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[Computational-biology] from a high school science teacher

Richard Kurtz via comp-bio%40net.bio.net (by RKurtz from commack.k12.ny.us)
Mon May 25 07:26:38 EST 2015

To whom it may concern,

I am a high school science teacher on Long Island, New York.  I work with students interested in conducting
science research.  I have a very talented and ambitious current 9th grade student who has made a proposal for
a research project.  It is in the area of computational biology.  The work that he is proposing is beyond my
experience so I decided to reach out to see if there is anyone in the computational biology world who may be willing to offer some help and/or advice.  Any help would be greatly appreciated.

Richard Kurtz
Science Teacher
Commack High School

Project Proposal by Daniel, May 22, 2015

General Areas: Computational Biology, Bioinformatics, Genetics, Mutations, Cancer, Computer Science

           Throughout the history of modern biology analysis of genetic mutations have been examined. Recently many new techniques have been developed to analyze structural variations (SVs) in genomes. SVs include Copy-Number Variation, inversion, insertion, deletion, and transposition mutations. I wish to develop new hybrid methods and tools to find Structural Variation by creating novel methods as well as building and improving upon previous existent methods so we can better infer detailed (fine-scale) Structure Variations from given sequencing reads from combinations or single sequencers such as Illumina (relatively short reads, but quite accurate), Pacbio (Long reads, but highly inaccurate), and nanopole (nanopole is still in development). Certain studies also show hybrid error fixing sequencing methods using Illumina and Pacbio that can be utilized instead of standard sequencing [Koren, et al., 2012].
         The importance of identifying mutations in especially cancerous cells is so we can identify drugs targets to kill, identify, find, or neutralize cancer. Cancer is known to be able to adapt to modern treatment methods and they evolve, become resistant, and can metastasize to other organs further increasing the necessity for more gene and mutation targeting methods.
What do I need:

  1.  A mentor of some sort and guidance.
  2.  A way to sequence genomes from cancerous human cells or access to required previous existing sequencing reads to test the code and methods' ability to infer mutations.

        Campbell, I., Shaw, C., Stankiewicz, P., & Lupski, J. (2015). Somatic mosaicism: Implications for disease and transmission genetics. Trends in Genetics.
        Koren, S., Schatz, M., Walenz, B., Martin, J., Howard, J.,   Ganapathy, G., . . . Phillippy, A. (2012). Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30(7), 693-700.
        Li, Y., Zheng, H, Luo, R., Wu, H., Zhu, H., Li, R., . . . Wang, J. (2011). Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology, 29(8), 723-730.
       Tuzun, E., Sharp, A., Bailey, J., Kaul, R., Morrison, V., Pertz, L., . . . Eichler, E. (2005). Fine-scale structural variation of the human genome. Nat Genet Nature Genetics, 37(3), 727-732.

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