Duke Center for Systems Biology

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Duke Center for Systems Biology
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Origins

• A systems biologist views biological problems
  through the eyes of a systems engineer

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Timeline
2008
2004
2005
2006
2007
2003
First annual Retreat and SAB review
Biological Networks Group formed
First NIH proposal submitted
First DCSB Systems Biology Symposium
Named NIH National Center for Systems Biology
Regular meetings and mini- tutorials held
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Core faculty

• Pankaj Agarwal (Computer Science) Q
• Philip Benfey (Biology) E
• Herbert Edelsbrunner (Computer Science) Q
• Steve Haase (Biology) E
• John Harer (Mathematics) Q
• Alex Hartemink (Computer Science) Q
• Paul Magwene (Biology) E/Q
• Dave McClay (Biology) E
• Sayan Mukherjee (Statistics) Q
• Uwe Ohler (IGSP/Bioinformatics) Q
• Dave Schaeffer (Mathematics) Q
• Josh Socolar (Physics) Q
• Mike West (Statistics) Q
• Greg Wray (Biology) E
• Lingchong You (Biomedical Engineering) E/Q

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Herbert Edelsbrunner
Center for Systems Biology
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Herbert Edelsbrunner
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Herbert Edelsbrunner
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Herbert Edelsbrunner
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CSB associated faculty

• Jungsang Kim (Electrical Engineering)
• Jack Keene (MGM)
• Blanche Capel (Cell Biology)
• Dewey McCafferty (Chemistry)

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Activities

• CSB meetings
• Education
• Outreach
• Faculty recruitment
• Research

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Regular CSB activities

• Weekly meetings
• No stupid questions rule
• Weekly lunches
• Post-docs and grad students
• Journal club

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Educational activities

• Grew out of internal mutual education activities
• Quantitative reasoning for biologists
• Biological processes for quantitative scientists

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Undergraduate

• HHMI grant
• 2 million
• Courses
• Modeling Certificate
• Structure/Function
• Introductory Biology
• Intro to Systems Biology

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Mentored research

• Vertically Integrated Partner (VIP) teams
• 2 faculty, 2 grad students, 2 undergraduates
• Summer research
• Independent study

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Graduate

• Integration into existing programs
• CBB
• UPGG
• Developmental Biology
• Cell and Molecular Biology

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Graduate courses

• Modeling and engineering gene circuits
• Lingchong You
• Computational biology of gene regulation
• Uwe Ohler
• Computational systems biology
• Alex Hartemink

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Outreach

• Annual Systems Biology Symposia
• Workshops
• Postdoctoral Fellows program
• Sabbatical visitors

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Partnership with NCCU

• Course Complex traits and systems biology
• Summer Research Internships

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Worldwide Network of Systems Biology Centers

• Bridging the quantitative/experimental divide
• Systems biology curriculum development
• Establishing, maintaining and sharing systems
  biology databases

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Faculty recruitment

• Cluster hire
• Interdisciplinary
• Cross-school

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Recruitment

• Over 150 applicants
• Interviewed 10
• Two offers made
• Biology - accepted
• Physics declined

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Research projects

• Network dynamics

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Time scales

• Cell cycle
• Minutes to hours
• Development
• Hours to months
• Evolution
• Millions of years