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  Current Area
      - Computational Biology / Bioinformatics

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      - External-Memory / Cache-Efficient / Cache-Oblivious
      - Multicore Computing
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  Dissertation
      1. Rezaul Alam Chowdhury, "Cache-efficient Algorithms and Data Structures: Theory and Experimental Evaluation", PhD Thesis, Department of Computer Sciences, The University of Texas at Austin, 2007.
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  Journal Papers
      1. Rezaul Alam Chowdhury, Hai-Son Le, and Vijaya Ramachandran, "Cache-oblivious Dynamic Programming for Bioinformatics", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7 (3), pp. 495-510, 2010.
        Preliminary Version
               View: Abstract
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      2. Chandrajit Bajaj, Rezaul Alam Chowdhury, and Vinay Siddavanahalli, "F2Dock: Fast Fourier Protein-Protein Docking", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8 (1), pp. 45-58, 2011.
        Preliminary Version
               View: Abstract
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      3. Chandrajit Bajaj, Rezaul Alam Chowdhury, and Muhibur Rasheed, "A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics", Bioinformatics, vol. 27 (1), pp. 55-62, 2011.
        Preliminary Version
               View: Abstract
               Download: PDF


  Conference Papers
      1. Rezaul Alam Chowdhury and Chandrajit Bajaj, "Multi-level Grid Algorithms for Faster Molecular Energetics", Proceedings of the ACM Symposium on Solid and Physical Modeling (SPM 2010), Haifa, Israel, pp. 147-152, 2010.
      2. Chandrajit Bajaj, Rezaul Alam Chowdhury, and Muhibur Rasheed, "A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics", Proceedings of the ACM Symposium on Solid and Physical Modeling (SPM 2009), San Francisco, California, pp. 259-270, 2009.
        View: Abstract
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      3. Rezaul Alam Chowdhury and Vijaya Ramachandran, "Cache-Oblivious Dynamic Programming", Proceedings of the 17th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2006), Miami, Florida, pp. 591-600, 2006.
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  Poster(s)
      1. Rezaul Alam Chowdhury, Hai-Son Le, and Vijaya Ramachandran, "Cache-Oblivious String Algorithms for Bioinformatics", 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), San Francisco, California, 2007.
        Full Paper
               View: Abstract
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  Under Review
      1. Rezaul Alam Chowdhury and Chandrajit Bajaj, "Algorithms for Faster Molecular Energetics, Forces and Interfaces", 2010.
        View: Abstract
      2. Rezaul Alam Chowdhury, Donald Keidel, Maysam Moussalem, Muhibur Rasheed, Arthur Olson, Michel Sanner, and Chandrajit Bajaj, "Protein-Protein Docking with F2Dock 2.0 and GB-rerank", 2010.
        View: Abstract


  Technical Reports
      1. Chandrajit Bajaj, Rezaul Alam Chowdhury, and Vinay Siddavanahalli, "F3Dock: A Fast, Flexible and Fourier Based Approach to Protein-Protein Docking", The University of Texas at Austin, Institute for Computational Engineering and Sciences (ICES), Report 08-01, January 2008 (Updated: April 2009), 27 pages.
        View: Abstract
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      2. Rezaul Alam Chowdhury, Hai-Son Le, and Vijaya Ramachandran, "Efficient Cache-Oblivious String Algorithms for Bioinformatics", The University of Texas at Austin, Department of Computer Sciences, TR-07-03, Feb. 2007, 26 pages.
        View: Abstract
        Download: PS,  PDF
      3. Rezaul Alam Chowdhury, "Experimental Evaluation of a Cache-Oblivious LCS Algorithm", The University of Texas at Austin, Department of Computer Sciences, TR-05-43, Oct. 2005, 12 pages.
        View: Abstract
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  Under Preparation
      1. Donald Keidel, Rezaul Alam Chowdhury, Maysam Moussalem, Arthur Olson, Michel Sanner, and Chandrajit Bajaj, "Comparative Study of the Scoring Methods of Three FFT-based Protein-Protein Docking Programs", 2010.
      2. Maysam Moussalem, Rezaul Alam Chowdhury, Donald Keidel, Arthur Olson, Michel Sanner, and Chandrajit Bajaj, "Comparative Study of Three Reranking Methods for Fast Fourier Transform-Based Protein-Protein Docking Programs", 2010.