Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice

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

Ben Langmead, Cole Trapnell, Mihai Pop et al. · Genome biology · 2009 · 22.5K citations · Full text

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 · 16.1K citations

Developmental Biology, Functional Genomics, Rna Biology +10

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber · Genome biology · 2010 · 16.1K citations · Full text

Engineering, Genomics, Gene Expression Profiling +19

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

Cole Trapnell, Adam Roberts, Loyal A. Goff et al. · Nature Protocols · 2012 · 12.6K citations · Full text

Differential Gene, Natural Sciences, Genetics +11

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D. Young, Matthew J. Wakefield, Gordon K. Smyth et al. · Genome biology · 2010 · 7.6K citations · Full text