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ISCB Overton Prize Keynote

Cole Trapnell

Cole Trapnell

Assistant Professor, Department of Genome Sciences, University of Washington
United States

Presentation Title: Reconstructing and deforming developmental landscapes
Time: Saturday July 7, 8:30 am - 9:30 am
Room: Grand Ballroom C-F

The Overton Prize recognizes the research, education, and service accomplishments of early to mid-career scientists who are emerging leaders in computational biology and bioinformatics. The Overton Prize was instituted in 2001 to honor the untimely loss of G. Christian Overton, a leading bioinformatics researcher and a founding member of the ISCB Board of Directors. Cole Trapnell is being recognized as the 2018 winner of the Overton Prize.


Developing embryos are comprised of highly plastic individual cells that shift from one functional state to another, often reversibly so. A cell executes a different gene expression program for each of its possible roles, switching between them as needed throughout its life. How does the genome encode the developmentally intended sequence of program switches? Which gene regulatory events are crucial for a given cell fate decision? Quantifying each gene’s contribution in governing even one developmental step is a staggeringly difficult challenge. However, massively scalable single-cell transcriptome and epigenome profiling offers a way to quantitatively dissect developmental regulatory circuits. I will discuss new assays and algorithms developed by my laboratory to realize this goal, and offer some lessons from several of our recent projects.


Cole Trapnell is an Assistant Professor in the Department of Genome Sciences at the University of Washington. Trapnell received his bachelor’s degree and PhD in Computer Science from the University of Maryland. As a graduate student, he was co-advised by Steven Salzberg, and Lior Pachter from the University of California, Berkeley, where he spent several years as a visiting student. While working with Salzberg and Pachter, Trapnell wrote TopHat and Cufflinks, and assisted Ben Langmead with Bowtie.

Dr. Trapnell studies stem cells and differentiation, primarily using high throughput transcriptome sequencing. He is the principal developer of several widely used open-source software tools for analyzing high-throughput sequencing experiments. At the University of Washington, his lab focuses on finding genes that govern stem cell maintenance and cell differentiation, primarily through single-cell genomics.