making toward improving precision medicine. The key areas CFD has been applied to in the pulmonary system are in predicting fluid transport and aerosol distribution within the airways. Here we focus our discussion on fluid flows and in particular on image-based clinically focused CFD in the ventilatory system. We discuss studies spanning from the paranasal sinuses through the conducting airways down to the level of the alveolar airways. The combination of imaging and CFD is enabling improved device design in aerosol transport, improved biomarkers of lung function in clinical trials, and improved predictions and assessment of surgical interventions in the nasal sinuses. WIREs Syst Biol Med 2017, 9:e1392. doi: 10.1002/wsbm.1392 For further resources related to this article, please visit the WIREs website.

个性化医疗的发展和实施对于提高患者护理的效率和疗效至关重要。在呼吸系统中,功能很大程度上是由空气和血液到气体交换表面的精心设计的运动决定的。空气通过口或鼻从上呼吸道开始,并在肺泡界面终止,同时血液从心脏流到肺泡,然后再流回来。计算流体动力学(CFD)是一种成熟的预测复杂系统内流体流动和压力分布的工具。传统上,CFD一直用于帮助有效或改进系统或设备的设计;然而,它越来越多地应用于基于生物和医学的应用,进一步扩大了这种计算技术的范围。本文综述了CFD在呼吸系统中的应用进展,以及CFD在改善精准医疗方面的贡献。CFD在肺系统中应用的关键领域是预测气道内的流体输送和气溶胶分布。在这里,我们集中讨论流体流动,特别是基于图像的临床聚焦CFD在通气系统。我们讨论的研究跨越从鼻窦通过传导气道到肺泡气道的水平。成像和CFD的结合可以改善气溶胶运输的设备设计,改善临床试验中肺功能的生物标志物,并改善鼻窦手术干预的预测和评估。中国生物医学工程学报,2017,39(9):1392 - 1392。doi: 10.1002 / wsbm.1392有关与本文相关的更多资源,请访问WIREs网站。
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引用次数: 20
Genome-scale metabolic models applied to human health and disease. 应用于人类健康和疾病的基因组尺度代谢模型。
IF 7.9 Q1 Medicine Pub Date : 2017-11-01 Epub Date: 2017-06-23 DOI: 10.1002/wsbm.1393
Daniel J Cook, Jens Nielsen

Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner. Several approaches that researchers are taking to address these challenges include using proteomic and transcriptomic-informed methods to build GEMs for individual organs, diseases, and patients and using constraints on model behavior during simulation to match observed metabolic fluxes. We review the challenges facing researchers in the use of GEMs, review the approaches used to address these challenges, and describe advances that are on the horizon and could lead to a better understanding of human metabolism. WIREs Syst Biol Med 2017, 9:e1393. doi: 10.1002/wsbm.1393 For further resources related to this article, please visit the WIREs website.

基因组测序、基因和蛋白质表达水平的高通量测量、数据可及性和计算能力的进步使得基因组尺度代谢模型(GEMs)成为了解与许多不同疾病相关的代谢改变的有用工具。尽管GEMs的效用已得到证实,但研究人员在使用GEMs、将其应用于人类健康和疾病、以器官特异性和疾病特异性方式构建和模拟GEMs方面面临着多重挑战。研究人员正在采取的几种方法来应对这些挑战,包括使用蛋白质组学和转录组学的方法来为单个器官、疾病和患者构建GEMs,以及在模拟过程中使用模型行为约束来匹配观察到的代谢通量。我们回顾了研究人员在使用GEMs时面临的挑战,回顾了用于解决这些挑战的方法,并描述了即将出现的进展,这些进展可能会导致对人类代谢的更好理解。中国生物医学工程学报,2017,29(4):393 - 393。doi: 10.1002 / wsbm.1393有关与本文相关的更多资源,请访问WIREs网站。
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引用次数: 31
The best models of metabolism. 最好的新陈代谢模型。
IF 7.9 Q1 Medicine Pub Date : 2017-11-01 Epub Date: 2017-05-19 DOI: 10.1002/wsbm.1391
Eberhard O Voit

Biochemical systems are among of the oldest application areas of mathematical modeling. Spanning a time period of over one hundred years, the repertoire of options for structuring a model and for formulating reactions has been constantly growing, and yet, it is still unclear whether or to what degree some models are better than others and how the modeler is to choose among them. In fact, the variety of options has become overwhelming and difficult to maneuver for novices and experts alike. This review outlines the metabolic model design process and discusses the numerous choices for modeling frameworks and mathematical representations. It tries to be inclusive, even though it cannot be complete, and introduces the various modeling options in a manner that is as unbiased as that is feasible. However, the review does end with personal recommendations for the choices of default models. WIREs Syst Biol Med 2017, 9:e1391. doi: 10.1002/wsbm.1391 For further resources related to this article, please visit the WIREs website.

生化系统是数学建模最古老的应用领域之一。跨越一百多年的时间,构建模型和形成反应的选项库一直在不断增长,然而,仍然不清楚某些模型是否或在何种程度上比其他模型更好,以及建模者如何在它们之间进行选择。事实上,对于新手和专家来说,各种各样的选择已经变得势不可挡,难以驾驭。这篇综述概述了代谢模型的设计过程,并讨论了建模框架和数学表示的众多选择。尽管它不可能是完整的,但它试图具有包容性,并以一种尽可能公正可行的方式介绍了各种建模选项。然而,审查结束时,对默认模型的选择提出了个人建议。中国生物医学工程杂志,2017,29(4):391 - 391。doi: 10.1002 / wsbm.1391有关与本文相关的更多资源,请访问WIREs网站。
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引用次数: 38
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