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

Ben Langmead, Cole Trapnell, Mihai Pop, +1

Genome biology

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

Cole Trapnell, Brian A. Williams, Geo Pertea, +6

Nature Biotechnology

Developmental BiologyFunctional GenomicsRna BiologyRna-seq RevealsTranscriptomics Technology +8

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

Daehwan Kim, Geo Pertea, Cole Trapnell, +3

Genome biology

BioinformaticsGene Sequence AnnotationNatural SciencesGeneticsSequence Analysis +12

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

Cole Trapnell, Adam Roberts, Loyal A. Goff, +7

Nature Protocols

Differential GeneNatural SciencesGeneticsRna BiologyMolecular Biology +9

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell, Lior Pachter, Steven L. Salzberg

Bioinformatics

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

Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, +7

Nature Biotechnology

Pattern FormationDevelopmental BiologyCell DivisionCell InteractionSingle-cell Biology +10

Reversed graph embedding resolves complex single-cell trajectories

Xiaojie Qiu, Qi Mao, Ying Tang, +4

Nature Methods

Graph TheoryMedicineBiological NetworkComputational BiologyNetwork Analysis +4

The single-cell transcriptional landscape of mammalian organogenesis

Junyue Cao, Malte Spielmann, Xiaojie Qiu, +9

Nature

Cell LineageDevelopmental BiologySingle Cell SequencingMedicineSingle-cell Transcriptional Landscape +5

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

Cole Trapnell, David G. Hendrickson, Martin Sauvageau, +3

Nature Biotechnology

BioinformaticsNatural SciencesGeneticsGene RegulationMolecular Biology +8

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

Moran N. Cabili, Cole Trapnell, Loyal A. Goff, +4

Genes & Development