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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

A Mortazavi, Brian A. Williams, Kenneth McCue, +2

Nature Methods

Functional GenomicsGeneticsTranscriptomics TechnologyMammalian TranscriptomesLong Non-coding Rna +5

Alternative isoform regulation in human tissue transcriptomes

Eric T. Wang, Rickard Sandberg, Shujun Luo, +6

Nature

Gene RegulationSystems BiologyMedicineFunctional GenomicsGene Expression +2

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia, Sina Ghaemmaghami, J. Robert Newman, +1

Science

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

Qun Pan, Ofer Shai, Leo J. Lee, +2

Nature Genetics

Long-read SequencingFunctional GenomicsDeep SurveyingGeneticsHigh-throughput Sequencing +13

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

Nucleic Acids Research

Microarray Sample PoolEngineeringTranscriptomics TechnologyGenomicsSpatial Omics +16

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

John C. Marioni, Christopher E. Mason, Shrikant Mane, +2

Genome Research

GeneticsMolecular BiologyTranscriptomics TechnologyIllumina SequencingGenomics +17

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

Ryan Lister, Ronan C. O’Malley, Julian Tonti‐Filippini, +4

Cell

BiologyChromatinGeneticsEpigenomicsSingle-base Resolution Maps +5

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

Leighton J. Core, Joshua J. Waterfall, John T. Lis

Science

GeneticsRna SplicingMolecular BiologyGene TranscriptionTranscriptional Regulation +14

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

Marc Sultan, Marcel H. Schulz, Hugues Richard, +13

Science

GeneticsRna SplicingMolecular BiologyTranscriptomics TechnologyGenomics +21