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Duke Center for Systems Biology

Duke Center for Systems Biology. Origins. “A systems biologist views biological problems through the eyes of a systems engineer”. Timeline. 2004. 2005. 2006. 2007. 2008. 2003. First annual Retreat and SAB review. Biological Networks Group formed. First NIH proposal

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Duke Center for Systems Biology

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  1. Duke Center for Systems Biology

  2. Origins “A systems biologist views biological problems through the eyes of a systems engineer”

  3. Timeline 2004 2005 2006 2007 2008 2003 First annual Retreat and SAB review Biological Networks Group formed First NIH proposal submitted Became IGSP Center for Systems Biology. Move to FFSC space First DCSB Systems Biology Symposium Named NIH National Center for Systems Biology Regular meetings and mini- tutorials held

  4. 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

  5. Philip Benfey Mike West Steve Haase Lingchong You Joshua Socolar Sayan Mukherjee Alex Hartemink Uwe Ohler John Harer David Schaeffer Greg Wray Paul Magwene Pankaj Agarwal David McClay Herbert Edelsbrunner Center for Systems Biology

  6. Philip Benfey Mike West Steve Haase Lingchong You Joshua Socolar Sayan Mukherjee Alex Hartemink Uwe Ohler John Harer David Schaeffer Greg Wray Paul Magwene David McClay Pankaj Agarwal Herbert Edelsbrunner

  7. Statistical Science Biology Philip Benfey Mike West Steve Haase Physics Medicine Lingchong You Joshua Socolar Sayan Mukherjee Alex Hartemink Computer Science Uwe Ohler Mathematics David Schaeffer John Harer Greg Wray Paul Magwene Pankaj Agarwal David McClay Herbert Edelsbrunner

  8. Statistical Science Biology Philip Benfey Mike West Steve Haase Physics Medicine Lingchong You Joshua Socolar Sayan Mukherjee Alex Hartemink Computer Science Uwe Ohler Mathematics David Schaeffer John Harer Greg Wray Paul Magwene Pankaj Agarwal David McClay Computational Biology and Bioinformatics Herbert Edelsbrunner

  9. CSB associated faculty • Jungsang Kim (Electrical Engineering) • Jack Keene (MGM) • Blanche Capel (Cell Biology) • Dewey McCafferty (Chemistry)

  10. Activities • CSB meetings • Education • Outreach • Faculty recruitment • Research

  11. Regular CSB activities • Weekly meetings • “No stupid questions” rule • Weekly lunches • Post-docs and grad students • Journal club

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

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

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

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

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

  17. Outreach • Annual Systems Biology Symposia • Workshops • Postdoctoral Fellows program • Sabbatical visitors

  18. Partnership with NCCU • Course: “Complex traits and systems biology” • Summer Research Internships

  19. Worldwide Network of Systems Biology Centers • Bridging the quantitative/experimental divide • Systems biology curriculum development • Establishing, maintaining and sharing systems biology databases

  20. Faculty recruitment • Cluster hire • Interdisciplinary • Cross-school

  21. Recruitment • Over 150 applicants • Interviewed 10 • Two offers made • Biology - accepted • Physics – declined

  22. Research projects Network dynamics

  23. Time scales • Cell cycle • Minutes to hours • Development • Hours to months • Evolution • Millions of years

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