Streaming fragment assignment for real-time analysis of sequencing experiments

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N. Dewey · BMC Bioinformatics · 2011 · 23.4K citations · Full text

Life Sciences, Bioinformatics, Molecular Biology +15

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

Ben Langmead, Cole Trapnell, Mihai Pop et al. · Genome biology · 2009 · 23K citations · Full text

Life Sciences, Bioinformatics, High-performance Computing +15

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

Cole Trapnell, Brian A. Williams, Geo Pertea et al. · Nature Biotechnology · 2010 · 16.5K citations

Life Sciences, Cell Biology, Molecular Biology +16

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber · Genome biology · 2010 · 16.4K citations · Full text

Life Sciences, Bioinformatics, Biostatistics +15

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

Cole Trapnell, David G. Hendrickson, Martin Sauvageau et al. · Nature Biotechnology · 2012 · 3.7K citations · Full text

Life Sciences, Genetics, Molecular Biology +16