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Project TitleBioinformatics Analysis for Cancer Gene Mutations
SummaryThe intern is expected to improve existing software applications and to write new codes on the Blue Waters supercomputer to analyze whole exome DNA sequence data and identify putative genetic variants involved in cancer.
Job DescriptionAdvances of next-generation sequencing technologies in the past few years have greatly facilitated research studies on many human diseases at the genomic level. While the exome, consisting of all the exons (i.e., protein-coding regions), represents less than 3\\% of the entire genome, whole exome sequence analyses in many recent studies have proven to be an efficient way of identifying novel genetic alterations associated with various types of cancer. At the cancer bio-repository housed at The University of Texas at El Paso, an increasing number of tissue samples from patients with cancer in local hospitals have been collected. We have recently initiated a research project to develop a bioinformatics pipeline that uses a combination of scoring functions, visualization tools, and statistical methods to filter through multiple cancer mutations and identify a short list of exonic variants for focused experimental investigation in the wet lab. However, the computations involved in our current evolution-based scoring function generally requires over a week to complete the analysis of the data from a single individual. The work in this internship will involve exploring the use of parallel programming and Blue Water resources to speed up the computations and complete the analysis much more efficiently.
Conditions/QualificationsThe intern should be familiar with C, JAVA, and Python, with good quantitative skills and a working knowledge of molecular biology, especially those related to nucleic acids, their sequences, and structural properties. The applicant must be available to attend a two-week workshop in late May of 2016 at the National Center for Supercomputing Applications (NCSA) facilities on the University of Illinois Urbana-Champaign campus.
Start Date06/01/2016
End Date05/31/2017
LocationUndergraduate Participation in Bioinformatics Training (UPBiT) Program, The University of Texas at El Paso, El Paso, Texas
Mariana Vasquez