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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 zak@che.udel.edurishi@capsl.udel.edu

mailto:zak@che.udel.edumailto:rishi@capsl.udel.edumailto:rishi@capsl.udel.edumailto:zak@che.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