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