Sunday, January 14

3:00pm-6:00pm

Registration and Hotel Check-in

6:00pm-7:00pm

Welcome Reception

7:00pm-7:15pm

Introductory Remarks:  Matt DeLisa (Cornell U) and
Jason Haugh (NC State U)

7:15pm-8:15pm

Opening Keynote Address: 
David Baker (U. of Washington)
Prediction and Design of Macromolecular
Structures and Interactions

8:15pm-10:00pm

Monday, January 15

7:00am-8:30am

Breakfast

Session 1:  Evolutionary Engineering of
Proteins
Co-chairs:   Marc Ostermeier (Johns Hopkins U) and
Andy Nixon (Dyax Corp)

8:30am-9:10am

Sachdev Sidhu (Genentech) Invited
Insights into Molecular Recognition
from Minimalist Synthetic Antibodies

9:10am-9:30am 

David Wood, A Gillies and G. Skretas 
(Princeton U) 
Generation, Mechanisms and Application of
Chimeric Allosteric Hormone Sensors

9:30am-9:50am

Paul O'Maille, N. Dellas and J.P. Noel 
(Jack H. Skirball Center for
Chemical Biology and Proteomics and
Howard Hughes Medical Institute) 
Connecting Sequence Space and Chemical Space:
Traversing Divergent Evolutionary Pathways in
Terpene Cyclases

9:50am-10:30am

George Georgiou (University of Texas, Austin) 
Invited Engineering Restriction-like
Proteases for Proteomic and
Therapeutic Applications

10:30am-10:50am

Break

Session 2:  Biomolecular Probes as
Diagnostic & Therapeutic Reagents
Co-chairs: Patrick S. Daugherty
(UC, Santa Barbara) and 
Bala Rao (NC State University)

10:50am-11:30am

Charles Wilson (Archemix) Invited

11:30am-11:50am

Charles Roth (Rutgers U) 
Molecular Design and Cellular
Delivery of Oligonucleotides 

10:50am-12:10pm

A.M. Levin, R.H. Kimura and Jennifer Cochran
(Stanford U) Engineered High Affinity Integrin
Binding Peptides for Tumor Targeting &
Molecular Imaging Applications

12:10pm-12:30pm

Ichiro Matsumura & R. O'Loughlin 
(Georgia Institute of Tech) 
Identification of a Pentapeptide that Inhibits
HIV Protease Dimerization 

12:30pm-2:00pm

Lunch

Session 3:  Evolutionary and Combinatorial
Approaches to Metabolic Pathway and
Strain Improvement
Co-chairs: Claudia Schmidt-Dannert
(U Minnesota) & Patrick Cirino (Penn State U)

2:00pm-2:40pm

Chaitan Khosla (Stanford U) 
Structural and Evolutionary Approaches for
Engineering Polyketide Biosynthesis

2:40pm-3:00pm

Holly Jessen (Cargill) 
Microbial Production of 3-Hydroxypropanoic Acid: 
A New Platform Chemical from Carbohydrates

3:00pm-3:20pm

Ryan Gill, T. Warnecke, M.D. Lynch & A. Singh
(U of Colorado) 
Using Genomics to Direct Strain Selections

3:20pm-3:40pm

Jeffrey Dietrick, Y. Yoshikuni, K. Fisher, and
Jay Keasling (UC Berkeley) 
Production of Artemisinic-11,12-Epoxide by
Engineered Cytochrome P450 Bm3

3:40pm-5:30pm

Poster Session  with Refreshments
Chairs: Hal Alper (MIT), Mattheos Koffas
(SUNY, Buffalo), and Yi Tang (UCLA)

5:30pm-9:00pm

Dinner 
Keynote Address:  J. Craig Venter
(J. Craig Venter Institute)

Tuesday, January 16

7:00am-8:30am

Breakfast                                                                       

Session 4:  Experimental and Computational
Tools for the Design and
Engineering of Biomolecules
Co-chairs:Eric Boder (U Penn) and
Jeff Gray (Johns Hopkins U)

8:10am-8:50am

Stephen Mayo (Caltech)                                          
Design and Evaluation of Computationally-
Inspired Protein Combinatorial Library Methods

8:50am-9:10am 

H.K. Fung and Christodoulos Floudas
(Princeton U)  
Redesigning Complement 3a and
an HIV-1 Gp41 Inhibitor Using a New De Novo
Protein Design Approach           

9:10am-9:30am

Andreas Lehmann, G.M. Bender, H.C. Fry,
D.E. Engel, M.J. Therien,
W.F. DeGrado, Jeff Saven (U of Pennsylvania) 
Computational Design of Single-Chain
Four-Helix Bundle Proteins That Bind
Non-Biological Cofactors

9:30am-10:10am

K. Dane Wittrup (MIT) Invited
Protein Engineering in Biomedicine

10:10am-10:30am

Break

Session 5:  Intracellular and Intercellular
Signaling Pathways and Networks  
Co-chairs:Anand Asthagiri  (Caltech) and
Bart Hendriks (Pfizer)

10:30am-11:10am

Frances Arnold, C. Tracewell and
K. Brenner (Caltech) Invited  
Constructing Bacterial Multicellular Systems with
Engineered Signaling Pathways  

11:10am-11:30am

Brian Harms, A. Lee, R. Paxson, U. Nielsen, and
B. Schoeberl(Merrimack Pharmaceuticals) 
Applications of Sensitivity Analysis for
Drug Discovery and Development in the
Erbb Receptor Network 

11:30am-11:50am

David Schaffer, J. Burnett, and
A.P. Arkin (UC Berkeley) 
Stochastic Effects Regulate the
Establishment of HIV-1 Latency

11:50am-12:30pm

Tobias Meyer (Stanford U) Invited
Second Messenger Signaling Systems

12:30pm-2:00pm

Lunch

Session 6:  Biophysical and Microscale
Analyses of Molecular and Cellular Function
Co-chairs: Ravi Kane (Rensselaer Polytechnic
Institute) and Josh Molho (Caliper Life Sciences)

2:00pm-2:40pm

Stephen Quake (Stanford U) Invited
Biological Large Scale Integration

2:40pm-3:00pm

Nimisha Srivastava, J.S. Brennan,
D.J. Throckmorton, S. Branda,
Z. Zhang, and A.E. Herr
(Sandia National Laboratories) 
Investigating the Tlr4 Signaling Pathway in
Macrophage Cells Using
Microfluidically-Enabled Flow Cytometry

3:00pm-3:20pm

Arpan Nayak, A. Dutta, C. C. Lee, M. Sorci,
G. J. McRae, and
Georges Belfort
(Rensselaer Polytechnic Institute) 
Fibrillation Kinetics of Recombinant
Human Insulin at Interfaces and with
Osmolytes: Experiments and Kinetic Modeling

3:20pm-3:40pm

T. Lele, S. Kumar, and Donald Ingber
(Childrens Hospital and
Harvard Medical School) 
Mechanical Control of Molecular
Binding Kinetics in Cell-Substrate Adhesion

3:40pm-4:00pm

David Colby  and S. Prusiner
(UC San Francisco) 
Structural Basis of Prion Infectivity

4:00pm-5:30pm

Poster Session  with Refreshments
Chairs:   Hal Alper (MIT), Mattheos Koffas
(SUNY, Buffalo), and Yi Tang (UCLA)

Free Evening

Wednesday, January 17

7:00am-8:30am

Breakfast

Session 7:  Computational Systems Biology
Co-chairs: Jeffrey D. Varner (Cornell U) and
Anthony Burgard (Genomatica)

8:30am-9:10am

Linda Petzold (UC, Santa Barbara) Invited
Multiscale Simulation of Biochemical Systems

9:10am-9:30am 

Zheng Li, Shireesh Srivastava, Fobert Findland, and
Christina Chan (Michigan State U)  
Using Dynamic Analysis of Module Mapping to
Identify Targets That Modulate Free Fatty Acids and
Tumor Necrosis Factor (Tnf)-a Induced Cytotoxicity

9:30am-9:50am

Jennifer Reed, Trina Patel, Keri Chen, Andrew Joyce,
Margaret Applebee, Christopher Herring, Olivia Bui,
Eric Knight, Stephen Fong, and
Bernhard Palsson (UC, San Diego) 
Combining Computational and
Experimental Methods to Identify Genes with
Metabolic Functions

9:50am-10:30am

Colin Hill (Gene Network Sciences) Invited
Reverse Engineering Regulatory Networks to
Determine Mode of Action and
Efficacy Markers for Multi Targeted-Kinase
Inhibitors

10:30am-10:50am

Break

Session 8:  Synthetic Biology  
Co-chairs:  Christina Smolke (Cal Tech) and
Jeremy Minshull (DNA 2.0)

10:50am-11:30am

Wendell Lim (UC, San Francisco) Invited    
The Modular Logic of Cell Signaling Systems

11:30am-11:50am

Justin Gallivan(Emory U) 
Engineered Bacterial Chemonavigation 

11:50am-12:10pm

John C. Anderson, Adam Arkin, and
Chris Voigt (UC, San Francisco) 
Design of Tumor-Killing Bacteria

12:10pm-12:30pm

Philippe Marguet, Eric Spitz, and
Linchong You (Duke U) 
Suicide Design, Oscillations, and
Host Interactions in a
Synthetic Gene Circuit

12:30pm-2:00pm

Lunch

2:00pm-3:30pm

Poster Session 
Chairs:  Hal Alper (MIT),
Mattheos Koffas (SUNY, Buffalo), and
Yi Tang (UCLA)

Session 9: Genomics, Proteomics and
Metabolomics Approaches for
Modifying Cellular Processes
Co-chairs: Ryan Gill (U of Colorado) and
Ranjan Patnaik (DuPont)

3:30pm-4:10pm

Gregory Stephanopoulos and
Hal Alper (MIT)Invited
Global Transcriptional Machinery
Engineering (Gtme): a New Powerful Tool for
Metabolic and Cell Engineering

4:10pm-4:30pm

Thomas Wood and  Jintae Lee (Texas A&M U) 
Discovery and Control of Signaling in
Pathogenic Biofilms

4:30pm-4:50pm

Kelvin Lee, Pat Lee and
Prateek Gupta (Cornell U) 
Engineered Protein Hypersecretion
Via mRNA and Protein Expression Profiling

4:50pm-5:10pm

Robert Kelly (North Carolina State U)  
Functional Genomic Approaches for
Determining the Role of
Protein/Peptide-Encoding Small
Open Reading Frames (Orfs) in
Microbial Genomes 

5:10pm-5:30pm

Stephen Van Dien, Anthony Burgard,
Christophe Schilling (Genomatica) 
An Integrated Platform for Model-Driven
Strain Design

5:30pm-6:00pm

Break

6:00pm-7:00pm

Reception

7:00pm-9:00pm

Dinner 
Keynote Address: 
Willem ‘Pim’ Stemmer (Amunix)

Thursday, January 18

7:00am-8:30am

Breakfast

Session 10:  Experimental and Computational
Tools for the Design and Engineering of
Biomolecules II

8:30am-8:50am

James Schneider, Jeffrey Savard, and
Shane Grosser (Carnegie Mellon U)
Separation and Identification of Biomolecules
Using Nucleic-Acid Amphiphiles in Micellar
Electrokinetic Chromatography

8:50am-9:10am 

Di Gao and Jerome Schultz (UC, Riverside)
Novel High-Throughput
Surface Plasmon Resonance
Methodology for Proteomics

9:10am-9:30am

9:30am-9:50am

Maung Nyan Win and Christina Smolke (Caltech)
Engineering New Molecular Sensors and
Switches for Programming Cellular Systems

9:50am-10:10am

A. James Link, Georgios Skretas,  Nandini Aiyappan,
and Goerge Georgiou (U Texas, Austin)
Engineering E. coli for Membrane Protein Biogenesis

10:10am-10:30am

Break

10:30am-10:50am

Wilfred Chen, Ashok Mulchandani, and
U. Loi Lao (UC, Riverside) Simple Conjugation
and Purification of Quantum Dot-Antibody
Complexes Using a Thermally Responsive
Elastin-Protein L Scaffold as
Immunofluorescent Agents

10:50am-11:10am

Kathryn Armstrong and Bruce Tidor (MIT) 
Computationally Mapping Sequence Space for
Evolutionary Protein Design

11:10am-11:30am

Yasuo Yoshikuni and Jay Keasling (UC, Berkeley) 
Designed Divergent Evolution of Enzyme Function

11:30am-11:50am

Huimin Zhao, K. Chockalingam, M. McLachlan, and
K.C. Lai (University of Illinois, Urbana-Champaign)
Protein Engineering of Gene Switches

11:50am-12:30pm

Close and Discussion of Future Programming

12:30pm-1:30pm

Session Chairs and Future Meeting Chairs Luncheon