Bioinformatics/Modeling/Biostatistics Core

生物信息学/建模/生物统计学核心

基本信息

批准号：
10593162
负责人：
David Wesley Dowdy
金额：
$ 12.38万
依托单位：
JOHNS HOPKINS UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-03-16 至 2027-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10593162
关键词：
Acceleration Accountability Address Area Bioinformatics Biometry Biostatistics Core Clinical Clinical Data Clinical Research Cloud Computing Collaborations Communicable Diseases Complex Computational Technique Computer Models Computing Methodologies Data Data Science Data Set Development Disease Educational workshop Engineering Ensure Epidemic Epidemiology FAIR principles Faculty Fostering Genomics Goals Granuloma Health Healthcare Heterogeneity High Performance Computing Human Subject Research Individual Infectious Diseases Research Institution Interdisciplinary Study Knowledge Learning Macrophage Medical Medicine Mentors Modeling Modernization Mycobacterium tuberculosis Organization administrative structures Performance Population Predisposition Process Productivity Proteomics Research Research Design Research Personnel Research Project Grants Resources Series Services Training Tuberculosis Universities Vision Waxes Writing bioinformatics tool career computing resources dynamic system epidemiology study experience genome-wide high dimensionality human pathogen innovation insight interest mathematical model meetings next generation recruit success synergism technology development training opportunity transmission process

项目摘要

ABSTRACT — JHU TRAC BIOINFORMATICS, MODELING AND BIOSTATISTICS CORE (BMBC) Mycobacterium tuberculosis has evolved with humankind for centuries; as such, tuberculosis (TB) is arguably one of the most complex infectious diseases to represent analytically. From within-host processes (e.g., macrophage heterogeneity and granuloma formation) to clinical presentation (e.g., latency and a prolonged waxing-and-waning disease course) to population-level dynamics (e.g., slow epidemics driven by heterogeneous transmission and susceptibility), TB presents distinctive challenges for modeling. By the same token, however, advances in the development of computational models – including systems dynamics, statistical, and epidemiological approaches – offer an unparalleled opportunity for developing new quantitative insights into the dynamics of this uniquely human pathogen. The overall goal of the Johns Hopkins University (JHU) TRAC Bioinformatics, Modeling and Biostatistics Core (BMBC) is to ensure that innovative TB research is accelerated by access to the most recent advances in computational methods for infectious disease research. These include bioinformatics to make use of genomic, proteomic, and other high-throughput, genome-scale data; modeling, to turn these data sets into mechanistic models; and biostatistics, for expertise in applying computational methods to clinical and epidemiological research. To ensure the ability of the BMBC to achieve these goals, we have recruited leaders whose expertise spans these areas. Dr. Joel Bader, Core Director, has extensive experience in bioinformatics and modeling applied to infectious disease, as well as a long record of technology development. Co-Director Dr. David Dowdy spans mathematical modeling and epidemiology; Co-Director Dr. Aletta Nonyane has expertise in biostatistics and high-dimensional clinical data. Additional Core faculty provide deeper expertise in key content areas, including genomics, biostatistics, mechanistic modeling (within-host and population-level), systems dynamics, bioinformatics, and data science. The BMBC will achieve its overall goal and provide added value to the JHU TRAC by enabling New Investigators (NI) and Early Stage Investigators (ESI) to achieve independence in their research, whether by learning to perform computational research themselves or by establishing productive partnerships with computational counterparts. The BMBC will assist NI/ESI, as well as researchers new to the TB field, in gaining access to the high-performance computing facilities required for modern studies. Additional examples of services the BMBC will provide include partnership with NI/ESI to navigate computationally intensive components of their research, assistance with study design and/or analytical approaches relevant to specific research questions, and linkage to formal training opportunities for interested investigators. In addition, the BMBC faculty will provide synergy with the other JHU TRAC Cores and foster multi-disciplinary collaborations by participating in the weekly TRAC Seminar Series, with a focus on computational approaches to addressing critical TB knowledge gaps, as well as NI/ESI-focused Writing Accountability Groups, TRAC K-Club and K2R Club, and the annual TB Scientific Meeting and TRAC Data Fair.

摘要 — JHU TRAC 生物信息学、建模和生物统计核心 (BMBC) 结核分枝杆菌与人类一起进化了几个世纪，因此结核病 (TB) 是有争议的。从宿主内部过程（例如，巨噬细胞异质性和肉芽肿形成）到临床表现（例如潜伏期和延长的时间）疾病的盛衰过程）到人口层面的动态（例如，由异质性驱动的缓慢流行病）传播和易感性），结核病给建模带来了独特的挑战。计算模型发展的进步——包括系统动力学、统计和流行病学方法——为开发新的定量见解提供了无与伦比的机会这种独特的人类病原体的动态。约翰·霍普金斯大学 (JHU) TRAC 的总体目标。生物信息学、建模和生物统计学核心 (BMBC) 将确保加速创新性结核病研究通过获取传染病研究计算方法的最新进展。生物信息学利用基因组、蛋白质组和其他高通量、基因组规模的数据来建模；将这些数据集转化为机械模型；以及生物统计学，以获得应用计算方法的专业知识为确保 BMBC 实现这些目标的能力，我们有能力进行临床和流行病学研究。聘请了专业知识涵盖这些领域的领导者，核心总监 Joel Bader 博士拥有丰富的经验。在应用于传染病的生物信息学和建模领域，以及长期的技术开发记录。联合主任 David Dowdy 博士负责数学建模和流行病学；联合主任 Aletta Nonyane 博士拥有生物统计学和高维临床数据方面的专业知识，其他核心教师可提供更深入的专业知识。在关键内容领域，包括基因组学、生物统计学、机制建模（宿主和群体水平）， BMBC 将实现其总体目标并提供额外的服务。通过帮助新研究者 (NI) 和早期研究者 (ESI) 实现以下目标，为 JHU TRAC 带来价值研究中的独立性，无论是通过学习自己进行计算研究还是通过 BMBC 将协助 NI/ESI 以及计算合作伙伴建立富有成效的合作伙伴关系。结核病领域的新研究人员，在获得结核病所需的高性能计算设施方面 BMBC 将提供的其他服务示例包括与 NI/ESI 合作，以导航研究的计算密集型部分，协助研究设计和/或分析与具体研究问题相关的方法，以及与感兴趣的正式培训机会的联系此外，BMBC 教师将与其他 JHU TRAC 核心人员进行协同合作并培养。通过参加每周一次的 TRAC 研讨会系列来促进多学科合作，重点关注解决关键结核病知识差距的计算方法以及以 NI/ESI 为重点的写作问责小组、TRAC K-Club 和 K2R 俱乐部，以及年度 TB 科学会议和 TRAC 数据博览会。