8 Result(s)

Article

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis

Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantificat...

Mohamed K Gunady, Stephen M Mount, Héctor Corrada Bravo in BMC Bioinformatics (2019)

Article

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana

Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regul...

**ao-Ning Zhang, Yifei Shi, Jordan J. Powers, Nikhil B. Gowda, Chong Zhang… in BMC Genomics (2017)

Article

Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

Theodore R. Gibbons, Stephen M. Mount, Endymion D. Cooper… in BMC Bioinformatics (2015)

Article

Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been th...

Theodore R. Gibbons, Stephen M. Mount, Endymion D. Cooper… in BMC Bioinformatics (2015)

Article

Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease

There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, t...

Lipika R Pal, Chen-Hsin Yu, Stephen M Mount, John Moult in BMC Genomics (2015)

Article

Features generated for computational splice-site prediction correspond to functional elements

Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and int...

Rezarta Islamaj Dogan, Lise Getoor, W John Wilbur, Stephen M Mount in BMC Bioinformatics (2007)

Article

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana

Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been ...

Mihaela Pertea, Stephen M Mount, Steven L Salzberg in BMC Bioinformatics (2007)

Article

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (...

Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount… in BMC Genomics (2006)