Search Results - Cole Trapnell

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  1. 1
    Defining cell types and states with single-cell genomics

    Defining cell types and states with single-cell genomics by Cole Trapnell

    Published 2015
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  2. 2
    Single-cell transcriptome sequencing: recent advances and remaining challenges

    Single-cell transcriptome sequencing: recent advances and remaining challenges by Serena Liu, Cole Trapnell

    Published 2016
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  3. 3
    Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation

    Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation by Jonathan S. Packer, Cole Trapnell

    Published 2018
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  4. 4
    Optimizing data intensive GPGPU computations for DNA sequence alignment

    Optimizing data intensive GPGPU computations for DNA sequence alignment by Cole Trapnell, Michael C. Schatz

    Published 2009
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  5. 5
    How to map billions of short reads onto genomes

    How to map billions of short reads onto genomes by Cole Trapnell, Steven L. Salzberg

    Published 2009
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  6. 6
    TopHat: discovering splice junctions with RNA-Seq

    TopHat: discovering splice junctions with RNA-Seq by Cole Trapnell, Lior Pachter, Steven L. Salzberg

    Published 2009
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  7. 7
    Supervised classification enables rapid annotation of cell atlases

    Supervised classification enables rapid annotation of cell atlases by Hannah A. Pliner, Jay Shendure, Cole Trapnell

    Published 2019
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  8. 8
    Identification of novel transcripts in annotated genomes using RNA-Seq

    Identification of novel transcripts in annotated genomes using RNA-Seq by Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter

    Published 2011
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  9. 9
    Extreme heterogeneity of influenza virus infection in single cells

    Extreme heterogeneity of influenza virus infection in single cells by Alistair B. Russell, Cole Trapnell, Jesse D. Bloom

    Published 2018
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  10. 10
    Improving RNA-Seq expression estimates by correcting for fragment bias

    Improving RNA-Seq expression estimates by correcting for fragment bias by Adam Roberts, Cole Trapnell, Julie Donaghey, John L. Rinn, Lior Pachter

    Published 2011
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  11. 11
    Sci-fate characterizes the dynamics of gene expression in single cells

    Sci-fate characterizes the dynamics of gene expression in single cells by Junyue Cao, Wei Zhou, Frank J. Steemers, Cole Trapnell, Jay Shendure

    Published 2020
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  12. 12
    Dimensionality reduction by UMAP to visualize physical and genetic interactions

    Dimensionality reduction by UMAP to visualize physical and genetic interactions by Michael W. Dorrity, Lauren M. Saunders, Christine Queitsch, Stanley Fields, Cole Trapnell

    Published 2020
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  13. 13
    TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

    TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions by Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L. Salzberg

    Published 2013
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  14. 14
    Single-cell mRNA quantification and differential analysis with Census

    Single-cell mRNA quantification and differential analysis with Census by Xiaojie Qiu, Andrew J. Hill, Jonathan S. Packer, Dejun Lin, Yi-An Ma, Cole Trapnell

    Published 2017
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  15. 15
    Trajectory analysis quantifies transcriptional plasticity during macrophage polarization

    Trajectory analysis quantifies transcriptional plasticity during macrophage polarization by Serena X. Liu, Heather H. Gustafson, Dana L. Jackson, Suzie H. Pun, Cole Trapnell

    Published 2020
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  16. 16
    Differential analysis of gene regulation at transcript resolution with RNA-seq

    Differential analysis of gene regulation at transcript resolution with RNA-seq by Cole Trapnell, David G. Hendrickson, Martin Sauvageau, Loyal A. Goff, John L. Rinn, Lior Pachter

    Published 2012
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  17. 17
    Reversed graph embedding resolves complex single-cell developmental trajectories

    Reversed graph embedding resolves complex single-cell developmental trajectories by Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A. Pliner, Cole Trapnell

    Published 2017
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  18. 18
    Reversed graph embedding resolves complex single-cell trajectories

    Reversed graph embedding resolves complex single-cell trajectories by Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A. Pliner, Cole Trapnell

    Published 2017
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  19. 19
    A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

    A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition by José L. McFaline‐Figueroa, Andrew J. Hill, Xiaojie Qiu, Dana L. Jackson, Jay Shendure, Cole Trapnell

    Published 2019
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  20. 20
    Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity

    Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity by Amy Tresenrider, Akshayalakshmi Sridhar, Kiara C. Eldred, Sophia A. Cuschieri, Dawn Hoffer, Cole Trapnell, Thomas A. Reh

    Published 2023
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