Hunt, Anthony

C. Anthony Hunt Major Research Interest: Bioinformatics, Genomics and Proteomics (also, Biomathematics and Biological Systems Modleing; and Biomedical Imaging) Phone: 415-476-2455 Email: This e-mail address is being protected from spam bots, you need JavaScript enabled to view it Web site: http://biosystems.ucsf.edu Date Available: N/A Project Type    Funding    Rotation Yes NIH Yes Summer Yes Private Foundation Yes Thesis Yes Other Yes Project Titles: Microarray Measures of Gene Expression Tissue Specific Targeted Drug Delivery Therapeutic Engineering: Toward Optimized Individual Treatments Microarray Measures of Gene Expression Abstract: See http://genetics.nature.com/chips_interstitial.html A device is used to scan the fluorescence intensity of thousands of micron scale features on a "GeneChip." Typically, the information from several features is used to calculate the level of expression of each gene in a biological sample. Typically, similar measurements are made as a function of time or treatment. A key question is, what are the informative patterns of gene expression? Several different pattern extraction algorithms and software are available, but we would welcome your ideas for a new one. This will be a computational rotation project. There is flexibility in specifying the rotation goals. We especially need help in two areas: contrasting the information arising from different pattern extraction approaches, and using related data and knowledge to provide informed guidance to the pattern extraction approaches. The level of commitment is expected to be about 1-2 days per week. There is a reasonable chance that results from a well designed and executed rotation project will be publishable or presentable at a regional scientific meeting. Collaboration with one of several companies is an option. Tissue Specific Targeted Drug Delivery Abstract: Because of the variability between and within individuals, the expected advantage of targeting is eroded somewhat when release of active agent (drug) at the target site is biologically controlled, e.g., via enzyme cleavage from the carrier. The same is true when accumulation at the target is biologically controlled, e.g., the drug carrier attaches to a specific cell surface protein. The engineering problem is made more interesting when there is a therapeutic window - a minimum effective delivered dose and maximally tolerated toxic dose. The possibilities and basic principles are being computationally explored. The scope of this rotation project is expected to be mostly computational. There is flexibility in specifying the rotation goals. There are opportunities for both the novice and someone already knowledgeable of drug delivery. The level of commitment is expected to be about 1-2 days per week. There is a reasonable chance that results from a well designed and executed rotation project will be publishable or presentable at a regional scientific meeting. Collaboration with a local company is an option. Therapeutic Engineering: Toward Optimized Individual Treatments Abstract: We are developing a framework that eventually will be capable of generating a large population of simulated, resetable objects that have individual attributes (e.g., age, blood chemistries, tumor properties) that are similar to those of real patients, and as such serve as surrogate patients. Each object will be a series of nested, connected modules that model essential features of the individual or disease process. Working together, they will be capable of generating realistic response values when given (input corresponding to) one of several treatment options. The resulting simulated response data will be indistinguishable from (but not identical to) available data from real patients (e.g., from a breast cancer clinical trial) when the attributes of the real and surrogate patients are reasonably matched. Thus, a hypercell of surrogate patients can be used to approximate how a new, real patient is likely to respond should she elect to follow any one of the treatment options. The hypercell can also be used to visualize changes in expected treatment outcomes in response to a variety of "what if" questions. There are several options for rotation projects depending on which aspect the project is of most interest. Examples include building algorithms, visualizing high dimensional data sets, interface design, using available data to generate simulated patient data, subsystem modeling and simulation. Thus, there is flexibility in specifying the rotation goals. The level of commitment is expected to be about 1-2 days per week. There is a reasonable chance that results from a well designed and executed rotation project will be publishable or presentable at a regional scientific meeting. Collaboration with one of several companies is an option.