Papers in bold were led or co-led by members of the Trapnell lab.

2024
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis

Hasegawa & Franks, et al. 2024.

Science Advances

Multiplexed single cell transcriptomics optimizes mesodermal patterning and hemogenic endothelial output from murine embryonic stem cells

Varnum-Finney, et al. 2024.

bioRxiv

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

Lalanne & Regalado, et al. 2024.

Nature Methods

A single-cell time-lapse of mouse prenatal development from gastrula to birth

Qiu, et al. 2024.

Nature

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

McFaline-Figueroa, et al. 2023.

Cell Genomics

2023
High-Capacity sample multiplexing for single cell chromatin accessibility profiling

Booth, et al. 2023.

BMC Genomics

Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Huang, et al. 2023.

Nature

Embryo-scale reverse genetics at single-cell resolution

Saunders, Srivatsan, et al. 2023.

Nature

Proteostasis governs differential temperature sensitivity across embryonic cell types

Dorrity, et al. 2023.

Cell

A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia

Tresenrider, et al. 2023.

bioRxiv

Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity

Tresenrider, et al. 2023.

Cell Reports Methods

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

Shi, et al. 2023.

eLife

2022
Optimized single-nucleus transcriptional profiling by combinatorial indexing

Martin, et al. 2022.

Nature Protocols

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

Rubin, et al. 2022.

Journal of Experimental Medicine

The continuum of Drosophila embryonic development at single-cell resolution

Calderon, et al. 2022.

Science

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

Huang & Henck, et al. 2022.

bioRxiv

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

Read, et al. 2022.

bioRxiv

Nuclear oligo hashing improves differential analysis of single-cell RNA-seq

Kim, Booth, et al. 2022.

Nature Communications

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

Vanderwall, et al. 2022.

Scientific Reports

Systematic reconstruction of cellular trajectories across mouse embryogenesis

Qiu, et al. 2022.

Nature Genetics

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

Shima, et al. 2022.

American Journal of Physiology-Lung Cellular and Molecular Physiology

2021
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Bonora, et al. 2021.

Genome Biology

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

Dignum, et al. 2021.

Cell Reports

Embryo-scale, single-cell spatial transcriptomics

Srivatsan, Regier, et al. 2021.

Science

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

O'Connor, et al. 2021.

Molecular systems biology

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

Aman, Saunders, et al. 2021.

bioRxiv

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

Hadland, et al. 2021.

bioRxiv

2020
A human cell atlas of fetal chromatin accessibility

Domcke, Hill, Daza, et al. 2020.

Science

A human cell atlas of fetal gene expression

Cao, et al. 2020.

Science

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

Calderon, et al. 2020.

BioRxiv

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

Gabrovsek, et al. 2020.

Journal of Biological Chemistry

Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

Liu, et al. 2020.

Scientific Reports

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

Hasle, et al. 2020.

Molecular Systems Biology

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

Furlan, et al. 2020.

Blood Advances

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

Cao, et al. 2020.

Nature Biotechnology

The promise of single-cell genomics in plants

McFaline-Figueroa, Trapnell, & Cuperus. 2020.

Current opinion in plant biology

Dimensionality reduction by UMAP to visualize physical and genetic interactions

Dorrity, Saunders et al. 2020.

Nature Communications

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

Qiu et al. 2020.

Cell Systems

Connect-seq to superimpose molecular on anatomical neural circuit maps

Hanchate, Lee et al. 2020.

PNAS

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

Sridhar, et al. 2020.

Cell Reports

2019
Massively multiplex chemical transcriptomics at single cell resolution

Srivatsan, McFaline-Figueroa, Ramani, et al. 2019.

Science

Supervised classification enables rapid annotation of cell atlases

Pliner et al. 2019.

Nature Methods

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

Packer, Zhu et al. 2019.

Science

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

McFaline-Figueroa, et al. 2019.

Nature Genetics

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Saunders et al. 2019.

eLife

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development

Sharon et al. 2019.

Cell Reports

Dynamics of gene expression in single root cells of Arabidopsis thaliana

Jean-Baptiste et al. 2019

The Plant Cell

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

Sinnamon, Torkenczy et al. 2019.

Genome Research

The single-cell transcriptional landscape of mammalian organogenesis

Cao, Spielmann et al. 2019.

Nature

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

Sharon, Chawla et al. 2019.

Cell

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

Gasperini et al. 2019.

Cell

2018
Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome

Cacciarelli et al. 2018.

Cell Systems

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

Cao et al. 2018.

Science

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

Wray-Dutra et al. 2018.

Journal of Experimental Medicine

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

Pliner et al. 2018.

Molecular Cell

A single-cell atlas of in vivo mammalian chromatin accessibility

Cusanovich et al. 2018.

Cell

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

Packer and Trapnell 2018.

Trends in Genetics

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

Cusanovich et al. 2018.

Nature

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

Hill et al. 2018.

Nature Methods

Extreme heterogeneity of influenza virus infection in single cells

Russell et al. 2018.

eLife

2017
Reversed graph embedding resolves complex single-cell trajectories

Qiu et al. 2017.

Nature methods

Comprehensive single-cell transcriptional profiling of a multicellular organism

Cao et al. 2017.

Science

Single-cell mRNA quantification and differential analysis with Census

Qiu et al. 2017.

Nature Methods

2016
Single-cell transcriptome sequencing recent advances and remaining challenges

Liu and Trapnell 2016.

F1000 Research

2015
Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

Hanchate et al. 2015.

Science

Defining cell types and states with single-cell genomics

Trapnell. 2015.

Genome Research

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Cacciarelli, Trapnell, & Ziller et al. 2015.

Cell

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

Cusanovich et al. 2015.

Science

2014
Pulmonary macrophage transplantation therapy

Suzuki et al. 2014.

Nature

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

Trapnell, Cacchiarelli et al. 2014.

Nature Biotechnology

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

Hacisuleyman, Goff et al. 2014.

Nature Structural & Molecular Biology

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

Silverman et al. 2014.

Genome Biology

2013
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells

Gifford, Ziller et al. 2013.

Cell

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

Kim et al. 2013.

Genome Biology

Long noncoding RNAs regulate adipogenesis

Sun et al. 2013.

Proceedings of the National Academy of Sciences

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

Trapnell, Hendrickson et al. 2013.

Nature Biotechnology

2012
SHAPE–Seq: High‐Throughput RNA Structure Analysis

Mortimer et al. 2012.

Current Protocols in Chemical Biology

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

Trapnell et al. 2012.

Nature Protocol

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

Mercer et al. 2012.

Nature Biotechnology

2011
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili et al. 2011.

Genes & Development

Identification of novel transcripts in annotated genomes using RNA-Seq

Roberts et al. 2011.

Bioinformatics

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

Lucks et al. 2011.

Proceedings of the National Academy of Sciences

Modeling and automation of sequencing-based characterization of RNA structure

Aviran et al. 2011.

Proceedings of the National Academy of Sciences

Computational methods for transcriptome annotation and quantification using RNA-seq

Garber et al. 2011.

Nature Methods

Improving RNA-Seq expression estimates by correcting for fragment bias

Roberts et al. 2011.

Genome Biology

2010
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Trapnell et al. 2010.

Nature Biotechnology

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

Bradley et al. 2010.

PLoS Biology

2009
Optimizing data intensive GPGPU computations for DNA sequence alignment

Trapnell & Schatz, 2009.

Parallel Computing

TopHat: discovering splice junctions with RNA-Seq

Trapnell et al. 2009.

Bioinformatics

How to map billions of short reads onto genomes

Trapnell & Salzberg 2009.

Nature Biotechnology

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

Langmead et al. 2009.

Genome Biology

2008
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Salzberg et al. 2008.

BMC genomics

2005
A peer-to-peer blacklisting strategy inspired by leukocyte-endothelial interaction

BC Trapnell, Jr., 2005.

Proceedings of the 4th International Conference on Artificial Immune Systems