Shared Resource Director
Ramana V. Davuluri, PhD
Professor, Department of Biomedical Informatics, Stony Brook University
Overview
The Bioinformatics Shared Resource (BI-SR) provides Cancer Center investigators with database management, software applications support, and expertise in analyses and computational modeling of biomedical research data. Under the scientific direction of Dr. Ramana Davuluri, Professor of Biomedical Informatics, the BI-SR is comprised of faculty, programmers, and data-science specialists. Functions of the BI-SR reflect the requirements of the Cancer Center research programs and are broadly divided into three areas: (I) data-management; (II) analyses and computational modeling of Next Generation Sequencing (NGS) data; and (III) advanced bioinformatics tools for integrative cancer biology.
Specific services offered by the Bioinformatics Shared Resource are to:
- provide computational support for use of database software and bioinformatics tools
- provide consulting support regarding design and data analyses for high-throughput experiments, such as those using NGS platforms
- provide shared archives for high throughput molecular (both microarray and sequencing) data, tissue related data, image data, and pharmacodynamics data
- adapt and implement cohesive analysis and machine-learning and deep-learning tools that allow for integration and cross-validation of the comprehensive molecular data used in integrative cancer biology research
- provide educational outreach to inform Cancer Center members how the available BI-SR services can benefit their research programs and provide specific training on certain software packages
The BI-SR has placed a high priority on integrating cancer research information representing a variety of data types, including clinical patient data, molecular data from NGS, and image data from digitized microscopy slides. Data security is a primary focus of the BI-SR in designing and implementing software systems. The BI-SR also provides computational bioinformatics support to assist in the analysis of genomic, molecular, and proteomic data using commercial and locally developed software packages.
Some specific activities that BI-SR will provide include:
- Provide data handling services to Cancer Center members and other shared facilities
- Provide computational resource training and access to Cancer Center members to the cloud computing resources
- Provide genomics analysis study design and analysis services to Cancer Center members, for example
- Gene expression (bulk RNA-seq, single cell RNA-seq, Nanostring)
- Gene regulation (ChIP-seq, ATAC-seq, epigenetic profiling, Hi-ChIP, HiC)
- Genome and transcriptome sequencing (alternative splicing, RNA editing, gene fusion, SNP and INDEL mutation detection, CNV)
- Biomarkers (discovering markers in mRNA, miRNA and protein expression data)
- Pathway and network analysis
- Integrative analyses of multi-platform data
- Other customized data analysis projects
Contact Details:
Jinyu Li, PhD, Staff Bioinformatician, jinyu.li@stonybrookmedicine.edu