San Diego Center for Systems Biology: From Maps to Models

圣地亚哥系统生物学中心：从地图到模型

• 批准号: 8957386
• 负责人: JEFF M HASTY
• 金额: $ 284.92万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-18 至 2019-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8957386
• 关键词: Address; Architecture; Area; Automobile Driving; Behavior; Bioinformatics; Biological; Biology; Biomedical Research; Biophysics; California; Cell Communication; Cell Nucleus; Cell physiology; Cells; Code; Communities; Coupled; Data; Data Set; Discipline; Disease; Ecosystem; Education and Outreach; Educational process of instructing; Educational workshop; Engineering; Environment; Event; Exhibits; Faculty; Funding; Genes; Genetic; Genome; Genomics; Genotype; Grant; Heterogeneity; Imagination; Institutes; Institution; International; Investigation; Journals; Laboratories; Libraries; Life; Link; Malignant Neoplasms; Maps; Medical Research; Metabolic; Methods; Mission; Modeling; Molecular; National Institute of General Medical Sciences; Network-based; Ontology; Organelles; Organism; Pharmaceutical Preparations; Phenotype; Positioning Attribute; Postdoctoral Fellow; Property; Recruitment Activity; Research; Research Infrastructure; Research Institute; Research Personnel; Research Project Grants; Science; Seeds; Series; Staging; Statistical Models; Stratification; Stress; Structure; Structure-Activity Relationship; System; Systems Biology; Techniques; Technology; Testing; Time; Tissues; Training; Training Programs; Training and Education; Universities; abstracting; anticancer research; biological systems; cell growth; genome-wide analysis; graduate student; innovation; interdisciplinary approach; interest; mathematical model; meetings; next generation; outreach; personalized medicine; predictive modeling; programs; protein complex; protein degradation; public health relevance; response; small molecule; spatiotemporal; symposium; synthetic biology

 DESCRIPTION (provided by applicant): The mission of the San Diego Center for Systems Biology (SDCSB; sdcsb.ucsd.edu) is to advance the discipline and application of systems biology in the greater San Diego area and to serve as a nucleus for systems biology education and training. The SDCSB brings together a community of 19 outstanding faculty, over 100 trainees and technical staff spanning four world-renowned institutions: the University of California San Diego, the Salk Institute for Biological Studies, the Sanford-Burnham Medical Research Institute and the Ludwig Institute for Cancer Research, all located on the Torrey Pines research mesa. The SDCSB has been supported as an NIGMS National Center for Systems Biology since 2010. Over the past five years our research has led to significant systems biology advances, including genome-wide studies of how stress remodels transcriptional and genetic networks, discovery of an independent metabolic clock coordinating cell growth through cycles of TOR1 activity, demonstration that much of the Gene Ontology can be inferred directly from `omics data, prediction of cancer survival time and drug response by an approach called Network Based Stratification and a series of major feats in engineering of synthetic coupled genetic circuits. We began two successful annual symposia, formal systems biology coursework, a seminar series and journal club, workshops on systems biology techniques and a faculty seed grant program that was used to recruit 10 new systems biology faculty to UCSD. We successfully trained more than 90 graduate students and postdoctoral fellows, seven who are now in independent positions. The theme of this renewal application - "From Maps to Models" - addresses an important challenge in systems biology: traversing between network maps and mathematical models, two very successful but so far mostly separate biological representations and modes of study. Network maps tend to be global, static, abstract and descriptive, whereas mathematical models tend to be local, dynamic, detailed and predictive. Guided by this overarching theme, four SDCSB research projects seek to develop a general library of maps and models relevant to fundamental cellular and super-cellular processes, including the spatiotemporal architecture of the genome (Project 1), protein turnover dynamics (Project 2), cell-cell communication and heterogeneity (Project 3) and environment-genome interactions (Project 4). These mapping and modeling activities are fueled by technologies advanced across three SDCSB core platforms, aspects of which serve as an exemplar for systems biology efforts nationally and internationally. This renewal application represents a tightly integrated set of research projects, cores and educational efforts. The keys to achieving this integration are four-fold: (1) A consistent theme of developing global network maps coupled to predictive models; (2) Support of an innovative systems biology core platform jointly developed and applied across all projects; (3) Cross-cutting faculty recruitment, postdoctoral and graduate programs in systems biology, from which the center recruits and staffs its projects; and (4) Outstanding symposia, retreats, journal clubs and workshops in which we all participate. The teams spearheading these efforts are comprised of investigators with diverse backgrounds and expertise, resulting in a multidisciplinary approach incorporating genomics, bioinformatics, synthetic biology and biophysics.

 描述（由申请人提供）：圣地亚哥系统生物学中心（SDCSB；sdcsb.ucsd.edu）的使命是在大圣地亚哥地区推进系统生物学的学科和应用，并作为系统生物学的核心SDCSB 汇集了来自四个世界知名机构的 19 名优秀教师、100 多名学员和技术人员：加州大学圣地亚哥分校、索尔克生物研究所。桑福德-伯纳姆医学研究所和路德维希癌症研究所均位于多利松研究平台，自 2010 年以来，SDCSB 一直作为 NIGMS 国家系统生物学中心得到支持。在过去的五年里，我们的研究取得了长足的进步。导致了系统生物学的重大进展，包括关于压力如何重塑转录和遗传网络的全基因组研究，发现了通过 TOR1 活动周期协调细胞生长的独立代谢时钟，证明了基因本体论的大部分内容可以直接从组学数据中推断出来，通过基于网络的分层方法预测癌症生存时间和药物反应，以及合成耦合遗传电路工程中的一系列重大成就我们开始了两次成功的年度研讨会，正式的系统生物学课程，我们成功地培训了 90 多名研究生和博士后研究员，其中 7 名现在是独立研究人员。这一更新应用程序的主题——“从地图到模型”——解决了系统生物学中的一个重要挑战：在网络地图和数学模型之间进行遍历，这两种非常成功但迄今为止大多是独立的生物表征和研究模式。数学模型倾向于全局、静态、抽象和描述性，而数学模型往往是局部的、动态的、详细的和预测性的。在这一总体主题的指导下，SDCSB 的四个研究项目寻求开发一个与基本细胞和超级相关的通用图谱和模型库。 - 细胞过程，包括基因组的时空结构（项目 1）、蛋白质周转动力学（项目 2）、细胞间通讯和异质性（项目 3）以及环境-基因组相互作用（项目 4）这些绘图和建模活动由三个方面的先进技术推动。 SDCSB 核心平台，其各个方面都是国内和国际系统生物学工作的典范。这一更新应用代表了一系列紧密集成的研究项目、核心和教育工作，实现这种集成的关键是。四个方面：（1）开发与预测模型相结合的全球网络图的一致主题；（2）支持在所有项目中联合开发和应用的创新系统生物学核心平台；（3）跨领域的教师招聘、博士后和系统生物学研究生项目，该中心从中招募人员并为其项目配备人员；（4）我们都参加的杰出研讨会、务虚会、期刊俱乐部和研讨会，带头这些工作的团队由具有不同背景和专业知识的研究人员组成。采取多学科方法结合基因组学、生物信息学、合成生物学和生物物理学。