SCHMIDT Bertil

Efficient and accurate OTU clustering with GPU-based sequence alignment and dynamic dendrogram cutting

Published date : 05 Oct 2015

De novo clustering is a popular technique to perform taxonomic profiling of a microbial community by grouping 16S rRNA amplicon reads into operational taxonomic units (OTUs). In this work, we introduce a new dendrogram-based OTU clustering pipeline called CRiSPy. The key idea used in CRiSPy to improve clustering accuracy is the application of an anomaly detection technique to obtain a dynamic distance cutoff instead of using the de facto value of 97 percent sequence similarity as in most existing OTU

type
Journal Paper
journal
IEEE/ACM Transactions on Computation Biology and Bioinformatics, Vol. 12, No. 5, Sept/Oct 2015
Impact Factor
1.438

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

Published date : 13 Sep 2015

Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing.

type
Journal Paper
journal
Nucleic Acids Research 2015, doi:10.1093/nar/gkv906
Impact Factor
9.112