Defining cell types and states with single-cell genomics

von Trapnell, Cole
Veröffentlicht in Genome Res (2015)

Single-cell transcriptome sequencing: recent advances and remaining challenges

von Liu, Serena, Trapnell, Cole
Veröffentlicht in F1000Res (2016)

Single cell multi-omics: an engine for new quantitative models of gene regulation

von Packer, Jonathan, Trapnell, Cole
Veröffentlicht in Trends Genet (2018)

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment

von Trapnell, Cole, Schatz, Michael C.
Veröffentlicht 2009

How to map billions of short reads onto genomes

von Trapnell, Cole, Salzberg, Steven L
Veröffentlicht 2009

TopHat: discovering splice junctions with RNA-Seq

von Trapnell, Cole, Pachter, Lior, Salzberg, Steven L.
Veröffentlicht 2009

Supervised classification enables rapid annotation of cell atlases

von Pliner, Hannah A., Shendure, Jay, Trapnell, Cole
Veröffentlicht in Nat Methods (2019)

Extreme heterogeneity of influenza virus infection in single cells

von Russell, Alistair B, Trapnell, Cole, Bloom, Jesse D
Veröffentlicht in eLife (2018)

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

von Langmead, Ben, Trapnell, Cole, Pop, Mihai, Salzberg, Steven L
Veröffentlicht 2009

The promise of single-cell genomics in plants

von McFaline-Figueroa, José L, Trapnell, Cole, Cuperus, Josh T
Veröffentlicht in Curr Opin Plant Biol (2020)

High-throughput sequence alignment using Graphics Processing Units

von Schatz, Michael C, Trapnell, Cole, Delcher, Arthur L, Varshney, Amitabh
Veröffentlicht 2007

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

von Cao, Junyue, Zhou, Wei, Steemers, Frank, Trapnell, Cole, Shendure, Jay
Veröffentlicht in Nat Biotechnol (2020)

Improving RNA-Seq expression estimates by correcting for fragment bias

von Roberts, Adam, Trapnell, Cole, Donaghey, Julie, Rinn, John L, Pachter, Lior
Veröffentlicht 2011

Single-cell mRNA quantification and differential analysis with Census

von Qiu, Xiaojie, Hill, Andrew, Packer, Jonathan, Lin, Dejun, Ma, Yi-An, Trapnell, Cole
Veröffentlicht in Nat Methods (2017)

Dimensionality reduction by UMAP to visualize physical and genetic interactions

von Dorrity, Michael W., Saunders, Lauren M., Queitsch, Christine, Fields, Stanley, Trapnell, Cole
Veröffentlicht in Nat Commun (2020)

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

von Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L
Veröffentlicht 2013

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

von Trapnell, Cole, Hendrickson, David G, Sauvageau, Martin, Goff, Loyal, Rinn, John L, Pachter, Lior
Veröffentlicht 2012

Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

von Liu, Serena X., Gustafson, Heather H., Jackson, Dana L., Pun, Suzie H., Trapnell, Cole
Veröffentlicht in Sci Rep (2020)

Reversed graph embedding resolves complex single-cell trajectories

von Qiu, Xiaojie, Mao, Qi, Tang, Ying, Wang, Li, Chawla, Raghav, Pliner, Hannah A., Trapnell, Cole
Veröffentlicht in Nat Methods (2017)

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

von McFaline-Figueroa, José L., Hill, Andrew J., Qiu, Xiaojie, Jackson, Dana, Shendure, Jay, Trapnell, Cole
Veröffentlicht in Nat Genet (2019)