Uma T. Shankavaram, Ph.D.
Staff Scientist

Dr. Shankavaram manages the Radiation Oncology Branch’s Microarray Core Facility (MCF), which provides services and access to new technologies to investigators from NCI and other NIH institutes. The MCF offers special expertise in gene expression array hybridization, statistical analysis, genetics/genomics, and technical support.

  • Gene Expression Arrays:   gene chip processing of cDNA and Affymetrix arrays
  • Boinformatics Analysis:  consultation with scientists prior to experiments, analysis of high-throughput sequencing, gene expression, metabolomics, proteomics and other biological data, including functional and gene set enrichment analysis
  • Application Development:  develops custom applications to enhance research through web applications for data analysis, databases, visualization, and custom analysis tools
  • Training:  informal training to assist researchers in using computational tools

 

Areas of Expertise
bioinformatics, genetics, genomics, high-throughput data analysis, statistical and computational methods, web application development

Contact Info

Uma T. Shankavaram, Ph.D.
Center for Cancer Research
National Cancer Institute
Building 10-CRC, Room B2-3677
Bethesda, MD 20892
301-451-8972
uma@mail.nih.gov

Biology is driven until recently by the study of individual biochemical compounds and genes. However, new technologies allow experimentalists to gather rapidly growing amounts of data at the scale of the entire cell, and a key challenge is now to integrate these data in order to progress towards a systems-level understanding of biological functions. In this framework, my research interests center around the field of cancer bioinformatics with special focus on radiation response on gene expression, pharmacogenomics and translational medicine. My other research interests are in the development of relational databases for biomedical projects, as well as the use of data mining and machine learning techniques for bioinformatic analyses. Following are the major topics my research projects: - Genomic data analysis and integration - Statistical pathway analysis - Target gene discovery - Bioinformatics tool development

Selected Publications
  1. Hayman TJ, Wahba A, Rath BH, Bae H, Kramp T, Shankavaram UT, Camphausen K, Tofilon PJ.
    Clin. Cancer Res.. 20: 110-9, 2014. [ Journal Article ]
  2. Ho J, Ondos J, Ning H, Smith S, Kreisl T, Iwamoto F, Sul J, Kim L, McNeil K, Krauze A, Shankavaram U, Fine HA, Camphausen K.
    PLoS ONE. 8: e70745, 2013. [ Journal Article ]
  3. Shankavaram U, Fliedner SM, Elkahloun AG, Barb JJ, Munson PJ, Huynh TT, Matro JC, Turkova H, Linehan WM, Timmers HJ, Tischler AS, Powers JF, de Krijger R, Baysal BE, Takacova M, Pastorekova S, Gius D, Lehnert H, Camphausen K, Pacak K.
    Neoplasia. 15: 435-47, 2013. [ Journal Article ]
  4. Johnson S, Issac B, Zhao S, Bisht M, Celiku O, Tofilon P, Camphausen K, Shankavaram U.
    PLoS ONE. 7: e51693, 2012. [ Journal Article ]
  5. Dan T, Hewitt SM, Ohri N, Ly D, Soule BP, Smith SL, Matsuda K, Council C, Shankavaram U, Lippman ME, Mitchell JB, Camphausen K, Simone NL.
    Breast Cancer Res. Treat.. 143: 41951, 2014. [ Journal Article ]

Dr. Uma Shankavaram received her Ph.D. in Human Genetics from India. She completed her postdoctoral research training at the Medical University of South Carolina, and National Institute of Dental and Craniofacial Research, National Institutes of Health. Combining her strong interest in biology, biostatistics, and computer programming, she worked as a Senior Research Fellow in the Genomics and Bioinformatics Group of Laboratory of Molecular Pharmacology, National Cancer Institute till 2007 and currently as a Staff Scientist at the Radiation Oncology Branch of National Cancer Institute.

Research

Biology is driven until recently by the study of individual biochemical compounds and genes. However, new technologies allow experimentalists to gather rapidly growing amounts of data at the scale of the entire cell, and a key challenge is now to integrate these data in order to progress towards a systems-level understanding of biological functions. In this framework, my research interests center around the field of cancer bioinformatics with special focus on radiation response on gene expression, pharmacogenomics and translational medicine. My other research interests are in the development of relational databases for biomedical projects, as well as the use of data mining and machine learning techniques for bioinformatic analyses. Following are the major topics my research projects: - Genomic data analysis and integration - Statistical pathway analysis - Target gene discovery - Bioinformatics tool development

Publications

Selected Publications
  1. Hayman TJ, Wahba A, Rath BH, Bae H, Kramp T, Shankavaram UT, Camphausen K, Tofilon PJ.
    Clin. Cancer Res.. 20: 110-9, 2014. [ Journal Article ]
  2. Ho J, Ondos J, Ning H, Smith S, Kreisl T, Iwamoto F, Sul J, Kim L, McNeil K, Krauze A, Shankavaram U, Fine HA, Camphausen K.
    PLoS ONE. 8: e70745, 2013. [ Journal Article ]
  3. Shankavaram U, Fliedner SM, Elkahloun AG, Barb JJ, Munson PJ, Huynh TT, Matro JC, Turkova H, Linehan WM, Timmers HJ, Tischler AS, Powers JF, de Krijger R, Baysal BE, Takacova M, Pastorekova S, Gius D, Lehnert H, Camphausen K, Pacak K.
    Neoplasia. 15: 435-47, 2013. [ Journal Article ]
  4. Johnson S, Issac B, Zhao S, Bisht M, Celiku O, Tofilon P, Camphausen K, Shankavaram U.
    PLoS ONE. 7: e51693, 2012. [ Journal Article ]
  5. Dan T, Hewitt SM, Ohri N, Ly D, Soule BP, Smith SL, Matsuda K, Council C, Shankavaram U, Lippman ME, Mitchell JB, Camphausen K, Simone NL.
    Breast Cancer Res. Treat.. 143: 41951, 2014. [ Journal Article ]

Biography

Dr. Uma Shankavaram received her Ph.D. in Human Genetics from India. She completed her postdoctoral research training at the Medical University of South Carolina, and National Institute of Dental and Craniofacial Research, National Institutes of Health. Combining her strong interest in biology, biostatistics, and computer programming, she worked as a Senior Research Fellow in the Genomics and Bioinformatics Group of Laboratory of Molecular Pharmacology, National Cancer Institute till 2007 and currently as a Staff Scientist at the Radiation Oncology Branch of National Cancer Institute.