NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

(2015) Qinghong Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonsense-mediated mRNA decay — Mechanisms of substrate mRNA recognition and degradation in mammalian cells

(2013) Christoph Schweingruber et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The functional consequences of intron retention: Alternative splicing coupled to NMD as a regulator of gene expression

(2013) Ying Ge et al.   BIOESSAYS

Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms

(2013) Karen Yap et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Inhibition of SMG-8, a subunit of SMG-1 kinase, ameliorates nonsense-mediated mRNA decay-exacerbated mutant phenotypes without cytotoxicity

(2013) F. Usuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The transcriptional landscape and mutational profile of lung adenocarcinoma

(2012) J.-S. Seo et al.   GENOME RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

(2010) Nicholas J McGlincy et al.   BMC GENOMICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Nonsense-mediated mRNA decay (NMD) mechanisms

(2009) Saverio Brogna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread Impact of Nonsense-Mediated mRNA Decay on the Yeast Intronome

(2008) Shakir Sayani et al.   MOLECULAR CELL

Translational control of intron splicing in eukaryotes

(2008) Olivier Jaillon et al.   NATURE

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

(2008) John C Castle et al.   NATURE GENETICS

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

(2008) Qun Pan et al.   NATURE GENETICS

Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?

(2008) Nicholas J. McGlincy et al.   TRENDS IN BIOCHEMICAL SCIENCES