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3. SYSTEMS BIOLOGY
Genomics
Opportunities in post-genomicsChallengesmethods, analysis
Systems Engineering + Genomics =
Systems BiologySynthesis and integration of data typesSystems analysis
Etc.etc.
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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 [email protected]@capsl.udel.edu
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Opportunities
Two current joint UD-TJU funding sources : BISTI andDARPA
Interface of systems engineering and genomics data
acquisition and data analysis Experimental opportunities
Modeling opportunities
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Objectives
Understanding, prediction and control of
human functional processes
Disease models and relevancy
Reverse engineering opportunities
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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
Outputsadaptive processes
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Characteristics
Consists of verycomplexinterconnections 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
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Engineers Viewpoint of Central Issue Biological system consists of processes
Process flowsheet encoded within genome;
not overt and explicit. (Can we decode andexploit?)
Ultimate objective: quantitative prediction of
cellular function; (for system-wide analysis and
novel synthesis and design).
Similarity to chemical processes can be
exploited!?
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SYSTEMS BIOLOGY: Projects
Multi-scale modeling and analysis of adaptive
cellular and system processes Mammalian systemsneurons, brains, brain
functions and diseases
CAKEa model benchmark tool, and a matrix ofsolutions for Genetic Regulatory Circuits.
Development and Analysis of kinetic signaling models
Link of signaling models to Genetic RegulatoryCircuits
Genetic Regulatory Circuits to neuronal electricalbehavior
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SYSTEMS BIOLOGY: Projects
Experimental
Development of useful mammalian microarray, promoter activityand proteomic datae.g.
New methods and applications - e.g. polynies
Analysis
CAKEcombining global datasets, experimental design, prediction
- e.g. genetic regulatory circuit, gene network prediction fromcombined data sets
Development and analysis of kinetic signaling models and e.g. linkof signaling models to genetic regulatory circuit
Genetic regulatory circuits to outpute.g. neuronal electrical
behavior and to biological neural network functionTools:
clone updater, PAINT, masliner II, qualitative modeling approaches,Bayes networks
The IT worldMDL BioSPICE scope, EWG ontologies
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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
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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