All Publications

  • Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress ONCOTARGET Oh, S., Flynn, R. A., Floor, S. N., Purzner, J., Martin, L., Do, B. T., Schubert, S., Vaka, D., Morrissy, S., Li, Y., Kool, M., Hovestadt, V., Jones, D. T., Northcott, P. A., Risch, T., Warnatz, H., Yaspo, M., Adams, C. M., Leib, R. D., Breese, M., Marra, M. A., Malkin, D., Lichter, P., Doudna, J. A., Pfister, S. M., Taylor, M. D., Chang, H. Y., Cho, Y. 2016; 7 (19): 28169-28182
  • Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis JOURNAL OF CLINICAL INVESTIGATION Howarth, M. M., Simpson, D., Ngok, S. P., Nieves, B., Chen, R., Siprashvili, Z., Vaka, D., Breese, M. R., Crompton, B. D., Alexe, G., Hawkins, D. S., Jacobson, D., Brunner, A. L., West, R., Mora, J., Stegmaier, K., Khavari, P., Sweet-Cordero, E. A. 2014; 124 (12): 5275-5290


    Chromosomal translocation that results in fusion of the genes encoding RNA-binding protein EWS and transcription factor FLI1 (EWS-FLI1) is pathognomonic for Ewing sarcoma. EWS-FLI1 alters gene expression through mechanisms that are not completely understood. We performed RNA sequencing (RNAseq) analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify gene targets of this oncoprotein. We determined that long noncoding RNA-277 (Ewing sarcoma-associated transcript 1 [EWSAT1]) is upregulated by EWS-FLI1 in pMPCs. Inhibition of EWSAT1 expression diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar, whereas EWSAT1 inhibition had no effect on other cell types tested. Expression of EWS-FLI1 and EWSAT1 repressed gene expression, and a substantial fraction of targets that were repressed by EWS-FLI1 were also repressed by EWSAT1. Analysis of RNAseq data from primary human Ewing sarcoma further supported a role for EWSAT1 in mediating gene repression. We identified heterogeneous nuclear ribonucleoprotein (HNRNPK) as an RNA-binding protein that interacts with EWSAT1 and found a marked overlap in HNRNPK-repressed genes and those repressed by EWS-FLI1 and EWSAT1, suggesting that HNRNPK participates in EWSAT1-mediated gene repression. Together, our data reveal that EWSAT1 is a downstream target of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes.

    View details for DOI 10.1172/JC172124

    View details for Web of Science ID 000345677200020

  • 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