Advanced Biomedical Computational Science

NextGen Sequencing 

• Specialize in next-generation sequencing data analysis and quality control, sequencing technology consultation, exploration and assessment of new protocols and technologies, and data analysis and management for the National Cancer Institute.  

• Work closely with CCR researchers and the CCR sequencing facility core and provide end-to-end bioinformatics support for next-generation sequencing projects. 

• Develop computational pipelines for both routine and custom NGS workflows 

• Provide processing, analysis, and interpretation of high-dimensional data sets. 

• Support the clinical sequencing facility in running CLIA pipelines including but not limited to targeted panels, RNA-Seq and Exome-Seq. 

• Support the Bioinformatics Training and Education Program, providing classes and workshops featuring subject matter experts, and training offered in bioinformatics and data visualization, to enable CCR researchers to analyze their own NGS data. 

Data Solutions and Systems Biology 

• Streamline and provide integrative and innovative solutions for the National Cancer Institute and National Institutes of Health community to access and use biological information collected across different sources and formats.  

• Develop interactive solutions for disease-agnostic data sharing, analysis, variant impact annotations, identifier conversions across species, clinical-genomics integration and visualization of multi-modal biomedical data.  

• Provide scientific infrastructure, scientific workflow management and innovative scientific web application and tool development support.  

• Create applications and web interfaces for dynamic queries and interaction with biomedical data and scientific applications.

Biomedical Image Analysis and Visualization 

• Support and accelerate basic research by developing and implementing technologies in image analysis and scientific visualization.  

• Use machine learning and deep learning for digital pathology 3D electron microscopy, light microscopy, image volume registration, and web-based, real-time visualization.  

• Facilitate data access, collaboration, and reuse to reduce duplicate efforts.  

Mathematical and Statistical Analysis 

• Collaborate on projects requiring mathematical and statistical analysis, study design, visualization of study results, and modeling of cancer and HIV/AIDS.  

• Create mathematical and statistical modeling for computational simulations, regression analysis, and survival analysis.  

• Provide study design consultation.  

• Provide training and outreach to increase awareness and understanding of statistics such as statistical reasoning seminars and tutorials, scientific programming seminars and tutorials, and software carpentry workshops.  

Computational Chemistry and Protein Modeling 

• Provide innovative solutions over a wide range of structure analysis and computational chemistry tools.  

• Develop tools and custom workflows for structural modeling including protein structures and drug interactions.  

• Assist in drug design with small molecule properties obtained from high-level quantum chemical calculations.  

• Develop algorithms and software for GAMESS.