Computational Genomics Group
The Computational Genomics Group at BSG/ABCC focuses on design, development and application of computational methods to support NCI initiatives including Next Generation Sequencing including Metagenomic and Microbiome projects. Members of the group participate in the design of experiments, data analysis and consulting for many NCI PI projects, helping with integration of heterogeneous data from different high-throughput platforms such as Roche/454, Illumina, SOLiD and fluidigm platforms. The group has successfully implemented and released into production an Automatic Variation Analysis Pipeline that efficiently replaces laborious manual work at Molecular Diagnostic Group at LMT. A Metagenomic Analysis pipeline has been implemented and applied for several NCI PI projects and has helped to confirm recently discovered polyoma viruses and identify previously unknown papiloma virus variants.
The group continues to work on development of computational methods for analysis of genomic variation and assessment of their contribution to the formation of the disease. New computational methods are in development for elucidating the role of non-coding RNAs and alternative splicing in cancer-related pathways.
- Tolstorukov M.Y. , Volfovsky N. , Stephens R.M. and Park P. (2011). Impact of chromatin structure on sequence variability in the human genome. In press. Nat Struct Mol Bio.
- Kearney M, Spindler J, Shao W, Maldarelli F, Palmer S, Hu SL, Lifson JD, KewalRamani VN, Mellors JW, Coffin JM, Ambrose Z.(2011). Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy.J Virol. 2011 Jan;85(2):1067-76.
- Volfovsky N. Oleksyk T.K.,Cruz KC,Truelove A.L. ,Stephens R.M. and Smith M.(2009). Genome and gene alterations by insertions and deletions in the evolution of human and chimpanzee chromosome 22. BMC Genomics 10:51
- Shao W, Kearney M, Maldarelli F, Mellors JW, Stephens RM, Lifson JD, KewalRamani VN, Ambrose Z, Coffin JM, Palmer SE (2009).
- RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy. Retrovirology, 6: 101
- Huppi K., Volfovsky N., Runfola T., Jones T.L., Mackiewicz M., Martin S.E., Mushinski J.F., Stephens R.M., and Caplen N.J.(2008). The Identification of Novel MicroRNAs in a Genomically Unstable Region of Human Chromosome 8q24 . Mol Cancer Res. 6(2):212-21