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

基本信息

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
项目类别：
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

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

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项目摘要

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（由应用程序提供）：圣地亚哥系统生物学中心（SDCSB; SDCSB.UCD.EDU）的使命是推进大圣地亚哥地区系统生物学的纪律和应用，并充当系统生物学教育和培训的核心。 SDCSB汇集了一个由19个杰出教职员工组成的社区，100多名受训人员和技术人员，涵盖了四个著名的机构：加利福尼亚大学圣地亚哥分校，萨克生物学研究所，桑福德·伯纳姆医学研究所和路德维格癌症研究所，均位于Torrey Pines Research Mesa上。 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 coordination 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通过一种称为基于网络的分层的方法，以及一系列合成耦合遗传回路工程的主要壮举。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，一个开创性的系列和期刊俱乐部，有关系统生物学技术的研讨会以及用于招募10个新系统生物学教师到UCSD的教师种子赠款计划。我们成功地培训了90多名研究生和博士后研究员，现在有7名现在处于独立职位。此更新应用的主题 - “从地图到模型” - 解决了系统生物学中的一个重要挑战：网络地图和数学模型之间的遍历，两个非常成功，但到目前为止主要是独立的生物学表示和研究模式。网络图往往是全局，静态，抽象和描述性的，而数学模型往往是局部，动态，详细和预测的。在这个总体主题的指导下，四个SDCSB研究项目旨在开发与基本细胞和超细胞过程相关的地图和模型库，包括基因组的时空结构（项目）1），蛋白质离职动力学（Project 2），细胞电池通信和杂项（项目3）和环境互动（项目3）和环境互动（项目4）。这些映射和建模活动源于在三个SDCSB核心平台上提出的技术，这些技术在国家和国际上是系统生物学工作的典范。该更新应用程序代表了一组紧密整合的研究项目，核心和教育工作。实现此集成的关键是四个方面：（1）开发与预测模型相连的全球网络图的一致主题；（2）在所有项目中共同开发和应用创新的系统生物学核心平台的支持；（3）系统生物学领域的跨裁判教师招聘，博士后和研究生课程，中心从中招募了其项目；（4）我们所有人都参加的杰出研讨会，务虚会，期刊俱乐部和研讨会。率领这些努力的团队由具有潜水员背景和专业知识的研究人员组成，导致了融合了基因组学，生物信息学，合成生物学和生物物理学的多学科方法。