Bioinformatics and Pathways Core

抽象生物信息学与路径核心 生物信息学和途径核心（BPC）将支持用户进行高水平的生物信息学分析， 通量实验，如RNA-seq，ChIP-seq和基因组分析，并提供统计支持， 实验的设计和解释。在COBRE的第一阶段和第二阶段，BPC支持 根据评审员的意见， 反馈BPC由Jonathan Wren博士领导，他是一位拥有19年经验的生物信息学家， 专注的博士学位-一级统计员和一名生物信息学家。我们的具体目标是： 目标1：为高质量、先进的数据分析服务创建具有成本效益的资源， 付费服务和合作模式。BPC人员拥有丰富的经验， 最先进的生物信息学方法，以及开发新型分析方法的记录。我们将提供 支持预实验研究设计，包括功效分析和利用新生物信息学， 统计工具来解决COBRE参与者提出的具体生物学问题。核心主任已 开发了一些新的工具，如软件：1）自动识别和分析相关的 感兴趣的实体（例如，基因、疾病、表型等）在已发表的文献中; 2）识别特征， 与感兴趣的基因组区域重叠的特性和实验; 3）识别和分析实验 在公共微阵列数据库，如NCBI的基因表达综合数据库（GEO），通过荟萃分析和4） 根据公共数据库中差异表达基因之间的相关性来解释它们。 目标2：提供一批具有多种技能和专业知识的经验丰富的分析师， 各种未来分析项目。COBRE使BPC能够开发新的软件， 具有一套广泛有用的技能，以帮助生物医学研究人员的人员。而且，正如我们的 在COBRE第一阶段和第二阶段的合作出版物中，我们成功地利用我们的能力， 帮助他人推进研究。第三阶段将使我们能够建立一个自我维持的机构核心。 目标3：继续开发、评估和改进数据分析和数据集成的新方法。 BPC将开发日益复杂和强大的技术，这些技术将随着以下需求而发展： 科学调查员。我们将改进对资源利用率的跟踪， 提供的数据和我们对数据的分析之间的在线互动，帮助调查人员使他们的数据 符合FAIR原则，开发评估基于网络的数据内聚性的方法，并推进 用于常见图像分析任务的机器学习方法。

ABSTRACT BIOINFORMATICS & PATHWAYS CORE The Bioinformatics and Pathways Core (BPC) will support users with bioinformatics analysis of high- throughput experiments such as RNA-seq, ChIP-seq, and genomic analyses, and provide statistical support in both the design and interpretation of experiments. During Phases I and II of this COBRE, BPC support has helped substantially to increase the competitiveness of Project Lead grant applications, based upon reviewer feedback. The BPC is led by Dr. Jonathan Wren, a bioinformatician with 19 years of experience and includes a dedicated Ph.D.-level Statistician and a Bioinformatics Scientist. Our Specific Aims are: Aim 1: Create a cost-effective resource for high-quality, advanced data analysis services, employing both fee-for-service and collaborative models. BPC personnel have extensive experience using state-of- the-art bioinformatics methods, as well as a track record of developing novel analysis methods. We will provide support for pre-experimental study design, including power analyses and utilize novel bioinformatics and statistical tools to solve specific biological questions posed by COBRE participants. The Core Director has developed a number of novel tools, such as software to: 1) Automate the identification and analysis of related entities of interest (e.g., genes, diseases, phenotypes, etc.) within the published literature; 2) Identify features, properties and experiments that overlap with genomic regions of interest; 3) Identify and analyze experiments in public microarray databases like NCBI’s Gene Expression Omnibus (GEO) through meta-analysis and 4) Interpret differentially expressed genes in terms of the correlations between them within public databases. Aim 2: Provide a set of experienced analysts with a diversity of skills and expertise to accommodate a variety of future analysis projects. This COBRE has enabled the BPC to develop novel software and to hire personnel with a set of skills broadly useful to helping biomedical researchers. And, as evidenced by our collaborative publications during COBRE Phases I and II, we have been successful at using our capabilities to help others advance their research. Phase III will enable us to establish a self-sustaining institutional Core. Aim 3: Continue to develop, evaluate, and refine new methods of data analysis and data integration. The BPC will develop increasingly sophisticated and powerful technologies that evolve with the demands of scientific investigators. We will improve tracking of resource utilization, advance technologies that improve online interactivity between the data provided and our analysis of it, help investigators make their data compliant with FAIR principles, develop methods for evaluating network-based data cohesion, and advance machine-learning methods for common image analysis tasks.