Duke Center for Systems Biology

杜克系统生物学中心

• 批准号: 8518136
• 负责人: Philip N Benfey
• 金额: $ 18.84万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-07-10 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8518136
• 关键词: Address; Arabidopsis; Biological; Biology; Cell Cycle; Cell Cycle Regulation; Cells; Cellular Structures; Characteristics; Collaborations; Complex; Development; Educational process of instructing; Embryonic Development; Exposure to; Faculty; Fellowship Program; Fostering; Graduate Education; Imagery; Life; Mammalian Cell; Mathematics; Measures; Methods; Modeling; Molecular; Nonlinear Dynamics; Organism; Physics; Plant Roots; Population; Process; Property; Regulator Genes; Relative (related person); Research; Research Personnel; Research Support; Scientist; Sea Urchins; Structure; Students; System; Systems Biology; Techniques; Variant; Yeast Model System; Yeasts; computer science; design; genetic manipulation; human disease; interdisciplinary approach; programs; statistics; symposium; theories; tool

The Duke Center for Systems Biology (DCSB) will support research collaborations aimed at discovering, modeling, and explaining the dynamical properties of biological networks. Using high throughput techniques, biologists can now determine nearly complete lists of many of the molecular components of cells, measure relative concentrations of these components, and determine which components interact with each other. A major challenge, however, is to understand how this complex network of interactions produces the orchestrated processes characteristic of living cells and higher organisms. DCSB will approach this challenge through interdisciplinary projects involving a wide array of experimental techniques, analysis tools, and modeling methods. Each project will be a collaboration between biologists and theorists with expertise in a relevant subfield of mathematics, computer science, statistics, or physics. DCSB projects will address three broad themes: (1) cell cycle control; (2) development and differentiation; and (3) population variation. In the first two, the emphasis will be on the dynamics determined by gene regulatory networks; in the third, on evolutionary dynamics of network structure. Six initial projects have been identified for support, covering networks involved in various model systems: the yeast cell cycle, mammalian cell cycle entry, Arabidopsis root development, sea urchin embryonic development, population variation in yeast, and population variation in sea urchin. Analysis and modeling efforts will draw from expertise in Bayesian statistics, nonlinear dynamics, computational topology and geometry, and visualization. DCSB will bring together outstanding researchers as collaborators and guest scientists through sabbatical and fellowship programs and through an annual symposium on a current systems biology theme. DCSB faculty will integrate systems biology themes into several existing graduate education programs that foster vertically integrated research teams and exposure to interdisciplinary approaches to biological problems. Faculty associated with DCSB will also teach several new undergraduate systems biology courses and administer a certificate program designed both for biology students and those students in mathematical/computational majors. The results will have substantial implications for treatment of human disease through manipulation of genetic regulatory systems, as well as for fundamental biology and theories of complex systems.

杜克系统生物学中心(DCSB)将支持旨在发现、建模和解释生物网络动态特性的研究合作。使用高通量技术，生物学家现在可以确定细胞许多分子成分的几乎完整的列表，测量这些成分的相对浓度，并确定哪些成分相互作用。然而，一个主要的挑战是理解这种复杂的相互作用网络是如何产生活细胞和高等有机体特有的精心安排的过程的。DCSB将通过涉及广泛的实验技术、分析工具和建模方法的跨学科项目来应对这一挑战。每个项目都将是生物学家和理论家之间的合作，他们在数学、计算机科学、统计学或物理学的相关子领域拥有专业知识。DCSB项目将涉及三个广泛的主题：(1)细胞周期控制；(2)发育和分化；(3)种群变异。在前两个方面，重点将放在由基因调控网络决定的动力学上；在第三个方面，将侧重于网络结构的进化动力学。已经确定了六个初步项目供支持，涵盖了涉及各种模型系统的网络：酵母细胞周期、哺乳动物细胞周期进入、拟南芥根发育、海胆胚胎发育、酵母中的种群变异和海胆中的种群变异。分析和建模工作将利用贝叶斯统计、非线性动力学、计算拓扑和几何以及可视化方面的专业知识。 DCSB将通过休假和奖学金计划以及关于当前系统生物学主题的年度研讨会，将杰出的研究人员聚集在一起，成为合作者和客座科学家。DCSB的教职员工将把系统生物学主题整合到几个现有的研究生教育项目中，这些项目培养垂直整合的研究团队，并接触到解决生物学问题的跨学科方法。与DCSB相关的教职员工还将教授几门新的本科系统生物学课程，并管理一项为生物学学生和数学/计算专业学生设计的证书课程。这一结果将对通过操纵基因调控系统治疗人类疾病以及基础生物学和复杂系统理论产生重大影响。

项目成果

Visualizing fitness landscapes.

• DOI: 10.1111/j.1558-5646.2011.01236.x
• 发表时间: 2011-06
• 期刊: Evolution; international journal of organic evolution
• 作者: McCandlish DM

Synergistic and tunable human gene activation by combinations of synthetic transcription factors.

合成转录因子组合对人类基因的协同和可调激活。

• DOI: 10.1038/nmeth.2361
• 发表时间: 2013-03
• 期刊: NATURE METHODS
• 影响因子: 48
• 作者: Perez-Pinera, Pablo;Ousterout, David G.;Brunger, Jonathan M.;Farin, Alicia M.;Glass, Katherine A.;Guilak, Farshid;Crawford, Gregory E.;Hartemink, Alexander J.;Gersbach, Charles A.
• 通讯作者: Gersbach, Charles A.

Boolean modeling of collective effects in complex networks.

• DOI: 10.1103/physreve.79.061908
• 发表时间: 2009-06
• 期刊: Physical review. E, Statistical, nonlinear, and soft matter physics
• 作者: Norrell J;Socolar JE
• 通讯作者: Socolar JE

Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology.

促进杜克大学系统生物学中心的跨学科合作研究。

• DOI: 10.1021/sb300036z
• 发表时间: 2012
• 期刊: ACS synthetic biology
• 影响因子: 4.7
• 作者: Stone,JanaE;Benfey,PhilipN;You,Lingchong
• 通讯作者: You,Lingchong

Evidence-ranked motif identification.

• DOI: 10.1186/gb-2010-11-2-r19
• 发表时间: 2010
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Georgiev S;Boyle AP;Jayasurya K;Ding X;Mukherjee S;Ohler U
• 通讯作者: Ohler U