A computational method for studying the relation between alternative splicing and DNA methylation

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Computational analysis of associations between alternative splicing and histone modifications

(2013) Yuki Shindo et al.   FEBS LETTERS

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors

(2013) Z. Ye et al.   NUCLEIC ACIDS RESEARCH

Epigenetic features are significantly associated with alternative splicing

(2012) Yuanpeng Zhou et al.   BMC GENOMICS

Genome-wide association between DNA methylation and alternative splicing in an invertebrate

(2012) Kevin Flores et al.   BMC GENOMICS

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

(2012) P. Yu et al.   GENOME RESEARCH

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

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

(2012) Cole Trapnell et al.   Nature Protocols

Pre-mRNA splicing in disease and therapeutics

(2012) Ravi K. Singh et al.   TRENDS IN MOLECULAR MEDICINE

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

(2011) Fabienne Brenet et al.   PLoS One

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

A global averaging method for dynamic time warping, with applications to clustering

(2010) François Petitjean et al.   PATTERN RECOGNITION

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Insights into the connection between cancer and alternative splicing

(2007) Eddo Kim et al.   TRENDS IN GENETICS