State University Data

VIJI SHANMUGAM PhD, MBA

Email: *************@*****.*** Phone: 480-***-**** Status: US citizen

Address: **** *. ***** ***, *******, AZ 85234

OBJECTIVE

Management/execution of research and development projects within an organization to develop new avenues in health sciences.

EDUCATION

2010: MBA (emphasis on entrepreneurship), W P Carey School of Business, Arizona State University.

2003: MS in Computer Engineering Technology, Arizona State University.

1997: Ph. D. Cell and Molecular Biology (Cancer Research),

Department of Biology, McGill University, Montreal, Canada.

B.Sc., M. Sc.: Biochemistry, Madras University, India.

WORK EXPERIENCE

June 2016 – Present: Sr. Mgr. Integrated Genomics, Systems Imagination, Inc. Scottsdale, Arizona.

Primary and secondary analysis of sequencing data.

Setting up the pipelines for the secondary analysis.

Knowledge mining of different data types from TCGA.

Scientific lead, planning and resource capturing

Project Management working with diverse customer needs.

Identify patent resources and design tools to extract information

Oct 2015 – May 2016: Scientist, Systems Imagination, Scottsdale, Arizona.

Sep 2010 – 2015: Project reviewer for BioAccel, Phoenix Arizona.

Review basic and applied research projects for funding bioscience discoveries to commercialize new business ventures.

Oct 2006 – Oct 2015: Staff scientist, Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGEN), Phoenix, Arizona.

Analysis of Next-Generation Illumina and SOLiD sequencing data in different Cancers: Sequence alignments using the different algorithms, SNP and indel calling using various tools, SNP annotations.

Analysis of Microarray gene expression data in Multiple Myeloma.

Identifying copy number variation using comparative genomic hybridization in Multiple Myeloma.

Identifying drug targets for Acute Myeloid Leukemia patients based on gene expression and copy number variations.

Nov 2003 – Sept 2006: Computational Scientist, Computational Biology Division, Translational Genomics Research Institute (TGEN), Phoenix, Arizona.

Microarray expression data analysis and cross platform comparisons.

Interaction with the software development team to develop tools and databases for TGen researchers.

Multimeric ligand project to identify receptors and ligands in pancreatic cancer.

Use of prior biological knowledge in classification, building gene regulatory networks and data fusion.

Nov 1997 – June 2000: Post-Doctoral training, Dr. Guy A Rouleau’s laboratory, Centre for Research in Neurosciences, The Montreal General Hospital Research Institute, Montreal, Canada.

Characterization of the PABP2 protein (Oculopharyngeal Muscular Dystrophy)

and its relation to other trinucleotide repeat disorders.

Production, purification and characterization of various polyclonal antibodies using ELISA.

Use of reporter gene GFP in COS-7 cells for localization studies.

Site-specific mutagenesis to generate various mutants of PABP2.

Expression of mutant proteins in established cell lines using inducible systems (tetracycline).

In situ localization of proteins by immunocytochemistry.

Supervision of students working on related aspects of my work.

Ph. D. – Dec 1997: Characterization of Osteopontin in RSV transformed Rat-1 cells and its role in cell transformation.

Use of various techniques (cell and tissue culture, protein purification and biochemical characterization, metabolic radiolabeling, immunoprecipitation, 2-D protein analysis, enzyme assays, in vitro radioiodination of cell surface proteins, Western blotting, Northern and Southern analyses, RT-PCR, DNA sequencing, cell transfections, immunostaining, immunofluorescence, and receptor binding analysis.

Characterization of the post-translational modifications of Osteopontin (OPN) in transformed cells.

Receptor mediated binding of the transformed and non-transformed forms of OPN.

Antisense inhibition of OPN to analyze the role of this protein in transformed cells.

AWARDS/TEACHING

Medical Research Council Graduate Fellowship, Canada.

Assistantship: McGill University Teaching Assistantship; 1990 – 1996, Department of Biology, McGill University, Canada.

COMPUTER SKILLS

Operating Systems: Windows, Macintosh, Unix

Biology Software: DNA Star, Bioinformatic Web Databases, GeneSpring for analysis of Microarray expression data, CGH Analytics

Use most of the Integrative BioInformatic Databases for interpretation of genes and proteins. Sequence Alignments and SNP calling using the various tools.

Statistical Programs: SAS, S-Plus

SELECTED PUBLICATIONS

Tibes, R., McDonagh, KT., Lekakis, L., Bogenberger, JM., Kim, S., Frazer, N., Mohrland, S., Bassett, D., Garcia, R., Schroeder, K., Shanmugam, V., Carpten, J., Hagelstrom, TR., Beaudry, C., Von Hoff, D., Shea, TC. (2015)

Phase I Study of the Novel Cdc2/CDK1 and AKT Inhibitor Terameprocol in Patients with Advanced Leukemias

Invest New Drugs, 33(2) 389-96

Shanmugam, V., Ramanathan, RK., Lavender, NA., Sinari, S., Chadha, M., Liang, W., Izatt, T., Christoforides, A., Benson, H., Phillips, L., Baker, A., Hostetter, G., Von Hoff, DD., Craig, D., Carpten,J. (2014)

Whole genome sequencing to find potential targets for therapy in patients with refractory Kras mutated metastatic colorectal cancer BMC Medical Genomics, 7:36

Ewing, CM., Ray AM., Lange, EM., Zulhlke, KA., Robbins, CM., Tembe, WD., Wiley, KE., Isaacs, SD., Johng, D., Wang, Y., Bizon, C., Yan, G., Gielzak, M., Partin, AW., Shanmugam, V., Izatt, T., Sinari, S., Craig, DW., Zheng, SL., Walsch, PC., Montie, JE., Xu, J., Carpten, JD., Isaacs, WB., Cooney, KA (2012)

Germline mutations in HOXB13 and prostate-cancer risk. N Engl J Med, 2012 Jan 12;366(2):141-9.

Balagurunathan, Y., Morse, D.L., Hostetter, G., Shanmugam, V., Stafford, P., Shack, S., Pearson, J., Trissal, M., Demeure, M., Von Hoff, D., Hruby, V.J., Gilles, R.J., and Han, H. (2008)

Gene expression profiling-based identification of cell-surface targets for developing multimeric ligands in pancreatic cancer. Molecular Cancer Therapeutics, 2008, 7 (9)

Dion, P., Shanmugam, V., Gaspar, C., Messaed, C., Meijer, I., Toulouse, A., Laganiere, J., Roussel, J., Rochefort, D., Laganiere, S., Allen, C., Karpati, G., Bouchard, J-P., Brais, B., and Rouleau, G.A. (2005).

Transgenic expression of an expanded (GCG)13 repeat PABPN1 leads to weakness and coordination defects in mice.

Neurobiology of Disease, 18: 528-536.

Shanmugam, V., Dion, P., Rochefort, D., Laganière, J., Brais, B., and Rouleau, G. (2000)

Polyalanine tract expansion of the PABP2 gene causes intranuclear inclusions in oculopharyngeal muscular dystrophy.

Annals of Neurology, Nov 2000, 798-802.

Shanmugam, V., Chackalaparampil, I., Kundu, G.C., Mukherjee, A.B.,and Mukherjee, B.B. (1997).

Altered Sialylation of Osteopontin Prevents Its Receptor-Mediated Binding on the Surface of Oncogenically Transformed tsB77 Cells.

Biochemistry, 36: 5729-5738.

Mukherjee, B. B., Nemir, M., Beninati, S., Cordella-Miele, E., Singh, K., Chackalaparampil, I., Shanmugam, V., DeVouge, M. W., and Mukherjee, A. B. (1995).

Interaction of Osteopontin with Fibronectin and Other Extracellular Matrix Molecules.

Annals of the New York Academy of Sciences, 760: 201-212.

Beninati, S., Senger, D., Cordella-Miele, D., Mukherjee, A. B., Chackalaparampil, I., Shanmugam, V., Singh, K., and Mukherjee, B. B. (1994)

Osteopontin: Its Transglutaminase-Catalysed Posttranslational Modifications and Cross-linking to Fibronectin.

Journal of Biochemistry, 115: 675-682.

Singh, K., Deonarine, D., Shanmugam, V., Senger, D., Mukherjee, A. B., Chang, P. L., Prince, C. W., and Mukherjee, B. B. (1993)

Calcium-Binding Properties of Osteopontin Derived from Non-Osteogenic sources.

Journal of Biochemistry, 114: 702-707.

CONFERENCE PRESENTATIONS

Shanmugam, V., Ramanathan, RK., Sinari, S., Chadha M 2, Liang, W., Kurdoglu, A., Izatt, T., Christoforides, A., Benson, H., Phillips, L., Baker, A., Hostetter, G., Von Hoff, DD., Craig, D., and Carpten, J. Genome sequencing of metastatic colorectal carcinomas to identify potential targets for therapy in patients. AACR Meeting, Apr 2012; 5072.

Ramanathan, RK., Shanmugam, V., Sinari, S., Chadha, M., Liang, W., Kurdoglu, A., Izatt., Cristoforides. A., Benson, H., Phillips, L., Baker, A., Hostetter, G., Von Hoff, DD., Craig, D., and Carpten, J.

Genome Sequencing to find Potential Targets for Therapy in Patients with Refractory Kras Mutated Metastatic Colorectal Cancer.

Molecular Targets and Cancer Therapeutics, Nov 2011.

Tibes, R., McDonagh, K. T., Lekakis, L., Frazer, N., Mohrland, S., Dawn, B., Garcia, R., Schroeder, K., Shanmugam, V., Carpten, J., Von Hoff, D., and Shea, T. C.

Phase I study of the Novel Survivin and cdc2/CDK1 Inhibitor Terameprocol in Patients with Advanced Leukemias.

Blood (ASH Annual Meeting), Nov 2009; 114: 1039.

Chapman, M. A., Brunet, J-P., Keats, J.J., Baker, A., Adli, M., Schinzel, A.C., Ahmann, G., Christina, H., Moore, A., Shanmugam, V., Perkins, L.M., Auclair, D., Hahn, W.C., Bernstein, B.E., Bergsagel, L., Fonseca, R., Carpten, J., Trent, J. and Golub, T.R.

HOXA9 Is a Novel Therapeutic Target in Multiple Myeloma.

Blood (ASH Annual Meeting), Nov 2009; 114: 832.

Chapman, M., Brunet, J-P., Baker, A., Keats, J., Ahmann, G., Schinzel, A.C., Moore, A., Shanmugam, V., Perkins, L.M., Auclair, D., Hahn, W.C., P. Bergsagel, L., Fonseca, R., Carpten, J., Trent, J., and Golub, T.R.

Interim Analyses of the MMRC Reference Collection Identifies Recurrent Genomic-Level Events in Multiple Myeloma and Demonstrates That CDKN2C/p18 Deletion Is the Pre-Eminent Copy Number Alteration in Poor Prognosis Disease.

Blood (ASH Annual Meeting), Nov 2008; 112: 497.

Tibes, R., Shanmugam, S., Henrichs, A., Baker, A., Azorsa, D., Robeson, A., Barrett, M., and Carpten, J.

Genomic vulnerabilities of acute myeloid leukemia cells.

AACR Meeting, Apr 2008; 2008: 1670.

Baker, A., Keats, J., Chapman, M., Moore, A., Shanmugam, V., Chng, W-J., Ahmann, G., Trudel, S., Siegal, D., Rajkumar, S.V., Alsina, M., Anderson, K., Auclair, D., Perkins, L., Fonseca, R., Trent, J., Carpten, J., and Golub, T.

Validation of NFkB pathway mutations in myeloma using data from the MMRF genomics initiative.

AACR Meeting, Apr 2008; 2008: 1678.

Chng, J., Shanmugam, V., Chesi, M., Bergsagel, L., Carpten, J., and Fonseca, R.

Identification of common and genetic subtype specific molecular programs associated with progression from monoclonal gammopathy of undetermined significance (MGUS) to myeloma (MM).

AACR Meeting, Nov 2007; 2007: B60.

Shanmugam, V., Stafford, P., and Suh, E. (2004)

Integration of Multi-Platform Microarray Expression Data.

Beyond Genome Conference, San Francisco, June 2004.

Shanmugam, V., Chackalaparampil, I., Mukherjee, B. B. (1994)

Differential Sialylation of Osteopontin Molecules Correlates with Tumorigenicity of RSV-Transformed Rat-1 Cells.

37th Annual Meeting of Canadian Federation of Biol Societies, Montreal, June 1994.

REFERENCES: will be provided on request

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