Cole Trapnell

Principal Investigator
Google Scholar

I’m an Assistant Professor in the Department of Genome Sciences at the University of Washington. I study cell differentiation, reprogramming and cell-cell communication. I also develop technologies to help identify genes that regulate these processes.

I received my bachelor’s degree and my PhD in Computer Science from the University of Maryland. As a graduate student, I was co-advised by Steven Salzberg, and Lior Pachter from the University of California, Berkeley, where I was a visiting student for several years. While working with Steven and Lior, I wrote TopHat and Cufflinks, and I helped Ben Langmead with Bowtie. I trained as postdoc in John Rinn’s lab at Harvard’s Department of Stem Cell and Regenerative Biology, where I learned to work with stem cells. Near the end of my time at Harvard, I worked with Davide Cacchiarelli on Monocle.


Reversed graph embedding resolves complex single-cell developmental trajectories

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

Single-cell mRNA quantification and differential analysis with Census

Single-cell transcriptome sequencing recent advances and remaining challenges

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

Defining cell types and states with single-cell genomics

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Pulmonary macrophage transplantation therapy

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Long noncoding RNAs regulate adipogenesis

Differential analysis of gene regulation at transcript resolution with RNA-seq

SHAPE–Seq: High‐Throughput RNA Structure Analysis

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Identification of novel transcripts in annotated genomes using RNA-Seq

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

Modeling and automation of sequencing-based characterization of RNA structure

Computational methods for transcriptome annotation and quantification using RNA-seq

Improving RNA-Seq expression estimates by correcting for fragment bias

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

Optimizing data intensive GPGPU computations for DNA sequence alignment

TopHat: discovering splice junctions with RNA-Seq

How to map billions of short reads onto genomes

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

A peer-to-peer blacklisting strategy inspired by leukocyte-endothelial interaction