SEED 2015 Program

Wednesday, June 10
8:00-12:15 Registration Check-In
9:00-9:30 Coffee served
9:30-9:45 Welcome - Dan Gibson, Synthetic Genomics 
9:45-10:00 Background on Mark Ptashne

Session 1: Systems Modelling

Chair:  Pam Silver, Harvard University

10:00-10:30 Georg Seelig, University of Washington - Learning the Sequence Determinants of Exon Definition from Millions of Random Synthetic Sequences
10:30-11:00 Howard Salis, Penn State - Scalable System-Wide Design of TF- and dCas9-Based Genetic Circuits
11:00-11:30 Andrea Weisse, University of Edinburgh - Quantifying Host-Circuit Interactions with a Mechanistic Chassis Model
11:30-12:00 John Fisk, Colorado State University - Biological Insights from a Computational Simulation of the M13 Bacteriophage Life Cycle
12:00-2:00 Lunch
2:00-4:00 Registration Check-In

Session 2: Biomedical Applications

Chair:  Ron Weiss, MIT

2:00-2:30 Jeff Way, Wyss Institute - Spatial and Quantitative Optimization of Engineered Multi-Element Therapeutic Proteins
2:30-3:00 Kyle Cady, SGI - Engineering Bacteriophage to Address Multidrug-Resistant Pathogens
3:00-3:30 Yvonne Chen, UCLA - Engineering Smarter and Stronger T Cells for Cancer Immunotherapy
3:30-4:00 Steve Shih, JBEI - µsynth: A Versatile Microfluidic Device for Automating the Synthetic Biology Process
4:00-4:30 Coffee Break

Session 3: Biological Circuits and Context

Chair:  Richard Murray, Caltech

4:30-5:00 John Dueber, UC Berkeley - Use of an enzyme-coupled biosensor to engineer a BIA fermentation pathway from glucose in Saccharomyces cerevisiae
5:00-5:30 Stanley Qi, Stanford University - CRISPR Genetic Circuits for Genome Control and Interfacing
5:30-6:00 Eric Klavins, University of Washington - Toward Synthetic Multicellular Behaviors in Yeast
6:00-6:30 Sri Kosuri, UCLA - Synthetic Approaches to Studying Cis-Regulation
6:30-7:30 Reception
Thursday, June 11
7:30-12:00 Registration Check-In
8:00-8:30 Breakfast
8:30-9:30 Keynote: Pam Silver, Harvard University - Designing Biology for a Healthy World 
9:30-10:00 Coffee Break

Session 4: Metabolism, Metabolomics and Engineering Metabolism

Chair:  Chris Voigt, MIT

10:00-10:30 Stephanie Culler, Genomatica - The development of platform-based technologies for the optimization of sustainably produced chemicals
10:30-11:00 Kris Prather, MIT - Metabolite Valves: Dynamic Control of Metabolic Flux for Pathway Engineering
11:00-11:30 Diego Oyarzun, Imperial College London - Gene Circuits for Self-Tuning Metabolic Pathways
11:30-12:00 Tammy Hsu, UC Berkeley - Protecting Groups for Improved Control of Indigo Biosynthesis
12:00-1:30 Lunch

Session 5: Agriculture and Water

Chair: Stephanie Culler, Genomatica

1:30-2:00 Virginia Ursin, Monsanto - What do Soybeans Have to do with Sustainable use of our Oceans?
2:00-2:30 Mary Dunlop, University of Vermont - Engineering Robust Hosts to Improve Microbial Biofuel Production
2:30-3:00 Huirong Gao, Pioneer - Targeted Integration of Genes into the Maize Genome Facilitated By Cas9-gRNA System
3:00-3:30 Coffee Break

Session 6: Advancing Synthetic Biology Tools, Automation and Analytical Technologies

Chair:  Alicia Jackson, DARPA

3:30-3:45 Introduction - Alicia Jackson, DARPA
3:45-4:10 Emily Leproust, Twist Bioscience - Broadband DNA Synthesis
4:10-4:35 Ben Gordon, MIT/Broad Foundry - Rapid Prototyping of Genetic Programs
4:35-5:05 Jacob Beal, Raytheon - Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communication of Synthetic Biology Designs
5:05-5:30 Ron Weiss, MIT
5:30-7:00 Poster Session A
Friday, June 12
7:30-12:00 Registration Check-In
8:00-8:30 Breakfast
8:30-9:30 Keynote: Jennifer Doudna, UC Berkeley - Re-writing Genomes: Discoveries to Applications
9:30-10:00 Coffee Break

Session 7: DNA and RNA Based Synthetic Biology

Chair:  Yvonne Chen, UCLA

10:00-10:30 Erik Winfree, Caltech - Designing and verifying molecular circuits made of DNA
10:30-11:00 Rebecca Schulman, Johns Hopkins University - Powered DNA Strand Displacement Circuits for Continuous Environmental Monitoring and Memory
11:00-11:30 Shaunak Sen, Indian Institute of Technology - Design of a Toolbox of RNA Thermometers
11:30-12:00 Niles Pierce, Caltech - Dynamic RNA Nanotechnology
12:00-2:00 Lunch and NIH Mentoring Session

Session 8: Minimal Systems

Chair: Barry Canton, Ginkgo Bioworks 

2:00-2:30 Elisa Franco, UC Riverside - Bottom Up Construction of Dynamic Biomolecular Materials
2:30-3:00 Michelle O'Malley, UC Santa Barbara - Reconstructing Anaerobic Microbiomes from the ‘Bottom-up': New Techniques to Decipher Interwoven Metabolism

Student Session

Chair:  Barry Canton, Ginkgo Bioworks

3:00-3:15 Daniel A. Martin-Alarcon, MIT - A Modular Protein Architecture for Generalized RNA Targeting: Development and Application to RNA Monitoring, Control, and Protein Scaffolding
3:15-3:30 Thomas Prescott, Oxford - Designing Conservation Relations in Layered Synthetic Biomolecular Networks
3:30-4:00 Coffee Break
4:00-4:15 Hoang Long Pham, National University of Singapore - Directed Evolution of Acid-Tolerant Phenotype Using an Engineered pH-Riboswitch
4:15-4:30 Neda Hassanpour, Tufts - Enabling Selection in Directed Evolution of Enzymes Via Cellular Engineering
4:30-4:45 Enoch Yeung, Caltech - Quantifying and Modeling Compositional Context Effects on Synthetic Biocircuits in E. coli

ACS Synthetic Biology Young Investigator Award Lecture

Chair:  Ranjini Prithviraj, ACS Synthetic Biology

5:15-6:45 Poster Session
7:00- Off site party at Ginkgo Bioworks
Saturday, June 13
7:30-9:30 Registration Check-In
8:00-8:30 Breakfast
8:30-9:30 Keynote: Martin Fussenegger, ETH Zurich - Prosthetic Gene Networks for Biomedical Applications

Session 9: Biological Parts

Chair:  Jeff Way, Wyss Institute for Biologically Inspired Engineering 

9:30-10:00 Caroline Ajo-Franklin, LBL - Controlling Organisms Electrically with Synthetic Biology
10:00-10:30 Stacy Anne-Morgan, UC Berkeley - Towards the High–Throughput Construction of Fluorescent Biosensors
10:30-11:00 Erik Carlson, Northwestern University - A System for Unprecedented Ribosome Engineering in Living E. coli
11:00-11:30 Coffee Break

Session 10: Microbial Communities and Microbiome Genomics

Chair:  Dan Gibson, Synthetic Genomics

11:30-12:00 Giles Oldroyd, John Innes Institute - Engineering nitrogen fixing symbiotic associations in cereals
12:00-12:30 Michael Fischbach, UCSF - Insights from a global view of secondary metabolism: Small molecules from the human microbiota
12:30-1:00 Peter Nguyen, Harvard University - Synthetic Biology Engineering of Biofilms As Nanomaterials Factories