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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

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

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

Researchers at the Seattle Hub for Synthetic Biology are developing experimental and computational tools to study how genes, cells, and tissues function over time within intact organisms. A central focus is molecular recording: genetically encoded systems that allow living cells to write information about their lineage, signaling, and environmental exposures into DNA, creating a durable record that can be read later using sequencing. In parallel, SeaHub performs large-scale, systematic perturbation experiments—altering genes, pathways, or environmental conditions in model organisms—and measures the resulting effects at single-cell resolution across development. By integrating these perturbation data with longitudinal recordings and computational modeling, SeaHub aims to uncover causal relationships between genes, cellular states, and organismal phenotypes that are difficult to infer from static or isolated measurements.

This work is focused on building foundational research technologies, datasets and computational models rather than immediate clinical applications. Over time, the resulting tools and models may inform how we interpret human biology, disease mechanisms, and environmental influences, and could eventually support more precise approaches to diagnosis or intervention. Core technologies underlying this effort include   DNA Typewriter, ENGRAM, and embryo-scale reverse genetics, technologies originally developed through the Allen Discovery Center for Cell Lineage Tracing.

“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 and Partners

Shendure Lab

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

Trapnell 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

Pepper Lab

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

Pepper Lab

Pinglay Lab

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

Pinglay Lab

Hamazaki 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

Brotman Baty Institute

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

Write 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

Sense Team

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

Sense Team

Read 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

In Vivo 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

SeaBridge

SeaBridge is a program to translate the Seattle Hub for Synthetic Biology’s cutting-edge technologies into real-world applications. We integrate a postdoctoral fellowship training program (SeaBridge Fellowship Program) with a translational research center (LaunchPad) to train the next generation of scientists while advancing the potential of Seattle Hub for Synthetic Biology’s unique genome engineering platform.

SeaBridge