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Kamalakar Gulukota , MBBS, PhD, MBA

Director, Center for Bioinformatics and Computational Biology

Contact Information



  • Undergraduate: MBBS, University of Madras, India
  • Graduate: PhD, Biophysics, University of Illinois at Urbana-Champaign, Urbana IL
                       MBA, Corporate Strategy, Auburn University, Auburn, AL
  • Post-Doctoral Fellowship: Boston University, Boston, MA

Research and Academic Interests

  • Omics Data Analysis
  • Cancer Genomics
  • Personalized Medicine

Career Summary

Wyeth, Cambridge MA and Princeton NJ - (1997-2002)
Staff Scientist, Principal Scientist and Leader of Bioinformatics Core Sciences

  • Led the effort to identify GPCR drug targets for Neuroscience therapeutic area (at Wyeth)
  • Led the effort to identify novel drug targets in the newly published human genome; Passed the targets on to therapeutic areas like Neuroscience and connective tissue disorders
  • Discovered (US patent 6,321,163) a better way to identify coding regions in genes

GVK Biosciences, Hyderabad, India -(2002 – 2005)
Head, Clinical Research and Development

  • Initiated and managed operations of a new bioequivalence center
  • Initiated and managed PCR-based diagnostic services for tuberculosis

Matrix Laboratories, Secunderabad, India - (2004-2005)
Vice President, Biopharmaceuticals

  • Initiated a new unit for novel biopharmaceuticals

GenomeQuest, Inc., Westborough, MA -(2005-2011)
Product Manager, Senior Product Evangelist and Director of Customer Support

  • Directed GenomeQuest product strategy
  • Leader for the technical support team
  • Navigated the GenomeQuest product from IP centric to more geomics centric
  • Technical lead for converting dozens of companies to GenomeQuest
  • Got GenomeQuest the recognition as a leader in patent sequence search

NorthShore University HealthSystem -(2011-)
Director, Center for Bioinformatics and Computational Biology

  • Bioinformatics strategy, managing genomics data center, bioinformatics support for the Next-Generation sequencing lab

Scholarly Work

Peer-Reviewed Publications

    1. Germline Mutations in ATM and BRCA1/2 Distinguish Risk for Lethal and Indolent Prostate Cancer and are Associated with Early Age at Death.  Rong Na, S. Lilly Zheng, Misop Han, Hongjie Yu, Deke Jiang, Sameep Shah, Charles M. Ewing, Liti Zhang, Kristian Novakovic, Jacqueline Petkewicz, Kamalakar Gulukota, Donald L. Helseth Jr, Margo Quinn, Elizabeth Humphries, Kathleen E. Wiley, Sarah D. Isaacs, Yishuo Wu, Xu Liu, Ning Zhang, Chi-Hsiung Wang, Janardan Khandekar, Peter J. Hulick, Daniel H. Shevrin, Kathleen A. Cooney, Zhoujun Shen, Alan W. Partin, H. Ballentine Carter, Michael A. Carducci, Mario A. Eisenberger, Sam R. Denmeade, Michael McGuire, Patrick C. Walsh, Brian T. Helfand, Charles B. Brendler, Qiang Ding, Jianfeng Xu, William B. Isaacs. Eur. Urol. 2016 Dec 9. (In Press) epub ahead of print: pii: S0302-2838(16)30885-5.   doi:
    2. Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples.  Subhajit Sengupta, Kamalakar Gulukota, Yitan Zhu, Carole Ober, Katherine Naughton, William Wentworth-Sheilds, and Yuan Ji.  Nucleic Acids Res. 2016 Feb 18; 44(3): e25.   doi:  10.1093/nar/gkv953.
    3. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data, Yitan Zhu, Yanxun Xu, Donald L Helseth, Kamalakar Gulukota, Shengjie Yang, Lorenzo L Pesce, Riten Mitra, Peter Müller, Subhajit Sengupta, Wentian Guo, Jonathan C Silverstein, Ian Foster, Nigel Parsad, Kevin P White, Yuan Ji, J Natl Cancer Inst. 2015 May 8;107(8). doi: 10.1093/jnci/djv129. Print 2015 Aug
    4. MAD Bayes for Tumor Heterogeneity – Feature Allocation with Exponential Family Sampling, Yanxun Xu, Peter Müller, Yuan Yuan, Kamalakar Gulukota, Yuan Ji, J Amer Stat Assoc 01/2015; DOI:10.1080/01621459.2014.995794
    5. BayClone: Bayesian nonparametric inference of tumor subclones using NGS data, Subhajit Sengupta, Jin Wang, Juhee Lee, Peter Mueller, Kamalakar Gulukota, Arunava Banerjee, Yuan Ji, 2015. Pacific Symposium on Biocomputing 20:467-478.
    6. Direct observation of genomic heterogeneity through local haplotyping analysis, Kamalakar Gulukota, Donald L Helseth Jr and Janardan D Khandekar, 2014. BMC Genomics, 15:418.
    7. Predicting GPCR - G protein coupling using hidden markov models, Kodangattil R. Sreekumar, Youping Huang, Mark H. Pausch and Kamalakar Gulukota, 2004. Bioinformatics, 20(18):3490-9.
    8. Immunoinformatics in personalized medicine, Kamalakar Gulukota 2003. Novartis Found Symp.254:43-50; discussion 50-6, 98-101, 250-2.
    9. Characterization of mGluR5R, a novel, metabotropic glutamate receptor 5-related gene, Bates B, Xie Y, Taylor N, Johnson J, Wu L, Kwak S, Blatcher M, Gulukota K, Paulsen JE, 2002, Brain Res Mol Brain Res, 109(1-2):18-33.
    10. Neural Network method for predicting peptides that bind major histocompatibility complex molecules, Kamalakar Gulukota and Charles DeLisi, 2001, Methods Mol Biol,156:201-9. “Antigen Processing and Presentation” Ed: Joyce C. Solheim., Humana Press.
    11. Skipping a step with neural nets, Kamalakar Gulukota, 1998, Nature Biotechnology, 16:722 723
    12. Computational determination of the structure of rat Fc bound to the neonatal Fc receptor, 1998, Zhiping Weng, Kamalakar Gulukota, Daniel E. Vaughn, Pamela J. Bjorkman and Charles DeLisi, 1998, Journal of Molecular Biology, Vol: 282(2) Pages: 217-225.
    13. Two complementary methods for predicting peptides binding major histocompatibility complex molecules, Kamalakar Gulukota, John Sidney, Alessandro Sette and Charles DeLisi, 1997, Journal of Molecular Biology, Vol: 267(5) Pages: 1258-1267.
    14. HLA Allele selection for designing peptide vaccines, Kamalakar Gulukota and Charles DeLisi, 1996, Genetic Analysis: Biomolecular Engineering, Vol: 13, Pages: 81 - 86.
    15. Peptide Docking using Dynamic Programming, Kamalakar Gulukota, Sandor Vajda and Charles DeLisi, 1995, Journal of Computational Chemistry, Vol: 17(4), Pages: 418-28.
    16. Statistical Mechanics of Kinetic Proofreading in Protein folding in vivo, Kamalakar Gulukota and Peter Wolynes, 1994, Proceedings of the National Academy of Sciences, USA Vol: 91, Pages: 9292-9296.
    17. Computational Approaches to understanding the ion channel-lipid system, See-Wing Chiu, Kamalakar Gulukota and Eric Jakobsson, 1992, Membrane Proteins: Structure, interactions and Models Pages: 315-338. Editors: Alberte Pullman, Joshua Jortner and Bernard Pullman.

Patent Publications

    1. US 6,321,163: Method and apparatus for analyzing nucleic acid sequences
    2. US 20060008831: Methods and systems for predicting protein-ligand coupling specificities
    3. US 20030215852: Novel pancortin-Pablo protein interactions and methods of use thereof
    4. US 20030103964: Methods for designing molecular conjugates and compositions thereof
    5. US 20030027139: Polynucleotides encoding novel secreted proteins
    6. US 20020142952: Polynucleotides encoding novel secreted proteins
    7. US 20020142330: Novel glutamate receptor modulatory proteins and nucleic acid molecules and uses thereof
    8. US 20020045170: Polynucleotides encoding novel secreted proteins
    9. US 20020039760: Polynucleotides encoding novel secreted proteins

Invited Talks

    1. Chaired round table discussion on “NGS in 5 years” at the CHI Next Generation Sequencing conference, Providence, RI (Sep 2009)
    2. Next Generation Sequencing: A solution in search of a problem? Bio-IT World 2008, Boston MA
    3. A Sequence Search Portal: Easy GUI and Power can co-exist. Bio-IT World 2007, Boston MA
    4. 3 Pillars of IP sequence search: Content, Search, Analysis. Franklin Pierce Law Center, Intellectual Property Summer Institute, Concord, NH, 2007
    5. Patent analysis of short sequences. Patent Information User’s Group Biotech workshop, Cambridge MA, 2007
    6. What ails Pharma Research in India? Badruka Institute of Foreign Trade, Hyderabad, India, 2004
    7. Immunoinformatics in personalized medicine. At the Symposium on Immunoinformatics, Novartis Foundation, London UK, 2003
    8. PCR diagnostics for tuberculosis. At Neurology Symposium, Care Hospital, Hyderabad, India, 2003


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