网络、生物学与系统工程：炎症方面的一个案例研究
NETWORKS, BIOLOGY AND SYSTEMS ENGINEERING: A CASE STUDY IN INFLAMMATION.
作者信息
Foteinou P T, Yang E, Androulakis I P
机构信息
Biomedical Engineering Department, Rutgers University, 599 Taylor Road Piscataway, NJ 08854.
出版信息
Comput Chem Eng. 2009 Dec 10;33(12):2028-2041. doi: 10.1016/j.compchemeng.2009.06.027.
Abstract
Biological systems can be modeled as networks of interacting components across multiple scales. A central problem in computational systems biology is to identify those critical components and the rules that define their interactions and give rise to the emergent behavior of a host response. In this paper we will discuss two fundamental problems related to the construction of transcription factor networks and the identification of networks of functional modules describing disease progression. We focus on inflammation as a key physiological response of clinical and translational importance.
摘要
生物系统可以被建模为跨多个尺度相互作用的组件网络。计算系统生物学中的一个核心问题是识别那些关键组件以及定义它们相互作用并引发宿主反应的涌现行为的规则。在本文中，我们将讨论与转录因子网络构建以及描述疾病进展的功能模块网络识别相关的两个基本问题。我们将重点关注炎症这一具有临床和转化重要性的关键生理反应。
相似文献
1
NETWORKS, BIOLOGY AND SYSTEMS ENGINEERING: A CASE STUDY IN INFLAMMATION.网络、生物学与系统工程：炎症方面的一个案例研究
Comput Chem Eng. 2009 Dec 10;33(12):2028-2041. doi: 10.1016/j.compchemeng.2009.06.027.
2
A structural approach for finding functional modules from large biological networks.一种从大型生物网络中寻找功能模块的结构化方法。
BMC Bioinformatics. 2008 Aug 12;9 Suppl 9(Suppl 9):S19. doi: 10.1186/1471-2105-9-S9-S19.
3
Pattern Discovery in Multilayer Networks.多层网络中的模式发现。
IEEE/ACM Trans Comput Biol Bioinform. 2022 Mar-Apr;19(2):741-752. doi: 10.1109/TCBB.2021.3105001. Epub 2022 Apr 1.
4
Emergence of dynamic properties in network hypermotifs.网络超模体中动态特性的涌现。
Proc Natl Acad Sci U S A. 2022 Aug 9;119(32):e2204967119. doi: 10.1073/pnas.2204967119. Epub 2022 Aug 1.
6
Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).大分子拥挤现象：化学与物理邂逅生物学（瑞士阿斯科纳，2012年6月10日至14日）
Phys Biol. 2013 Aug;10(4):040301. doi: 10.1088/1478-3975/10/4/040301. Epub 2013 Aug 2.
7
Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers.利用系统生物学破译宿主-病原体相互作用网络和预测生物标志物。
Clin Microbiol Infect. 2016 Jul;22(7):600-6. doi: 10.1016/j.cmi.2016.04.014. Epub 2016 Apr 22.
8
A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics.健康与疾病中的系统生物学概念综述：从生物网络到现代治疗学
Syst Synth Biol. 2014 Mar;8(1):99-116. doi: 10.1007/s11693-013-9125-3. Epub 2013 Sep 18.
9
Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science.发育工程：基于细胞产品设计和制造的新模式。第二部分：从基因到网络：从系统生物学和网络科学角度看组织工程。
Tissue Eng Part B Rev. 2009 Dec;15(4):395-422. doi: 10.1089/ten.TEB.2009.0461.
10
Arabidopsis thaliana as a model organism in systems biology.拟南芥作为系统生物学的模式生物。
Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):372-379. doi: 10.1002/wsbm.25.
引用本文的文献
1
Dynamical modeling of pro- and anti-inflammatory cytokines in the early stage of septic shock.脓毒性休克早期促炎和抗炎细胞因子的动力学建模
In Silico Biol. 2020;14(1-2):101-121. doi: 10.3233/ISB-200474.
2
On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.论复杂生物供应链分析：从过程系统工程到定量系统药理学
Comput Chem Eng. 2017 Dec 5;107:100-110. doi: 10.1016/j.compchemeng.2017.06.003. Epub 2017 Jun 3.
3
Computational modelling of the inflammatory response in trauma, sepsis and wound healing: implications for modelling resilience.创伤、脓毒症和伤口愈合中炎症反应的计算建模：对建模弹性的影响。
Interface Focus. 2014 Oct 6;4(5):20140004. doi: 10.1098/rsfs.2014.0004.
4
A Systems Engineering Perspective on Homeostasis and Disease.从系统工程角度看体内平衡与疾病
Front Bioeng Biotechnol. 2013 Sep 9;1:6. doi: 10.3389/fbioe.2013.00006. eCollection 2013.
5
Global sensitivity analysis of a mathematical model of acute inflammation identifies nonlinear dependence of cumulative tissue damage on host interleukin-6 responses.急性炎症数学模型的全局敏感性分析确定了累积组织损伤对宿主白细胞介素-6反应的非线性依赖性。
J Theor Biol. 2014 Oct 7;358:132-48. doi: 10.1016/j.jtbi.2014.05.036. Epub 2014 Jun 5.
6
A Biohybrid Device for the Systemic Control of Acute Inflammation.一种用于急性炎症全身控制的生物杂交装置。
Disrupt Sci Technol. 2012 May 14;1(1). doi: 10.1089/dst.2012.0001.
7
Sepsis: from pattern to mechanism and back.脓毒症：从模式到机制，再回归模式
Crit Rev Biomed Eng. 2012;40(4):341-51. doi: 10.1615/critrevbiomedeng.v40.i4.80.
8
A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes.砷(III)在肝细胞中的半机械论整合毒代动力学-毒效动力学（TK/TD）模型。
J Theor Biol. 2013 Jan 21;317:244-56. doi: 10.1016/j.jtbi.2012.09.019. Epub 2012 Oct 12.
本文引用的文献
1
Translational potential of systems-based models of inflammation.基于系统的炎症模型的转化潜力。
Clin Transl Sci. 2009 Feb;2(1):85-9. doi: 10.1111/j.1752-8062.2008.00051.x.
2
Reverse-engineering transcription control networks.转录调控网络的反向工程。
Phys Life Rev. 2005 Mar;2(1):65-88. doi: 10.1016/j.plrev.2005.01.001.
3
Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm.使用线性时间二分聚类算法识别时间序列基因表达数据中的调控模块。
IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):153-65. doi: 10.1109/TCBB.2008.34.
4
In silico simulation of corticosteroids effect on an NFkB- dependent physicochemical model of systemic inflammation.皮质类固醇对系统性炎症的NFkB依赖性物理化学模型影响的计算机模拟
PLoS One. 2009;4(3):e4706. doi: 10.1371/journal.pone.0004706. Epub 2009 Mar 10.
5
Transcription factor network reconstruction using the living cell array.利用活细胞阵列进行转录因子网络重建。
J Theor Biol. 2009 Feb 7;256(3):393-407. doi: 10.1016/j.jtbi.2008.09.040. Epub 2008 Oct 22.
6
Modeling endotoxin-induced systemic inflammation using an indirect response approach.使用间接反应方法模拟内毒素诱导的全身炎症。
Math Biosci. 2009 Jan;217(1):27-42. doi: 10.1016/j.mbs.2008.09.003. Epub 2008 Sep 20.
7
Mechanistic simulations of inflammation: current state and future prospects.炎症的机制模拟：现状与未来展望
Math Biosci. 2009 Jan;217(1):1-10. doi: 10.1016/j.mbs.2008.07.013. Epub 2008 Aug 26.
8
Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation.用于急性炎症动态知识表示的基于智能体的多尺度模块化架构介绍。
Theor Biol Med Model. 2008 May 27;5:11. doi: 10.1186/1742-4682-5-11.
9
Translational systems biology of inflammation.炎症的转化系统生物学
PLoS Comput Biol. 2008 Apr 25;4(4):e1000014. doi: 10.1371/journal.pcbi.1000014.
10
Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient.转化系统生物学：将工程学方法引入烧伤患者的病理生理学研究
J Burn Care Res. 2008 Mar-Apr;29(2):277-85. doi: 10.1097/BCR.0b013e31816677c8.
Zotero 插件