Bioinformatics/Modeling/Biostatistics Core

摘要- JHU TRAC生物信息学、建模和生物统计学核心（BMBC） 结核分枝杆菌已经与人类一起进化了几个世纪;因此，结核病（TB）可以说是一种 最复杂的传染病之一。从主机内进程（例如， 巨噬细胞异质性和肉芽肿形成）与临床表现（例如，潜伏期和延长的 盛衰病程）到群体水平动态（例如，由异质性驱动的缓慢流行病 传播和易感性），结核病提出了独特的挑战建模。然而，出于同样的原因， 在计算模型的发展-包括系统动力学，统计， 流行病学方法-提供了一个前所未有的机会，发展新的定量见解， 这种独特的人类病原体的动力学。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）旨在确保加快创新性结核病研究 通过获得传染病研究的计算方法的最新进展。这些包括 生物信息学，利用基因组，蛋白质组学和其他高通量，基因组规模的数据;建模， 将这些数据集转化为机械模型;以及生物统计学，用于应用计算方法的专业知识 临床和流行病学研究。为确保大厦管理委员会有能力达致这些目标，我们 招聘的领导人的专业知识涵盖这些领域。核心总监Joel Bader博士拥有丰富的经验 在生物信息学和传染病建模方面，以及技术发展的长期记录。 联合主任大卫道迪博士跨越数学建模和流行病学;联合主任Aletta Nonyane博士 在生物统计学和高维度临床数据方面拥有专业知识。额外的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（宿主内和人群水平）， 系统动力学、生物信息学和数据科学。BMBC将实现其总体目标，并提供更多 通过使新研究者（NI）和早期研究者（ESI）能够实现 在他们的研究中，无论是通过学习自己进行计算研究，还是通过 与计算机同行建立富有成效的伙伴关系。BMBC将协助NI/ESI，以及 研究人员新的结核病领域，在获得所需的高性能计算设施， 现代研究。BMBC将提供的其他服务包括与NI/ESI的合作伙伴关系， 导航其研究的计算密集型组件，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 investigators.此外，BMBC教师将提供与其他JHU TRAC核心的协同作用，并促进 通过参加每周一次的TRAC系列研讨会，开展多学科合作，重点是 解决关键的结核病知识差距的计算方法，以及NI/ESI为重点的写作 问责小组、TRAC K-Club和K2 R Club以及年度结核病科学会议和TRAC数据博览会。

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.