(6ar) Daniel Cook - Understanding and Treating Progressive Diseases at the Levels of Single Cells and Single Patients Though Systems Biology

I am interested in understanding and predicting treatments for progressive diseases including liver diseases and cancers through high-throughput data analysis, characterization of single cells and cell populations, and genome-scale metabolic modeling.

Briefly, heterogeneity is emerging as a defining feature of biology. This biological heterogeneity can be seen at multiple characteristic scales – from individual patients to single cells – and at multiple regulatory levels – genomic, transcriptomic, proteomic, and metabolomic. Originally perceived as “biological noise”, this heterogeneity is now being leveraged to understand fundamental principles of biology and design more complete and effective therapies to treat diseases.

My work uses computational methods to use biological heterogeneity at multiple scales to understand disease progression, understand dynamic regulation of disease processes, and predict more effective disease therapies and personalized therapies. Specifically, I use a combination of “big data” analyses from individual patients, single-cell RNA-seq and proteomic analyses, and personalized genome-scale metabolic modeling to understand dynamic metabolic regulation in and predict therapies for multiple diseases including non-alcoholic fatty liver disease and breast cancer in individual patients and in patient populations.

Teaching Interests:

I am most interested in teaching the following courses: Systems biology and personalized medicine, Controls, Statistics for chemical & life science engineering, Reaction Engineering, Numerical methods and Introduction to programming, and Metabolic Engineering.

I believe that the most important skills an engineering teacher can impart are analytical problem solving, creative thinking, and lifelong learning. Overall, my theory of teaching is that these skills can be developed best by student immersion in engineering thought and repetition of skills. In engineering, as in language studies, immersion and repetition facilitates faster learning, better outcomes, more creative approaches, and an appreciation of how much more one still has to learn. In my view, it is the responsibility of the teacher to create an environment where immersion is possible and repetition of theory and practice is encouraged. It is the students’ responsibility to practice repeatedly until “fluency” is reached.