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A cell simulator platform: the cell collective.细胞模拟平台：细胞群体。
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The Cell Collective: toward an open and collaborative approach to systems biology.细胞集体：迈向系统生物学的开放协作方法。
BMC Syst Biol. 2012 Aug 7;6:96. doi: 10.1186/1752-0509-6-96.
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The cell in an era of systems biology.系统生物学时代的细胞
Cell. 2011 Mar 18;144(6):850-4. doi: 10.1016/j.cell.2011.02.045.
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Network news: innovations in 21st century systems biology.网络新闻：21 世纪系统生物学的创新。
Cell. 2011 Mar 18;144(6):844-9. doi: 10.1016/j.cell.2011.03.008.
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BioXyce: an engineering platform for the study of cellular systems.BioXyce：用于细胞系统研究的工程平台。
IET Syst Biol. 2009 Mar;3(2):77-89. doi: 10.1049/iet-syb.2007.0086.
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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.基于约束模型的细胞代谢定量预测：COBRA工具箱
Nat Protoc. 2007;2(3):727-38. doi: 10.1038/nprot.2007.99.
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Computational modeling in systems biology.系统生物学中的计算建模
Methods Mol Biol. 2010;662:97-120. doi: 10.1007/978-1-60761-800-3_5.
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sbv IMPROVER: Modern Approach to Systems Biology.SBV改进者：系统生物学的现代方法。
Methods Mol Biol. 2017;1613:21-29. doi: 10.1007/978-1-4939-7027-8_2.
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Guaranteed error bounds for structured complexity reduction of biochemical networks.生物化学网络结构复杂度降低的有保证误差界。
J Theor Biol. 2012 Jul 7;304:172-82. doi: 10.1016/j.jtbi.2012.04.002. Epub 2012 Apr 9.
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Network-based methods for identifying critical pathways of complex diseases: a survey.基于网络的复杂疾病关键通路识别方法综述
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A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.大规模布尔模型的类风湿关节炎成纤维样滑膜细胞预测药物协同作用在关节炎关节。
NPJ Syst Biol Appl. 2023 Jul 15;9(1):33. doi: 10.1038/s41540-023-00294-5.
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Normalizing Input-Output Relationships of Cancer Networks for Reversion Therapy.正常化癌症网络的输入-输出关系以进行逆转治疗。
Adv Sci (Weinh). 2023 Aug;10(24):e2207322. doi: 10.1002/advs.202207322. Epub 2023 Jun 2.
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The nonlinearity of regulation in biological networks.生物网络调控的非线性。
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A multiscale mechanistic model of human dendritic cells for investigation of immune responses and novel therapeutics discovery.用于研究免疫反应和新型治疗药物发现的人类树突状细胞的多尺度机械模型。
Front Immunol. 2023 Mar 10;14:1112985. doi: 10.3389/fimmu.2023.1112985. eCollection 2023.
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Metabolomics meets systems immunology.代谢组学与系统免疫学相遇。
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RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.运行生物模拟：一个可扩展的网络应用程序，可模拟各种计算建模框架、算法和格式。
Nucleic Acids Res. 2021 Jul 2;49(W1):W597-W602. doi: 10.1093/nar/gkab411.
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A practical guide to mechanistic systems modeling in biology using a logic-based approach.使用基于逻辑的方法对生物学中的机制系统建模的实用指南。
Brief Bioinform. 2021 Jul 20;22(4). doi: 10.1093/bib/bbaa236.
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HIV and Proteomics: What We Have Learned from High Throughput Studies.HIV 和蛋白质组学：高通量研究的启示。
Proteomics Clin Appl. 2021 Jan;15(1):e2000040. doi: 10.1002/prca.202000040. Epub 2020 Oct 14.
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Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.为生物学逻辑模型的编纂和注释设定最佳实践和标准的基础——[BC]2 2019 年 CoLoMoTo/SysMod 研讨会的亮点。
Brief Bioinform. 2021 Mar 22;22(2):1848-1859. doi: 10.1093/bib/bbaa046.
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Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes.通过细胞过程逻辑模型中的决定性力量识别生物学上的关键节点
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本文引用的文献
1
Bio-logic builder: a non-technical tool for building dynamical, qualitative models.生物逻辑构建器：一种构建动态、定性模型的非技术性工具。
PLoS One. 2012;7(10):e46417. doi: 10.1371/journal.pone.0046417. Epub 2012 Oct 17.
2
Dynamics of influenza virus and human host interactions during infection and replication cycle.流感病毒和人类宿主在感染和复制周期中的相互作用动态。
Bull Math Biol. 2013 Jun;75(6):988-1011. doi: 10.1007/s11538-012-9777-2. Epub 2012 Oct 19.
3
The Cell Collective: toward an open and collaborative approach to systems biology.细胞集体：迈向系统生物学的开放协作方法。
BMC Syst Biol. 2012 Aug 7;6:96. doi: 10.1186/1752-0509-6-96.
4
A whole-cell computational model predicts phenotype from genotype.全细胞计算模型从基因型预测表型。
Cell. 2012 Jul 20;150(2):389-401. doi: 10.1016/j.cell.2012.05.044.
5
Emergent decision-making in biological signal transduction networks.生物信号转导网络中的应急决策
Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1913-8. doi: 10.1073/pnas.0705088105. Epub 2008 Feb 4.
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