Bioinformatics/Modeling/Biostatistics Core

生物信息学/建模/生物统计学核心

• 批准号: 10431025
• 负责人: Joel S. Bader
• 金额: $ 12.26万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 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/10431025
• 关键词: Accountability; Address; Area; Bioinformatics; Biometry; Biostatistics Core; Clinical; Clinical Data; Clinical Research; Cloud Computing; Collaborations; Communicable Diseases; Complex; Computational Technique; Computer Models; Computing Methodologies; Consult; 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; Institutes; Interdisciplinary Study; Knowledge; Learning; Medical; Medicine; Mentors; Modeling; Modernization; Mycobacterium tuberculosis; Organization administrative structures; Performance; Population; Predisposition; Process; Proteomics; Research; Research Design; Research Personnel; Research Project Grants; Resources; Series; Services; System; Training; Training Support; Tuberculosis; Universities; Vision; Waxes; Writing; bioinformatics tool; career; computing resources; epidemiology study; experience; genome-wide; high dimensionality; human pathogen; innovation; insight; interest; macrophage; mathematical model; meetings; next generation; recruit; success; synergism; technology development; training opportunity; transmission process

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) 可以说是 分析起来最复杂的传染病之一。来自主机内部进程（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。然而，出于同样的原因， 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）旨在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。这些包括 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；建模，以 将这些数据集转化为机械模型；和生物统计学，应用计算方法的专业知识 临床和流行病学研究。为了确保 BMBC 有能力实现这些目标，我们有 招募了具有这些领域专业知识的领导者。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 博士的研究领域涵盖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）， 系统动力学、生物信息学和数据科学。 BMBC 将实现其总体目标并提供额外的 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 与计算同行建立富有成效的伙伴关系。 BMBC 将协助 NI/ESI 以及 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 现代研究。 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 调查人员。此外，BMBC 教师将与其他 JHU TRAC 核心人员提供协同作用，并培养 通过参加每周一次的 TRAC 研讨会系列来开展多学科合作，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。