sysbio_projects

3. SYSTEMS BIOLOGY : 

3. SYSTEMS BIOLOGY Genomics Opportunities in post-genomics Challenges – methods, analysis Systems Engineering + Genomics = Systems Biology Synthesis and integration of data types Systems analysis Etc.etc.

Bio-medical Science + Engineering : 

Bio-medical Science + Engineering Background (www.dbi.tju.edu) New Program at the interface Biomedical option Nascent core curriculum: biomed courses TJU tech courses UD and new course(s) Work across-between campuses (SEPTA, I95) joint advisorship Dan Zak and Rishi Khan zak@che.udel.edu rishi@capsl.udel.edu

Opportunities : 

Opportunities Two current joint UD-TJU funding sources : BISTI and DARPA Interface of systems engineering and genomics data acquisition and data analysis Experimental opportunities Modeling opportunities

Objectives : 

Objectives Understanding, prediction and control of human functional processes Disease models and relevancy Reverse engineering opportunities

Multi-scale Model Problem : 

Multi-scale Model Problem Organizational Structure in Biology Single Cells (Building blocks) Tissues (organization of multiple cells) Organism Fundamental Cellular Processes Inputs (Signal Transduction) Transcription Translation Outputs – adaptive processes

Slide 6: 

Characteristics Consists of very complex interconnections of large number of “processes” Structure and function encoded in DNA sequences in the genome. Similar to Chemical Processes but on a significantly more elaborate scale

Slide 7: 

Engineer’s Viewpoint of Central Issue Biological “system” consists of “processes” “Process flowsheet” encoded within genome; not overt and explicit. (Can we decode and exploit?) Ultimate objective: quantitative prediction of cellular function; (for system-wide analysis and novel synthesis and design). Similarity to chemical processes can be exploited !?

SYSTEMS BIOLOGY: Projects : 

SYSTEMS BIOLOGY: Projects Multi-scale modeling and analysis of adaptive cellular and system processes Mammalian systems – neurons, brains, brain functions and diseases CAKE – a model benchmark tool, and a matrix of solutions for Genetic Regulatory Circuits. Development and Analysis of kinetic signaling models Link of signaling models to Genetic Regulatory Circuits Genetic Regulatory Circuits to neuronal electrical behavior

SYSTEMS BIOLOGY: Projects : 

SYSTEMS BIOLOGY: Projects Experimental Development of useful mammalian microarray, promoter activity and proteomic data – e.g. New methods and applications - e.g. polynies Analysis CAKE – combining global datasets, experimental design, prediction - e.g. genetic regulatory circuit, gene network prediction from combined data sets Development and analysis of kinetic signaling models and e.g. link of signaling models to genetic regulatory circuit Genetic regulatory circuits to output – e.g. neuronal electrical behavior and to biological neural network function Tools: clone updater, PAINT, masliner II, qualitative modeling approaches, Bayes networks The IT world – MDL BioSPICE scope, EWG ontologies

Relevance : 

Relevance Biological understanding and prediction: e.g. principles of gene regulation; relating neuron dynamics to neural network function Disease: e.g. addiction; homeostasis; mental illness and mood; liver disease; heart disease Reverse engineering: following slides

Path Forward : 

Path Forward Talk to us, talk to Dan/Rishi, visit TJU Explore opportunities in the Systems Biology problem space and define a project direction Projects can extend ongoing work Projects can initiate new work