Cu Nguyen

Staff Scientist

Biography

Mr. Cu Nguyen is a staff scientist at CBIIT within the Computational Genomics and Biomedical Informatics Group. Mr. Nguyen has over 18 years of experience at NCI, during which he has collaborated on many projects and with many groups, including the Laboratory of Population Genetics. He has also supported the NCI Cloud Resources (formerly known as Cloud Pilots), the Therapeutically Applicable Research to Generate Effective Treatments’ (TARGET) Acute Myeloid Leukemia and Kidney Tumor projects, and the Environment and Genetics in Lung Cancer Etiology (EAGLE) project. Mr. Nguyen has designed Cloud and high-performance computing next-generation sequence analysis workflows and curate and evaluate mutation and copy number variation calling methods for the Food and Drug Administration Sequencing Quality Control Phase II project. He also conducts RNA-Seq analysis training classes at the NIH Library of Medicine. Before coming to NCI, he was a lead software engineer working for the National Aeronautics and Space Administration at the Goddard Space Flight Center, the U.S. Agency for International Development, and the American Registry for Internet Number. Mr. Nguyen received his bachelor’s degree in electrical and electronic technology from Capitol College in Laurel, Maryland and has completed graduate computer science courses at Johns Hopkins University in Baltimore, Maryland.

Projects

  • Computational Genomics and Bioinformatics Group

Publications

  • Fan, Y., Hu, Y., Nguyen, C., Yan, C., Ries, R.E., Bolouri, H., Smith, J.L., Chen, Q., Anders Kolb, E., Meshinchi, S., and Meerzaman, D. Altered Transcriptome Uniquely Associated with AML Vs. Normal Hematopoiesis. Blood (2017) 130:3792.
  • Schuback, H.L., Alonzo, T.A., Gerbing, R.B., Brodersen, L.E., Loken, M.R., Kahwash, S.B., Raimondi, S.C., Hirsch, B.A., Nguyen, C., Chen, Q., Meerzaman, D., Ostronoff, F., Appelbaum, F.R., Gamis, A.S., and Meshinchi, S. Prevalence and prognostic significance of the CBFA2T3-GLIS2 fusion transcript in childhood AML: a report from the Children’s Oncology Group. Clinical Cancer Research (in press).
  • Gadd, S., Huff, V., Walz, A.L., Ooms, A., Armstrong, A., Gerhard, D.S., Smith, M.A., Guidry Auvil, J.M., Meerzaman, D., Chen, Q.R., Hsu, C.H., Yan, C., Nguyen, C., Hu, Y., Hermida, L., Davidsen, T., Ma, Y., Zong, Z., Mungall, A.J., Moore, R.A., Marra, M.A., Dome, J.S., Mullighan, C.G., Ma, J., Wheeler, D.A., Hampton, O.A., Ross, N., Gastier-Foster, J.M., Arnold, S., Perlman, E.J. The Genetic Landscape of Wilms Tumor. Nature Genetics (August 2017); doi:10.1038/ng.3940.
  • Shi, J., Hua, X., Zhu, B., Ravichandran, S., Wang, M., Nguyen, C., Brodie, S., Jones, K., Zhou, W., Boland, J., Hicks, B., Risch, A., Bennet, H., Luke, B., Song, L., Duan, J., Liu, P., Kohno, T., Chen, Q., Meerzaman, D., Marconett, C., Laird-Offringa, I., Mills, I., Gail, M.H., Caporaso, N.E., Consonni, D., Alberto Bertazzi, P., Chanock, S., Landi, M.T. Somatic Genomic Landscape of Lung Adenocarcinoma and its Association with Clinical Outcomes. PLoS Med (2016) 6;13(12):e1002162. doi: 10.1371/journal.pmed.1002162. eCollection 2016.
  • Hsu, C.H., Nguyen, C., Yan, C., Ries, R., Chen, Q., Hu, Y., Ostronoff, F., Stirewalt, D., Arceci, R., Komatsoulis, G., Levy, S., Meerzaman, D., Meshinchi, S. M.A. Transcriptome Profiling of Pediatric Core Binding Factor AML.PLoS One (September 2015). 10(9):e0138782. doi: 10.1371/journal.pone.0138782. eCollection 2015.
  • Gooskens, S.L, Gadd, S., Guidry Auvil, J., Gerhard, D.S., Khan, J., Patidar, R., Meerzaman, D., Chen, Q., Hsu, C.H., Yan, C., Nguyen, Cu., Hu, Y., Mullighan, C.G., Ma, J., de Krijger, R., van den Heuvel-Eibrink, M.M., Smith, M.A., Ross, N., Gastier-Foster, J.M., Perlman, E.J. TCF21 hypermethylation in genetically quiescent Clear Cell Sarcoma of the Kidney. Oncotarget (June 2015).
  • Perlman, E., Gadd, S., Arold, S., Radhakrishnan, A., Gerhard, D., Jennings, L.J., Huff, V., Guidry Auvil, J., Davidsen, T., Dome, J., Meerzaman, D., Hsu, C.H., Nguyen, C., Anderson, J., Ma, Y., Mungall, A., Moore, R., Marra, M., Mullighan, C., Ma, J., Wheeler, D., Hampton, O., Gastier-Foster, J., Ross, Nicole, and Smith, M. MLLT1 (ENL) YEATS Domain Mutations in Clinically Distinctive Favorable Histology Wilms Tumors. Nature Communications 04 (December 2015). Article number:10013 doi:10.1038/ncomms10013.
  • Finney, R.P., Chen, Q.R., Nguyen, C.V., Hsu, C.H., Yan, C., Hu, Y., Abawi, M., Bian, X., Meerzaman, D.M. Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files, 13 (September 2015). PMID:26417198  PMCID: PMC4573065.
  • Walz, A., Ooms, A., Gadd, S., Gerhard, D.S., Smith, M.A., Guidry Auvil, J.M., Meerzaman, D., Chen, Q., Hsu, C.H., Yan, C., Nguyen, C., Hu, Y., Bowlby, R., Brooks, D., Ma, Y., Mungall, A.J., Moore, R.A., Schein, J., Marra, M.A., Huff, V., Dome, J.S., Mullighan, C.G., Ma, J., Ross, N., Gastier-Foster, J.M., Perlman, E.J. Recurrent Somatic and Germline DGCR8, DROSHA, XPO5, DICER1, and SIX homeodomain Mutations in Favorable Histology Wilms Tumors.Cancer Cell Volume 27, Issue 2, 9 (February 2015): 286–297. 
  • Meerzaman, D., Yan, C., Chen, Q., Edmonson, M., Schaefer, C., Clifford, R., Dunn, B., Li, D., Finney, R., Cultraro, C., Hu, Y., Yang, Z., Nguyen, C., Kekkey, J., Cai, S., Zhang, H., Zhang, J., Wilson, R., Messmer, L., Chung, Y., Kim., J., Park, NH., Lyu, M., Song, IH., Komatsoulis, G., and Buetow, K. Genome-wide transcription sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma. 11-12, (January 2014). PMID:24633315 Cancer Genomics Proteomics.
  • Gooskens, S.L., Gadd, S., Guidry-Auvil, J., Gerhard, D., Khan, J., Meerzaman, D., Chen, Q.R., Hsu, C.H., Yan, C., Nguyen, C., Hu, Y., Mullighan, C.G., Jing, M., de Krijger, R., van den Heuvel-Eibrink, M.M., Smith, M., Perlman, E.J. 46th Congress of the Internal Society of Paediatric Oncology: Comprehensive Molecular Characterization of Clear Cell Sarcoma of the Kidney (October 22, 2014).
  • Kuhn, J., Meerzaman, D., Ries, R.E., Milano, F., Gamis, A.S., Alonzo, T.A., Guidry-Auvil, J., Davidsen, T.M., Smith, M.A., Yan, C., Hsu, C.H., Nguyen, C., Gerhard, D.S., Wai, D., Arceci, R.J., Meshinchi, S. Journal of the American Society of Hematology:  PIM3-SCO2 Fusion Is a Novel Transcription-Induced Chimera That Is Highly Prevalent In Childhood AML. Blood 15, Vol. 122 No. 21 2549 (November 2013).
  • Clifford, R.J., Zhang, J., Meerzaman, D.M., Lyu, M.S., Hu, Y., Cultraro, C.M. Finney, R.P., Kelley, J.M., Efroni, S., Greenblum, S.I., Nguyen, C.V., Rowe, W.L., Sharma, S., Wu, G., Yan, C., Zhang, H., Chung, Y.H., Kim, J.A., Park, N.H., Song, I.H., Buetow, K.H. Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma (HCC) in a Korean population (2011).
  • Meerzaman, D., Yan, C., Edmonson, M., Shaefer, C., Clifford, R., Funn, B., Dong, L., Finney, R., Cultraro, C., Hu, Y., Yan, Z., Nguyen, C., Kelley, J., Cai, S., Zhang, H., Zhang, J., Wilson, R., Messmer, L., Chen, Q., Chun, Y., Kim, J., Park, N.H., Lyu, M.S., Song, H., Buetow, K. Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma (HCC). Plos one (December 2011). PMID: 24633315.
  • Zhang, J., Finney, R., Edmonson, M., Schaefer, C., Rowe, W., Yan, C., Clifford, R., Greenblum, S., Wu, G., Zhang, H., Liu, H., Nguyen, C., Hu, Y., Madhavan, S., Ding, L., Wheeler, D.A., Gerhard, D.S. and Buetow, K.H. The Cancer Genome Workbench: Identifying and Visualizing Complex Genetic Alterations in Tumors. NCI-Nature Pathway Interaction Database (2010). doi:10.1038/pid.2010.1. 
  • Zhang, J., Finney, R., Edmonson, M., Schaefer, C., Rowe, W., Yan, C., Clifford, R., Greenblum, S., Wu, G., Zhang, H., Liu, H., Nguyen, C., Hu, Y., Madhavan, S., Ding, L., Wheeler, D.A., Gerhard, D.S. and Buetow, K.H. Identifying and Visualizing Complex Tumor Alterations through Integration of Diverse Data from the Cancer Genome Atlas (TCGA) Project. Nature Methods (2008).
  • Clifford, R.J., Edmonson, M.N., Nguyen, C., Buetow, K.H. Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics (2004).
  • Clifford, R.J., Edmonson, M.N., Nguyen, C., Scherpbier, T., Hu, Y., and Buetow, K.H. Bioinformatics tools for single nucleotide polymorphism discovery and analysis. Ann. N. Y. Acad. Sci. (2004).