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.
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.
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