Cole Trapnell

Principal Investigator
Google Scholar

I’m an Associate Professor in the Department of Genome Sciences at the University of Washington. I develop new technologies that allow biologists to study gene regulation and cell-cell communication in development and disease. My lab is currently focused mostly on single-cell genomic technologies.

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.


Embryo-scale reverse genetics at single-cell resolution

Proteostasis governs differential temperature sensitivity across embryonic cell types

Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy

High-Capacity sample multiplexing for single cell chromatin accessibility profiling

Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis

Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes

Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters

Optimized single-nucleus transcriptional profiling by combinatorial indexing

Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish

The continuum of Drosophila embryonic development at single-cell resolution

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart

Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication

Systematic reconstruction of cellular trajectories across mouse embryogenesis

A murine model of hereditary pulmonary alveolar proteinosis caused by homozygous Csf2ra gene disruption

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo

Embryo-scale, single-cell spatial transcriptomics

Neural G0 - a quiescent‐like state found in neuroepithelial‐derived cells and glioma

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin

Engineering a niche supporting haematopoietic stem cell development using integrated single cell transcriptomics

A human cell atlas of fetal chromatin accessibility

A human cell atlas of fetal gene expression

TransMPRA - A framework for assaying the role of many trans-acting factors at many enhancers

A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface

Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity

IL-2 enhances ex vivo–expanded regulatory T-cell persistence after adoptive transfer

Sci-fate characterizes the dynamics of gene expression in single cells

The promise of single-cell genomics in plants

Dimensionality reduction by UMAP to visualize physical and genetic interactions

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

Connect-seq to superimpose molecular on anatomical neural circuit maps

Single-cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures

Massively multiplex chemical transcriptomics at single cell resolution

Supervised classification enables rapid annotation of cell atlases

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

Dynamics of gene expression in single root cells of Arabidopsis thaliana

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

The single-cell transcriptional landscape of mammalian organogenesis

A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets

A genome-wide framework for mapping gene regulation via cellular genetic screens

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

A single-cell atlas of in vivo mammalian chromatin accessibility

Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation

The cis-regulatory dynamics of embryonic development at single-cell resolution

On the design of CRISPR-based single-cell molecular screens

Extreme heterogeneity of influenza virus infection in single cells

Reversed graph embedding resolves complex single-cell trajectories

Comprehensive single-cell transcriptional profiling of a multicellular organism

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

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