duke center for systems biology. origins “a systems biologist views biological problems through...
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Duke Center for Systems Biology
Origins
“A systems biologist views biological problems through the eyes of a systems engineer”
Timeline
2003 20082004 2005 2006 2007
Biological Networks Group formed
First NIHproposal submitted
Named NIHNational Center forSystems Biology
First DCSBSystemsBiologySymposium
Regularmeetingsand mini-tutorialsheld
Became IGSPCenter for SystemsBiology. Move to FFSC space
First annualRetreat and SAB review
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
Greg Wray
Mike West
Philip Benfey
Steve Haase
LingchongYou
Sayan Mukherjee
Uwe Ohler
Alex Hartemink
Joshua Socolar
Paul Magwene
David Schaeffer
PankajAgarwal
DavidMcClay
John Harer
Center for Systems Biology
HerbertEdelsbrunner
Greg Wray
Mike West
Philip Benfey
Steve Haase
LingchongYou
Sayan Mukherjee
Uwe Ohler
Alex Hartemink
Joshua Socolar
Paul Magwene
David Schaeffer
PankajAgarwal
DavidMcClay
John Harer HerbertEdelsbrunner
Mathematics
Medicine
Computer Science
StatisticalScience
Physics
Greg Wray
Mike West
Philip Benfey
Steve Haase
LingchongYou
Sayan Mukherjee
Uwe Ohler
Alex Hartemink
Joshua Socolar
Paul Magwene
David Schaeffer
PankajAgarwal
DavidMcClay
John Harer
Biology
HerbertEdelsbrunner
Mathematics
Medicine
Computer Science
StatisticalScience
Physics
Greg Wray
Mike West
Philip Benfey
Steve Haase
LingchongYou
Sayan Mukherjee
Uwe Ohler
Alex Hartemink
Joshua Socolar
Paul Magwene
David Schaeffer
PankajAgarwal
DavidMcClay
John Harer
Biology
Computational Biology and Bioinformatics
HerbertEdelsbrunner
CSB associated faculty
• Jungsang Kim (Electrical Engineering)
• Jack Keene (MGM)
• Blanche Capel (Cell Biology)
• Dewey McCafferty (Chemistry)
Activities
• CSB meetings
• Education
• Outreach
• Faculty recruitment
• Research
Regular CSB activities
• Weekly meetings– “No stupid questions” rule
• Weekly lunches– Post-docs and grad students
• Journal club
Educational activities
• Grew out of internal mutual education activities– Quantitative reasoning for biologists– Biological processes for quantitative
scientists
Undergraduate
• HHMI grant– $2 million
• Courses– Modeling Certificate– Structure/Function– Introductory Biology– Intro to Systems Biology
Mentored research
• Vertically Integrated Partner (VIP) teams
– 2 faculty, 2 grad students, 2 undergraduates– Summer research– Independent study
Graduate
• Integration into existing programs– CBB– UPGG– Developmental Biology– Cell and Molecular Biology
Graduate courses
• Modeling and engineering gene circuits – Lingchong You
• Computational biology of gene regulation– Uwe Ohler
• Computational systems biology– Alex Hartemink
Outreach
• Annual Systems Biology Symposia
• Workshops
• Postdoctoral Fellows program
• Sabbatical visitors
Partnership with NCCU
• Course: “Complex traits and systems biology”
• Summer Research Internships
Worldwide Network of Systems Biology Centers
• Bridging the quantitative/experimental divide
• Systems biology curriculum development
• Establishing, maintaining and sharing systems biology databases
Faculty recruitment
• Cluster hire– Interdisciplinary– Cross-school
Recruitment
• Over 150 applicants
• Interviewed 10
• Two offers made– Biology - accepted– Physics – declined
Research projects
Network dynamics
Time scales
• Cell cycle– Minutes to hours
• Development– Hours to months
• Evolution– Millions of years