Research Publications

    
    Peer-Reviewed Journal Articles ( >500 Citations ) 
  1. Flanking bases influence the nature of DNA distortion by Platinum 1,2-Intrastrand (GG) cross-links. 
    Debadeep Bhattacharyya, Srinivas Ramachandran, Shantanu Sharma, et al. 
    PLoS One 2011 6(8):e23582. [PDF]

  2. Computational modeling and automation to study biomolecular dynamics. 
    Shantanu Sharma 
    Lambert Academic Publishing, 2009. [PDF]

  3. iFoldRNA: three-dimensional RNA structure prediction and folding. 
    Shantanu Sharma, Feng Ding, Nikolay V Dokholyan. 
    Bioinformatics 2008 24(17):1951-2. [PDF]

  4. Probing protein aggregation using discrete molecular dynamics. 
    Shantanu Sharma, Feng Ding, Nikolay V Dokholyan. 
    Frontiers in Bioscience 2008 13:4795-808. [PDF]

  5. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. 
    Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V Demidov, Natalia E Broude, Nikolay V Dokholyan. 
    RNA 2008 14(6):1164-73. [PDF]

  6. DNA sequence mediates nucleosome structure and stability. 
    Shantanu Sharma, Nikolay V Dokholyan. 
    Biophysical Journal 2007 94(1):1-3. [PDF]

  7. Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics. 
    Shantanu Sharma, Peng Gong, Brenda Temple, Debadeep Bhattacharyya, Nikolay V Dokholyan, Stephen G Chaney. 
    Journal of Molecular Biology 2007 373(5):1123-40. [PDF]

  8. Protein folding: then and now. 
    Shantanu Sharma*,  Yiwen Chen*, Feng Ding*, Huifen Nie*, Adrian W Serohijos*, Kyle C Wilcox*, Shuangye Yin*, Nikolay V Dokholyan*. 
    Archives of Biochemistry and Biophysics 2007 469(1):4-19. (* Equal Contribution) [PDF]

  9. Multiscale modeling of nucleosome dynamics. 
    Shantanu Sharma, Feng Ding, Nikolay V Dokholyan. 
    Biophysical Journal 2007 92(5) 1457-70. [PDF] 

  10. iFold: a platform for interactive folding simulations of proteins. 
    Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, Nikolay V Dokholyan. 
    Bioinformatics 2006 22: 2693-2694. [PDF] 

  11. The path of DNA in the kinetochore.
    Kerry S Bloom, Shantanu Sharma, Nikolay V Dokholyan. 
    Current Biology 2006 16:R276-R278. [PDF] 

  12. Structure alignment via delaunay tetrahedralization.
    Jeffrey Roach, Shantanu Sharma, Maryna Kapustina, Charles W Carter Jr. 
    Proteins: Structure, Function, and Bioinformatics 2005 60(1):66-81. [PDF] 

    Book Chapters
  1. Differences in conformation and conformational dynamics between cisplatin and oxaliplatin DNA adducts.
    Stephen G Chaney, Srinivas Ramachandran, Shantanu Sharma, Nikolay Dokholyan, Brenda Temple, Debadeep Bhattacharyya, Yibing Wu, Sharon Campbell 
    Platinum and Other Heavy Metal Compounds in Cancer Chemotherapy, Springer Press 2009. [PDF] 

  2. Best Practices in Biotechnology Education: Carolina Student Biotechnology Network.
    Jessica R McCann, Shantanu SharmaBrant Hamel, Justin T Brown.
    Logos Press 2008 335-342. [PDF] 

    Conference Articles & Abstracts
  1. Nucleosome dynamics in silico - role of DNA and histone tails.
    Shantanu Sharma, Nikolay V Dokholyan. 
    98th Annual Meeting of the American Society for Biochemistry & Molecular Biology 2007, Washington DC, USA, The FASEB Journal 21:516.1. 2007. [PDF]

  2. Effect of sequence context in platinum-DNA structure.
    Debadeep Bhattacharya, Candice L King, Shantanu Sharma, Brenda Temple, Sharon L Campbell, Stephen G Chaney. 
    98th Annual Meeting of the American Association for Cancer Research 2007, Los Angeles, USA, AACR Proceedings 2007:3166. 2007. [PDF] 

  3. Discrete molecular dynamics studies of nucleosomes.
    Shantanu Sharma, Feng Ding, Nikolay V Dokholyan. 
    51st Annual Meeting of the Biophysical Society 2007, Baltimore, MD, USA, Biophys. J. 2007: 15a. 2007. [PDF] 

  4. Histone variants and tail dynamics in chromatin organization.
    Shantanu Sharma, Nikolay V Dokholyan. 
    6th Biennial Carolina Biophysics Symposium 2006. Chapel Hill, NC, USA. 2006. [PDF] 

  5. Structural dynamics of a nucleosome.
    Shantanu Sharma, Nikolay V Dokholyan. 
    1st Annual Duke Systems Biology Symposium 2006. Durham, NC, USA. 2006. [PDF] 

  6. Structure and dynamics of centromere specific nucleosomes.
    Shantanu Sharma, Kerry S Bloom, Nikolay V Dokholyan. 
    1st Annual Atlantic Coast Chromatin Conference, Chapel Hill, NC, USA. 2006. [PDF] 

  7. Comparing unfolding and folding pathways for Eglin C, SH3, and Chymotrypsin Inhibitor-2.
    Tamara J James, Shantanu Sharma, Nikolay V Dokholyan. 
    Annual Meeting of the Partnership for Minority Students in Biomolecular Sciences 2005 (Sponsored by the Howard Hughes Medical Institute). Chapel Hill, NC, USA 2006. [PDF] 

  8. Multiple sequence and structure alignments
    Aram Kim, Shantanu Sharma, Jeffrey Roach, Charles W Carter Jr. 
    International Conference on Aminoacyl-tRNA Synthetases: Ancient Molecules for Future Biology and Medicine. Seoul, Korea. 2004. [PDF] 

  9. Delaunay tetrahedral decomposition structural alignment.
    Jeffrey Roach, Shantanu Sharma, Charles W Carter Jr. 
    American Crystallographic Association Annual Meeting (ACA-2004; Chicago, USA), 2004. [PDF] 

  10. AAB: A generalized java-based algorithm animator builder.
    Shantanu Sharma, Vinay Choudhary, Ratan K Ghosh. 
    Proceedings of the Fifth International Conference of Information Technology (CIT-2002) 2002 Tata McGraw Hill, ISBN: 0070499926. [PDF] 

    Invited Talks 
  1. The odyssey of chromatin organization: histone tails and variants.
    Shantanu Sharma 
    Theoretical and Systems Biology Seminar Series, University of North Carolina at Chapel Hill. 2006, J. Logan Irvin Library, Mary Ellen Jones Bldg., Chapel Hill, NC, USA. [PDF] 

    Poster Presentations 
  1. Integrating multiscale modeling and simulations with scalable high performance computation. 
    Shantanu Sharma, Feng Ding, Nikolay V Dokholyan. 
    2007 Annual Symposium of the National Biomedical Computation Resource Summer Institute.La Jolla, CA, USA 2007. [PDF] 

  2. Structure and Dynamics of Centromere Specific Nucleosomes. 
    Shantanu Sharma, Kerry S Bloom, Nikolay V Dokholyan. 
    Annual Atlantic Coast Chromatin Symposium. Chapel Hill, NC, USA 2006. [PDF] 

  3. Structural Dynamics of a Nucleosome in silico.
    Shantanu Sharma, Nikolay V Dokholyan. 
    Annual Duke Systems Biology Symposium. Durham, NC, USA 2006. [PDF] 

  4. Multiple Sequence and Structure Alignments: Statistical Coupling Energies and Maximum Parsimony Analysis of Class I and Class II Synthetases.
    Aram Kim, Shantanu Sharma, Jeffrey Roach, Charles W Carter Jr. 
    International Conference on Aminoacyl-tRNA Synthetases: Ancient Molecules for Future Biology and Medicine (ARS2004). Seoul, Korea 2004. [PDF] 

    Technical Reports 
  1. A Novel Approach To Structural Comparison of Proteins. 
    Shantanu Sharma, Somenath Biswas. 
    Technical Report Undergraduate Thesis, Department of Computer Science and Engineering, IIT Kanpur 2004. [PDF]

  2. Independent Component Analysis in Real and Complex Fourier Space: An Application to Videos and Natural Scenes.
    Shantanu Sharma*, Nimit Kumar*.
    Technical Report CS698 - The Computational Brain, Department of Computer Science and Engineering, IIT Kanpur 2004. (* Equal Contribution) [PDF] 

  3. An active appearance model based face recognition system. 
    Shantanu Sharma*, Nitin Gupta*, Amitabha Mukherjee. 
    Technical Report Special Topics in Computer Science, IIT Kanpur 2003. (* Equal Contribution) [PDF] 

  4. Neural Network Applications in Sensor Fusion. 
    Shantanu Sharma*, Mathad S Apurva*, Ratan K Ghosh. 
    Technical Report Mobile Computing, IIT Kanpur 2003. (* Equal Contribution) [PDF] 

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