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Seattle Hub for Synthetic Biology

Cracking the code of how changes in our genes manifest as changes in health and disease

Research Overview

The Seattle Hub for Synthetic Biology is a collaboration between Allen Institute, Chan Zuckerberg Initiative and the University of Washington.

Reimagining how we study cells by turning them into their own recording devices

The Seattle Hub for Synthetic Biology is researching and designing cutting-edge technologies that will monitor and record genomic changes in millions of cells simultaneously in real time to unveil their complete cellular histories and reveal the complete chain of events that cause healthy cells to progress into disease. Unlocking this insight has the potential to revolutionize how we diagnose and ultimately treat illnesses and will provide unprecedented clarity into how our environment shapes our fundamental biology.

The work will be deployed at the scale of the whole organism and uncover how genetic or environmental changes give rise to specific characteristics in human cells and tissues, including those involved in disease. This team is also focused on developing technology that would not only diagnose disease, but also treat it.

Seattle Hub Cell Lineage

Research Overview

Reimagining living cells and genomes as devices for recording complex biological information over time.

Researchers at the Seattle Hub for Synthetic Biology are building cellular recording technology that records and captures live data from millions of cells responding to their environment at the scale of the whole organism. Using reverse genetics, the research goes a step further, systematically altering or perturbing genes to illuminate which genes cause which downstream changes. The work is focused on developing a research tool that could someday spawn  diagnostic or clinical tools to not just observe, but actively intervene to treat disease in real time.  Core technologies involved in this research include,  DNA Typewriter and ENGRAM, which were both developed as part of the Allen Discovery Center for Cell Lineage Tracing in Jay Shendure’s lab at UW Medicine.

Seattle Hub animation

“Imagine being able to put a smart watch into each of your cells to record the genome itself and everything that cell is experiencing.”

– Dr. Jay Shendure, Lead Scientific Director of the Seattle Hub for Synthetic Biology, professor of genome sciences and Scientific Director of the Brotman Baty Insitute at the University of Washington School of Medicine.

Meet our teams

This team is working to develop and apply new technologies and methods for genetics, genomics and molecular biology. Research by the Shendure Lab focuses on next-generation DNA sequencing to measure biological phenomena.

Shendure Lab

The Trapnell Lab at the University of Washington’s Department of Genome Sciences studies how genomes encode the program of vertebrate development and how that program goes awry in disease.

Trapnell Lab

Investigating antigen specific adaptive immune cells to better design vaccines and therapeutics.

Pepper Lab

We are a laboratory of biological tinkerers at the intersection of DNA synthesis, protein design and single-cell sequencing.

Pinglay Lab

We use and develop a stem-cell based embryo model that allow us to test out the synthesized DNA circuit in physiologically relevant context and to understand human developmental diseases.

Hamazaki Lab

The Brotman Baty Institute operationalizes and administers the University of Washington (UW) portion of the SeaHub project, and provides single-cell sequencing support to SeaHub teams in the Shendure, Trapnell, Pepper, Pinglay and Hamazaki labs at UW.

Brotman Baty Institute

We use and develop techniques that allow us to build many large pieces of DNA quickly inside cells. The Sense and Write teams use our synthetic DNAs.

Build Team

We take the barcodes from the Sense Team and create a permanent record (DNA Tape) in the cellular DNA. These records are stored in sequential order, enabling us to understand the relative timing of different cellular events.

Write Team

We develop sensors that convert cellular events into barcodes that can then be written into DNA.

Sense Team

We develop computational pipelines and methods to analyze sequencing data and to characterize lineage relationships and biological signaling between cells across various tissues.

Read Team

The In Vivo Team develops mouse models incorporating the technologies developed by the Build, Sense, and Write teams to record cellular events in genomic DNA during mammalian development and homeostasis

In Vivo

Science Programs at Allen Institute