UW Genome Sciences

Research:

Dr. Trapnell studies stem cells and differentiation, primarily using high throughput transcriptome sequencing. He earned his Ph.D. in Computer Science from the University of Maryland, College Park, where he was jointly advised by Steven Salzberg and Lior Pachter. As a postdoc in John Rinn’s lab at Harvard’s Stem Cell and Regenerative Biology department, he pioneered methods for analyzing differentiation with single cell 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 will focus on finding genes that govern stem cell maintenance and cell differentiation, primarily through single-cell genomics. The lab will operate at the interface between genomics and experimental cell biology to answer how cells make fate decisions.

Selected Publications:

KCole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen & John L Rinn, "The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells”, Nature Biotechnology, doi:10.1038/nbt.2859 (2014)

Lei Sun*, Loyal A Goff*, Cole Trapnell*, Ryan Alexander, Kinyui Alice Lo, Ezgi Hacisuleyman, Martin Sauvageau, Barbara Tazon-Vega, David R Kelley, David G Hendrickson, Bingbing Yuan, Manolis Kellis, Harvey F Lodish, John L Rinn, "Long noncoding RNAs regulate adipogenesis", PNAS, 2013 

Cole Trapnell*, David Hendrickson*, Martin Sauvageau, Loyal Goff, John Rinn, Lior Pachter, "Differential analysis of gene regulation at transcript resolution with RNA-seq", Nature Biotechnology, 2012  

Cole Trapnell, Brian A. Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J. van Baren, Steven L. Salzberg, Barbara J. Wold, and Lior Pachter. "Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms." Nature Biotechnology, 28, 511–515, doi:10.1038/nbt.1621 (2010)

Cole Trapnell, Lior Pachter, and Steven L. Salzberg, "TopHat: discovering splice junctions with RNA-Seq."Bioinformatics (2009), doi:10.1093/bioinformatics/btp120

Ben Langmead, Cole Trapnell, Mihai Pop, and Steven L. Salzberg, "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome." Genome Biology, 10:R25 (2009) 

additional publication listings available via PubMed