2015 - Fellow of Alfred P. Sloan Foundation
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead;Cole Trapnell;Mihai Pop;Steven L Salzberg.
Genome Biology (2009)
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell;Cole Trapnell;Brian A Williams;Geo Pertea;Ali Mortazavi.
Nature Biotechnology (2010)
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell;Lior Pachter;Steven L. Salzberg.
Bioinformatics (2009)
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Daehwan Kim;Daehwan Kim;Geo Pertea;Cole Trapnell;Cole Trapnell;Harold Pimentel.
Genome Biology (2013)
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell;Adam Roberts;Loyal Goff;Loyal Goff;Loyal Goff;Geo Pertea.
Nature Protocols (2012)
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
Cole Trapnell;Davide Cacchiarelli;Davide Cacchiarelli;Jonna L Grimsby;Prapti Pokharel.
Nature Biotechnology (2014)
Differential analysis of gene regulation at transcript resolution with RNA-seq
Cole Trapnell;David G Hendrickson;David G Hendrickson;Martin Sauvageau;Martin Sauvageau;Loyal Goff;Loyal Goff.
Nature Biotechnology (2013)
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Moran N. Cabili;Cole Trapnell;Cole Trapnell;Loyal Goff;Magdalena J. Koziol;Magdalena J. Koziol.
Genes & Development (2011)
Reversed graph embedding resolves complex single-cell trajectories.
Xiaojie Qiu;Qi Mao;Ying Tang;Li Wang.
Nature Methods (2017)
The single-cell transcriptional landscape of mammalian organogenesis
Junyue Cao;Malte Spielmann;Xiaojie Qiu;Xingfan Huang.
Nature (2019)
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University of Washington
University of Colorado Boulder
California Institute of Technology
Johns Hopkins University School of Medicine
Johns Hopkins University
Broad Institute
Fred Hutchinson Cancer Research Center
Max Planck Institute for Molecular Genetics
Johns Hopkins University
Broad Institute
Utrecht University
University of Oregon
Seoul National University
MIT
University of the Balearic Islands
Walter and Eliza Hall Institute of Medical Research
University of Queensland
KU Leuven
National Jewish Health
University of Colorado Anschutz Medical Campus
Oak Ridge National Laboratory
Centre for Addiction and Mental Health
Osaka University
World Bank
Goddard Space Flight Center
National Institute for Astrophysics