Skip to main content

Have you used our open science resources?

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.

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

Goals and Approach

The Trapnell Lab mission is to understand how the genome encodes the program of development and the role this program plays in disease. They develop and apply genomic tools, especially single-cell sequencing, to a variety of in vitro and animal model systems.

Their research strategy is to develop new algorithms and measurements technologies that will enable the community to quantitatively model how every gene is regulated in every cell type found in an animal. Lab members draw from computer science, statistics, and molecular cell biology to jointly develop both new assays and algorithms that fully exploit their capabilities. They are using their technologies to understand the genetic control of plasticity in zebrafish and other key model systems of development.

Trapnell Headshot
Cole Trapnell, Ph.D., Co-Director, Seattle Hub for Synthetic Biology; Associate Professor of Genome Sciences, University of Washington

Research Details

zebrafish scientific image

We are working to systematically perturb zebrafish embryonic development and read out the effects using massively multiplexed single-cell molecular profiling. These experiments will not only facilitate the mapping of the gene networks that control vertebrate development, but all shed light on how those networks buffer variability and confer robustness.

A greay and orange pixelated graph

We aim to use single-cell genomics experiments to train statistical and machine learning models that can explain how every gene is regulated in every cell in an entire animal. We are developing new algorithms that use ideas from statistics to reason about the genetic control of development and disease.

Genetic screening has been a cornerstone in efforts to dissect the program that controls how cells exert their function or breakdown in disease. Single-cell sequencing provides a means of interrogating the molecular consequences of genetic, chemical, or environmental perturbations, but limited sample multiplexing in commercial platforms makes screening infeasible. We have developed and continue to improve various methods for highly multiplexed single-cell sequencing experiments. We have applied these tools to study diverse biological systems including cancer cells and whole zebrafish embryos.

Science Programs at Allen Institute