Skip to main content
Trapnell Headshot

Cole Trapnell, Ph.D.

Co-Director, Seattle Hub for Synthetic Biology; Associate Professor of Genome Sciences, University of Washington


Cole Trapnell is a Professor of Genome Sciences at the University of Washington. He received his Ph.D in Computer Science at the University of Maryland and has formal training in both computational and experimental biology. As a graduate student with Steven Salzberg and Lior Pachter, Dr. Trapnell wrote "TopHat" and "Cufflinks", two widely used tools for transcriptome sequencing (RNA-seq) analysis. He also co-developed (with Ben Langmead) the ultrafast short read alignment program "Bowtie". As a postdoctoral fellow, Dr. Trapnell augmented his computational work with experimental training focused on analysis of cell differentiation, and developed “single-cell trajectory analysis”, an approach for studying cell differentiation using single-cell RNA-Seq. Dr. Trapnell’s lab has introduced computational tools extracting biological insights from single-cell data, such as “Monocle”, as well as experimental workflows for ultra-scalable single-cell molecular profiling experiments. The lab has used these tools to explore pancreatic islet development, olfactory neurogenesis, and thyroid hormone-dependent pigmentation, and is currently applying them to dissect the genetic program of zebrafish embryonic development.  Dr Trapnell is a recipient of ISCB Overton Prize (2018), NIH Director’s New Innovator Award and Alfred P. Sloan Foundation Research Fellowship (2015), Damon Runyon Dale F. Frey Award for Breakthrough Scientist (2014).

News & Events

    Science Programs at Allen Institute