Pre-meeting Workshop

Genome Editing

Genome Editing Workshop2018-07-18T20:48:03+00:00

Genome Editing: CRISPR/Cas9, transposons and other tools

Industrial strain improvement programs are often tasked with quickly (and cheaply) identifying beneficial genetic changes and stacking them into single strains. The ability to quickly, efficiently, and with great precision being able to insert, edit, delete and rearrange genomic information in living cells is a rapidly changing field that impacts microbes, plants, and mammalian cell lines on a multitude of levels. The tools to create these changes must be specific in where they edit the genome, flexible in their utility, and scalable. Additionally, some approaches work well for some hosts but not in all hosts necessitating many months of research and development to perform proof of principle and optimization experiments. Researchers are constantly on the lookout for searching for generic tools, much like a Swiss Army Knife, to help accelerate their research.

The last few years have seen a tidal wave of novel genetic engineering tools. Most famous among these tools include: RNA-guided endonucleases (e.g., CRISPR/Cas9 in its many formats), TALENs, Zinc fingers nucleases, meganucleases, and Flip In and transposons. Just like restriction enzymes in the NEB catalog, each genome editing tool has its pro’s and con’s. This workshop will focus broadly on the scope of the types of tools, with an emphasis on transposons – a somewhat forgotten genome engineering tool in the recent genome engineering gold rush. Much of what will be presented will be through the lens of industry and how traditional and next generation genetic engineering tools can (and are) applied in a high-throughput setting.

Who should attend?

The workshop should be attended by scientists new to genome engineering and interested in getting an overview of the emerging genome engineering toolbox. Experienced scientists will also appreciate the industrial angle the presenters provide. Topics will be discussed broadly so that non-scientists will be able to come away with an appreciation for emerging tools and technologies increasingly available to edit genomes with high precision.


  1. Quick introduction to the different classes of genome engineering tools
  2. General mechanism and process using CRISPR cas9 as case study
  3. High throughput biology meets strain improvement: A Zymergen case study
  4. Different applications in different hosts require different tools
  5. How to build your own genome engineering tool using Leap-In as case study

How to Register

You can register for the workshop with your Annual Meeting registration (online or registration form). For more info, go to the Annual Meeting registration page.

If you wish to attend the workshop only (and not the SIMB Annual Meeting), you may register online and select “Workshop Attendee Only” as your registration fee. Or, you may fill out the Annual Meeting registration form.

Walk-on registrations for the workshop will be accepted Sunday, August 12, from 7-8 am only. Space will be limited.


8:30 am – 4:00 pm


Hilton Chicago


Claes Gustafsson – ATUM

ATUM is pioneering the use of synthetic biology and machine learning to engineer genes, proteins and genomes across a multitude of commercial applications. As ATUMÆs Co-Founder and CCO, Dr. Gustafsson oversees all of the companyÆs partnered scientific programs for gene, protein and genome engineering. Prior to co-founding ATUM in 2003, Gustafsson developed fungal genome engineering technologies and led the bioinformatics team at Maxygen for five years. Claes has also held scientist positions at Kosan Biosciences where he engineered Streptomyces to produce novel polyketides, as well as positions at UC Santa Cruz under Prof Harry Noller and UC San Francisco under Prof Dan Santi. He holds ~50 issued US patents and has published ~50 scientific papers. Gustafsson received his PhD 1992 from the University of Umeσ, Sweden where he studied translation under Prof Glenn Bj÷rk.

Shawn Szyjka – Zymergen

Shawn Szyjka is currently an Associate Director within the Platform Research & Development group at Zymergen. The group’s core mission is to identify and test step-change technologies, which can then be deployed at production scale. At Zymergen, Shawn leads multiple genome editing projects leveraging biology, software, and automation to accelerate hit identification and stacking into a variety of industrial microbes. Previously, Shawn was at Sapphire Energy where he was responsible for developing genetic tools to edit algal genomes. During his time there, Shawn led the first outdoor piloting of a genetically engineered algal strain; a collaboration between Sapphire Energy, the Environmental Protection Agency, and UC San Diego. Shawn earned his Ph.D. in 2008 from the University of Southern California where he studied DNA replication fork dynamics and cell cycle checkpoints in Dr. Oscar Aparicio’s lab.

Limit: 30 attendees


Early registration
SIMB Member: $350
Nonmember: $525
Student: $225

Regular and onsite registration
SIMB Member $450
Nonmember: $625
Student: $225

Includes breakfast, lunch, 2 breaks and workshop materials.