网络动力学的单项式与盆状圆柱体
MONOMIALS AND BASIN CYLINDERS FOR NETWORK DYNAMICS.
作者信息
Austin Daniel, Dinwoodie Ian H
机构信息
Department of Neurology, Oregon Health & Science University, 3303 SW Bond Ave, MC: CH13B, Portland OR 97239.
Fariborz Maseeh Department of Mathematics and Statistics, 724 SW Harrison St, Portland State University, Portland OR 97201.
出版信息
SIAM J Appl Dyn Syst. 2015;14(1):25-42. doi: 10.1137/140975929.
Abstract
We describe methods to identify cylinder sets inside a basin of attraction for Boolean dynamics of biological networks. Such sets are used for designing regulatory interventions that make the system evolve towards a chosen attractor, for example initiating apoptosis in a cancer cell. We describe two algebraic methods for identifying cylinders inside a basin of attraction, one based on the Groebner fan that finds monomials that define cylinders and the other on primary decomposition. Both methods are applied to current examples of gene networks.
摘要
我们描述了识别生物网络布尔动力学吸引域内柱集的方法。此类集合用于设计调控干预措施，使系统朝着选定的吸引子演化，例如在癌细胞中引发凋亡。我们描述了两种用于识别吸引域内柱体的代数方法，一种基于找到定义柱体的单项式的格罗比纳扇，另一种基于素分解。这两种方法都应用于当前的基因网络示例。
相似文献
1
MONOMIALS AND BASIN CYLINDERS FOR NETWORK DYNAMICS.网络动力学的单项式与盆状圆柱体
SIAM J Appl Dyn Syst. 2015;14(1):25-42. doi: 10.1137/140975929.
2
COMPUTATIONAL METHODS FOR ASYNCHRONOUS BASINS.异步盆地的计算方法
Discrete Continuous Dyn Syst Ser B. 2016 Dec;21(10):3391-3405. doi: 10.3934/dcdsb.2016103. Epub 2016 Nov 1.
3
Algebraic model checking for Boolean gene regulatory networks.布尔基因调控网络的代数模型检查。
Adv Exp Med Biol. 2011;696:113-22. doi: 10.1007/978-1-4419-7046-6_12.
4
Sign-representation of Boolean functions using a small number of monomials.使用少量单项式的布尔函数的符号表示。
Neural Netw. 2009 Sep;22(7):938-48. doi: 10.1016/j.neunet.2009.03.016. Epub 2009 Apr 5.
5
Evaluation of attractors and basins of asynchronous random Boolean networks.异步随机布尔网络的吸引子和盆地评估
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 May;85(5 Pt 2):056105. doi: 10.1103/PhysRevE.85.056105. Epub 2012 May 4.
6
Minimal intervening control of biomolecular networks leading to a desired cellular state.最小干预控制生物分子网络，以达到预期的细胞状态。
Sci Rep. 2019 Sep 11;9(1):13124. doi: 10.1038/s41598-019-49571-6.
7
Algorithm to identify the optimal perturbation based on the net basin-of-state of perturbed states in Boolean network.基于布尔网络中受扰状态的净状态盆地来识别最优扰动的算法。
IET Syst Biol. 2018 Aug;12(4):148-153. doi: 10.1049/iet-syb.2017.0091.
8
Boolean network analysis through the joint use of linear algebra and algebraic geometry.布尔网络分析的线性代数和代数几何的联合使用。
J Theor Biol. 2019 Jul 7;472:46-53. doi: 10.1016/j.jtbi.2019.04.012. Epub 2019 Apr 15.
9
Identifying targets for intervention by analyzing basins of attraction.通过分析吸引域来确定干预目标。
Pac Symp Biocomput. 2011:350-61. doi: 10.1142/9789814335058_0036.
10
Precritical State Transition Dynamics in the Attractor Landscape of a Molecular Interaction Network Underlying Colorectal Tumorigenesis.结直肠癌发生所涉及分子相互作用网络吸引子景观中的临界前状态转变动力学
PLoS One. 2015 Oct 6;10(10):e0140172. doi: 10.1371/journal.pone.0140172. eCollection 2015.
引用本文的文献
1
COMPUTATIONAL METHODS FOR ASYNCHRONOUS BASINS.异步盆地的计算方法
Discrete Continuous Dyn Syst Ser B. 2016 Dec;21(10):3391-3405. doi: 10.3934/dcdsb.2016103. Epub 2016 Nov 1.
本文引用的文献
1
REST and stress resistance in ageing and Alzheimer's disease.衰老和阿尔茨海默病中的休息和抗压能力。
Nature. 2014 Mar 27;507(7493):448-54. doi: 10.1038/nature13163. Epub 2014 Mar 19.
2
Regularity and predictability of human mobility in personal space.个人空间中人类移动的规律性和可预测性。
PLoS One. 2014 Feb 27;9(2):e90256. doi: 10.1371/journal.pone.0090256. eCollection 2014.
3
Dynamics of p53 and NF-κB regulation in response to DNA damage and identification of target proteins suitable for therapeutic intervention.p53和NF-κB在响应DNA损伤时的调控动力学以及适合治疗干预的靶蛋白鉴定。
BMC Syst Biol. 2012 Sep 15;6:125. doi: 10.1186/1752-0509-6-125.
4
Modeling mechanistic biological networks: an advanced Boolean approach.建模机制生物网络：一种高级布尔方法。
Bioinformatics. 2012 Feb 15;28(4):557-63. doi: 10.1093/bioinformatics/btr697. Epub 2011 Dec 22.
5
Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia.动态和结构分析 T 细胞存活网络确定大颗粒淋巴细胞白血病的新候选治疗靶点。
PLoS Comput Biol. 2011 Nov;7(11):e1002267. doi: 10.1371/journal.pcbi.1002267. Epub 2011 Nov 10.
6
Dysfunction of TGF-β1 signaling in Alzheimer's disease: perspectives for neuroprotection.阿尔茨海默病中 TGF-β1 信号传导功能障碍：神经保护的展望。
Cell Tissue Res. 2012 Jan;347(1):291-301. doi: 10.1007/s00441-011-1230-6. Epub 2011 Aug 31.
7
Intelligent Systems For Assessing Aging Changes: home-based, unobtrusive, and continuous assessment of aging.智能系统评估衰老变化：基于家庭、非侵入式、持续评估衰老。
J Gerontol B Psychol Sci Soc Sci. 2011 Jul;66 Suppl 1(Suppl 1):i180-90. doi: 10.1093/geronb/gbq095.
8
Comparing signaling networks between normal and transformed hepatocytes using discrete logical models.使用离散逻辑模型比较正常和转化肝细胞之间的信号转导网络。
Cancer Res. 2011 Aug 15;71(16):5400-11. doi: 10.1158/0008-5472.CAN-10-4453. Epub 2011 Jul 8.
9
Cancer therapy design based on pathway logic.基于通路逻辑的癌症治疗设计。
Bioinformatics. 2011 Feb 15;27(4):548-55. doi: 10.1093/bioinformatics/btq703. Epub 2010 Dec 30.
10
From biological pathways to regulatory networks.从生物途径到调控网络。
Mol Biosyst. 2011 Mar;7(3):843-51. doi: 10.1039/c0mb00263a. Epub 2010 Dec 15.
Zotero 插件