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Cole Trapnell

University of California, BerkeleyORCID https://orcid.org/0000-0002-8105-4347

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Impact (2-yr)

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Top Publications

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

Genome biology200922,766 citations

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

Nature Biotechnology201016,341 citationsFirst authorCorresponding

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

Genome biology201313,586 citations

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

Nature Protocols201212,813 citationsFirst authorCorresponding

TopHat: discovering splice junctions with RNA-Seq

Bioinformatics200912,093 citationsFirst authorCorresponding

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

Nature Biotechnology20147,571 citationsFirst authorCorresponding

Reversed graph embedding resolves complex single-cell trajectories

Nature Methods20175,149 citations

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

Nature Biotechnology20123,712 citationsFirst author

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

Genes & Development20113,656 citations

Single-cell mRNA quantification and differential analysis with Census

Nature Methods20172,084 citations

Improving RNA-Seq expression estimates by correcting for fragment bias

Genome biology20111,812 citations

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

Nature Structural & Molecular Biology2014641 citations

Cole Trapnell · Scinovex