All Publications

  • NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets BIOINFORMATICS Breese, M. R., Liu, Y. 2013; 29 (4): 494-496


    NGSUtils is a suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.NGSUtils is available under a BSD license and works on Mac OS X and Linux systems. Python 2.6+ and virtualenv are required. More information and source code may be obtained from the website:

    View details for DOI 10.1093/bioinformatics/bts731

    View details for Web of Science ID 000315158500012

    View details for PubMedID 23314324

  • Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data BMC GENOMICS Zhou, A., Breese, M. R., Hao, Y., Edenberg, H. J., Li, L., Skaar, T. C., Liu, Y. 2012; 13


    Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing.We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. With a proper combination of alignment and transcript reconstruction tools, Alt Event Finder is capable of identifying novel splicing events in the human genome. We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure.Alt Event Finder is capable of identifying de novo splicing events from data-driven transcript annotation, and is a useful tool for studying splicing regulation.

    View details for DOI 10.1186/1471-2164-13-S8-S10

    View details for Web of Science ID 000312990300010

    View details for PubMedID 23281921

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