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      - External-Memory / Cache-Efficient / Cache-Oblivious
      - Computational Biology / Bioinformatics
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      - Compilers


  Journal Papers
      ¤ Michael Bender, Rezaul Chowdhury, Pramod Ganapathi, Samuel McCauley, and Yuan Tang, "The Range 1 Query (R1Q) Problem", Theoretical Computer Science (Special Issue for COCOON'14, Invited Paper), 2016.
      ¤ Rezaul Chowdhury, Dmitri Beglov, Mohammad Moghadasi, Ioannis Paschalidis, Pirooz Vakili, Sandor Vajda, Chandrajit Bajaj, and Dima Kozakov, "Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations", Journal of Chemical Theory and Computation, vol. 10(10), pp. 4449-4454, 2014.
      ¤ Michael Bender, Ritwik Bose, Rezaul Chowdhury, and Samuel McCauley, "The Kissing Problem: How to End a Gathering When Everyone Kisses Everyone Else Goodbye", Theory of Computing Systems (Special Issue for FUN'12, Invited Paper), vol. 54(4), pp. 715-730, 2014.
      ¤ Rezaul Chowdhury, Francesco Silvestri, Brandon Blakeley, and Vijaya Ramachandran, "Oblivious Algorithms for Multicores and Network of Processors", Journal of Parallel and Distributed Computing (Special issue dedicated to the Best Papers from IPDPS'10-12), vol. 73 (7), pp. 911-925, 2013.
      ¤ Rezaul Chowdhury, Muhibur Rasheed, Donald Keidel, Maysam Moussalem, Arthur Olson, Michel Sanner, and Chandrajit Bajaj, "Protein-Protein Docking with F2Dock 2.0 and GB-Rerank", PLoS One, vol. 8 (3), pp. e51307, 2013.
      ¤ Chandrajit Bajaj, Rezaul Chowdhury, and Muhibur Rasheed, "A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics", Bioinformatics, vol. 27 (1), pp. 55-62, 2011.
      ¤ Chandrajit Bajaj, Rezaul 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.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "The Cache-Oblivious Gaussian Elimination Paradigm: Theoretical Framework, Parallelization and Experimental Evaluation", Theory of Computing Systems (Special Issue for SPAA'07), vol. 47 (4), pp. 878-919, 2010.
      ¤ Rezaul 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.
      ¤ Camil Demetrescu, Mikkel Thorup, Rezaul Chowdhury, and Vijaya Ramachandran, "Oracles for Distances Avoiding a Failed Node or Link", SIAM Journal on Computing, vol. 37 (5), pp. 1299-1318, 2008.


  Refereed Conference / Workshop Papers with Published Proceedings
      ¤ Shachar Itzhaky, Rohit Singh, Armando Solar-Lezama, Kuat Yessenov, Yongquan Lu, Charles Leiserson, and Rezaul Chowdhury, "Deriving Divide-and-Conquer Dynamic Programming Algorithms Using Solver-Aided Transformations", Proceedings of the ACM SIGPLAN International Conference on Object-Oriented Programming, Systems, Languages & Applications (OOPSLA 2016), Amsterdam, Netherlands, pp. 145-164, 2016.
      ¤ Rezaul Chowdhury, Pramod Ganapathi, Vivek Pradhan, Jesmin Jahan Tithi, and Yunpeng Xiao, "An Efficient Cache-oblivious Parallel Viterbi Algorithm", Proceedings of the 22nd International European Conference on Parallel and Distributed Computing (EuroPar 2016), Grenoble, France, LNCS 9833, pp. 574-587, 2016.
      ¤ Michael Bender, Rezaul Chowdhury, Alexander Conway, Martín Farach-Colton, Pramod Ganapathi, Rob Johnson, Samuel McCauley, Bertrand Simon, and Shikha Singh, "The I/O Complexity of Computing Prime Tables", Proceedings of the 12th Latin American Theoretical Informatics Symposium (LATIN 2016), Ensenada, Mexico, LNCS 9644, pp. 192-206, 2016.
      ¤ Rezaul Chowdhury, Pramod Ganapathi, Jesmin Jahan Tithi, Charles Bachmeier, Bradley C. Kuszmaul, Charles E. Leiserson, Armando Solar-Lezama, and Yuan Tang, "AUTOGEN: Automatic Discovery of Cache- Oblivious Parallel Recursive Algorithms for Solving Dynamic Programs", Proceedings of the 21st ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 2016), Barcelona, Spain, article 10, 2016. (Invited to ACM Transactions on Parallel Computing Special Issue on Top Papers from PPoPP'16).
      ¤ Deukhyun Cha, Qin Zhang, Jesmin Jahan Tithi, Alexander Rand, Rezaul Chowdhury, and Chandrajit Bajaj, "Accelerated Molecular Mechanical and Solvation Energetics on Multicore CPUs and Manycore GPUs", Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2015), Atlanta, GA, pp. 222-231, 2015.
      ¤ Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther Arkin, Joseph Mitchell, and Steven Skiena, "Optimizing Read Reversals for Sequence Compression (Extended Abstract)", Proceedings of the 15th International Workshop on Algorithms in Bioinformatics (WABI 2015), Atlanta, GA, LNCS 9289, pp. 189-202, 2015 (Invited to Algorithms for Molecular Biology Special Issue on Top Papers from WABI'15).
      ¤ Jesmin Jahan Tithi, Pramod Ganapathi, Aakrati Talati, Sonal Aggarwal, and Rezaul Chowdhury, "High-Performance Energy-Efficient Recursive Dynamic Programming with Matrix-Multiplication-Like Flexible Kernels", Proceedings of the 29th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2015), Hyderabad, India, pp. 303-312, 2015.
      ¤ Yuan Tang, Ronghui You, Haibin Kan, Jesmin Jahan Tithi, Pramod Ganapathi, and Rezaul Chowdhury, "Cache-Oblivious Wavefront: Improving Parallelism of Recursive Dynamic Programming Algorithms without Losing Cache-efficiency", Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 2015), San Francisco, CA, pp. 205-214, 2015.
      ¤ Yuan Tang, Ronghui You, Haibin Kan, Jesmin Jahan Tithi, Pramod Ganapathi, and Rezaul Chowdhury, "Improving Parallelism of Recursive Stencil Computations without Sacrificing Cache Performance", Proceedings of the SPLASH Workshop on Stencil Computations (WOSC 2014), Portland, Oregon, 2014.
      ¤ Michael Bender, Rezaul Chowdhury, Pramod Ganapathi, Samuel McCauley, and Yuan Tang, "The Range 1 Query (R1Q) Problem", Proceedings of the 20th International Conference on Computing and Combinatorics (COCOON 2014), Atlanta, GA, pp. 116-128, 2014 (Invited to Theoretical Computer Science Special Issue on Top Papers from COCOON'14).
      ¤ Jesmin Jahan Tithi, Dhruv Matani, Gaurav Menghani, and Rezaul Chowdhury, "Avoding Locks and Atomic Instructions in Shared-Memory Parallel BFS using Optimistic Parallelization", Proceedings of the IPDPS Workshop on Multithreaded Architectures and Applications (MTAAP 2013), Boston, Massachusetts, May 2013.
      ¤ Jesmin Jahan Tithi and Rezaul Chowdhury, "Polarization Energy on a Cluster of Multicores", Proceedings of the IPDPS Workshop on High Performance Computational Biology (HiCOMB 2013), Boston, Massachusetts, May 2013.
      ¤ Michael Bender, Ritwik Bose, Rezaul Chowdhury, and Samuel McCauley, "The Kissing Problem: How to End a Gathering When Everyone Kisses Everyone Else Goodbye", Proceedings of the 6th International Conference on Fun with Algorithms (FUN 2012), Venice, Italy, pp. 28-39, 2012 (Invited to Theory of Computing Systems Special Issue on Top Papers from FUN'12).
      ¤ Yuan Tang, Rezaul Chowdhury, Bradley Kuszmaul, Chi-Keung Luk, and Charles Leiserson, "The Pochoir Parallel Stencil Compiler", Proceedings of the 23rd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2011), San Jose, California, pp. 117-128, 2011 (Most Cited Paper of SPAA'11).
      ¤ Yuan Tang, Rezaul Chowdhury, Chi-Keung Luk, and Charles Leiserson, "Coding Stencil Computations Using the Pochoir Stencil-Specification Language", Proceedings of the 3rd USENIX Workshop on Hot Topics in Parallelism (HotPar 2011), Berkeley, California, May 26-27, 2011.
      ¤ Rezaul 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.
      ¤ Rezaul Chowdhury, Francesco Silvestri, Brandon Blakeley, and Vijaya Ramachandran, "Oblivious Algorithms for Multicores and Network of Processors", Proceedings of the 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2010), Atlanta, Georgia, April 19-23, 2010 (Best Paper Award in the Algorithms Track).
      ¤ Chandrajit Bajaj, Rezaul 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.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "Cache-efficient Dynamic Programming Algorithms for Multicores", Proceedings of the 20th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2008), Munich, Germany, pp. 207-216, 2008.
      ¤ Guy Blelloch, Rezaul Chowdhury, Phillip Gibbons, Vijaya Ramachandran, Shimin Chen, and Michael Kozuch, "Provably Good Multicore Cache Performance for Divide-and-Conquer Algorithms", Proceedings of the 19th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2008), San Francisco, California, pp. 501-510, 2008.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "The Cache-Oblivious Gaussian Elimination Paradigm - Theoretical Framework, Parallelization and Experimental Evaluation", Proceedings of the 19th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2007), San Diego, California, pp. 71-80, 2007 (Invited to Theory of Computing Systems Special Issue on Top Papers from SPAA'07).
      ¤ Rezaul 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.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "External-Memory Exact and Approximate All-Pairs Shortest-Paths in Undirected Graphs", Proceedings of the 16th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2005), Vancouver, BC, Canada, pp. 735-744, 2005.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "Cache-Oblivious Shortest-Paths in Graphs Using Buffer Heap", Proceedings of the 16th Annual ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2004), Barcelona, Spain, pp. 245-254, 2004.
      ¤ Rezaul Chowdhury, Peter Djeu, Brandon Cahoon, James Burrill, and Kathryn S. McKinley, "The Limits of Alias Analysis for Scalar Optimizations", Proceedings of the 13th International Conference on Compiler Construction (CC 2004), Barcelona, Spain, pp. 24-38, 2004.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "Improved Distance Oracles for Avoiding Link-Failure", Proceedings of the 13th Annual International Symposium on Algorithms and Computation (ISAAC 2002), Vancouver, BC, Canada, LNCS 2518, pp. 523-534, 2002.


  Refereed Short Paper(s) / Brief Announcement(s) / Poster(s)
      ¤ Rezaul Chowdhury, Pramod Ganapathi, Yuan Tang, and Jesmin Jahan Tithi, "Provably Efficient Scheduling of Cache-Oblivious Wavefront Algorithms", To appear in the Proceedings of the 22nd SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 2017), Austin, Texas, 2017.
      ¤ Jesmin Jahan Tithi, Pramod Ganapathi, Rezaul Chowdhury, and Yuan Tang, "Cache-oblivious Wavefront Algorithms for Dynamic Programming Problems: Efficient Scheduling with Optimal Cache Performance and High Parallelism", High Performance Computing, Networking Storage and Analysis (SC 2016), 2016.
      ¤ Jesmin Jahan Tithi and Rezaul Chowdhury, "Efficient Computation of Distance Incorporated Codon Auto-correlation (DICA) Score using Fast Fourier Transform", Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2015), Atlanta, GA, pp. 515-516, 2015.
      ¤ Jesmin Jahan Tithi, Pramod Ganapathi, Aakrati Talati, and Rezaul Chowdhury, "High-performance Recursive Dynamic Programming for Bioinformatics using MM-like Flexible Kernels", Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2014), Newport Beach, CA, pp. 600-601, 2014.
      ¤ Jesmin Jahan Tithi and Rezaul Chowdhury, "Polarization Energy on a Cluster of Multicores", Proceedings of the High Performance Computing, Networking Storage and Analysis (SCCOMPANION 2012), pp. 1377-1378, 2012.
      ¤ Pramod Ganapathi, Rezaul Chowdhury, and Yuan Tang, "The R1Q Problem", 22nd Annual Fall Workshop on Computational Geometry (FWCG 2012), University of Maryland, College Park, MD, 2012.
      ¤ Rezaul 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.
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "The Cache-Oblivious Gaussian Elimination Paradigm - Theoretical Framework and Experimental Evaluation", Proceedings of the 18th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2006), Cambridge, Massachusetts, page 236, 2006.


  Book Article(s)
      ¤ Rezaul Chowdhury, "Equivalence Between Priority Queues and Sorting (Mikkel Thorup, 2002)", Encyclopedia of Algorithms, Ming-Yang Kao (Editor), Springer US, 2008.


  Technical Reports
      ¤ Rezaul Chowdhury, Francesco Silvestri, Brandon Blakeley, and Vijaya Ramachandran, "Oblivious Algorithms for Multicores and Network of Processors", The University of Texas at Austin, Department of Computer Sciences, TR-09-19, July 2009, 40 pages.
        View: Abstract
        Download: PS,  PDF
      ¤ Chandrajit Bajaj, Rezaul 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
        Download: PS,  PDF
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "Cache-efficient Dynamic Programming Algorithms for Multicores", The University of Texas at Austin, Department of Computer Sciences, TR-08-16, Apr. 2008, 21 pages.
        View: Abstract
        Download: PS,  PDF
      ¤ Mo Chen, Rezaul Chowdhury, Vijaya Ramachandran, David Lan Roche, and Lingling Tong, "Priority Queues and Dijkstra's Algorithm", The University of Texas at Austin, Department of Computer Sciences, TR-07-54, Oct. 2007, 25 pages.
        View: Abstract
        Download: PS,  PDF
      ¤ Rezaul 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
      ¤ Rezaul Chowdhury and Vijaya Ramachandran, "The Cache-Oblivious Gaussian Elimination Paradigm: Theoretical Framework and Experimental Evaluation", The University of Texas at Austin, Department of Computer Sciences, TR-06-04, Mar. 2006, 36 pages.
        View: Abstract
        Download: PS,  PDF
      ¤ Rezaul 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
        Download: PS,  PDF

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  Dissertation
      ¤ Rezaul Chowdhury, "Cache-efficient Algorithms and Data Structures: Theory and Experimental Evaluation", PhD Thesis, Department of Computer Sciences, The University of Texas at Austin, 2007.
        View: Abstract
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