Bioinformatics and Pathways Core

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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.