David A. Bader

Associate Professor
College of Computing
Georgia Tech
Atlanta, GA
30332

  
 

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Last updated: March 31, 2005

 




Computational Biology



Parallel Computing



Combinatorics

Peer-Reviewed Journal Publications

  1. D. A. Bader, J. JáJá , R. Chellappa. `` Scalable Data Parallel Algorithms for Texture Synthesis using Gibbs Random Fields,'' IEEE Transactions on Image Processing, 4(10):1456-1460, October 1995.

  2. D. A. Bader and J. JáJá . `` Parallel Algorithms for Image Histogramming and Connected Components with an Experimental Study,'' Journal of Parallel and Distributed Computing, 35(2)173-190, June 1996.

  3. D. A. Bader, D. R. Helman, and J. JáJá . `` Practical Parallel Algorithms for Personalized Communication and Integer Sorting,'' ACM Journal of Experimental Algorithmics, 1(3):1-42, 1996.

  4. D. A. Bader, J. JáJá , D. Harwood, and L.S. Davis. `` Parallel Algorithms for Image Enhancement and Segmentation by Region Growing with an Experimental Study,'' The Journal of Supercomputing, 10(2):141-168, 1996.

  5. D. R. Helman, D. A. Bader, and J. JáJá . `` A Randomized Parallel Sorting Algorithm With May 25, 2005 Journal of Parallel and Distributed Computing, 52(1):1-23, 1998.

  6. D.R. Helman, J. JáJá , D.A. Bader. `` A New Deterministic Parallel Sorting Algorithm With an Experimental Evaluation,'' ACM Journal of Experimental Algorithmics, 3(4):1-24, 1998.

  7. S.N.V. Kalluri, J. JáJá , D.A. Bader, Z. Zhang, J.R.G. Townshend, and H. Fallah-Adl. ``High Performance Computing Algorithms for Land Cover Dynamics Using Remote Sensing Data,'' International Journal of Remote Sensing, 21(6):1513-1536, 2000.

  8. D. A. Bader and J. JáJá `` SIMPLE: A Methodology for Programming High Performance Algorithms on Clusters of Symmetric Multiprocessors (SMPs),'' Journal of Parallel and Distributed Computing, 58(1):92-108, 1999.

  9. Z. Zhang, J. JáJá, D.A. Bader, S. Kalluri, H. Song, N. El Saleous, E. Vermote, and J. Townshend `` Kronos: A Software System for the Processing and Retrieval of Large-Scale AVHRR Data Sets,'' Photogrammetric Engineering & Remote Sensing, 66(9):1073-1082, 2000.

  10. David A. Bader and Robert Pennington, `` Cluster Computing: Applications,'' The International Journal of High Performance Computing, 15(2):181-185, May 2001.

  11. D.A. Bader, B. M.E. Moret, and M. Yan, `` A Linear-Time Algorithm for Computing Inversion Distance Between Two Signed Permutations with an Experimental Study,'' Journal of Computational Biology, 8(5):483-491, 2001.

  12. Y. Sun, X. Lin, Y. Pan, R.W.H. Lau, D.A. Bader, and P.Y.S. Cheung, `` Generalized Block Shift Network for Clusters,'' IEEE Trans. Circuits and Systems I, 49(4):543-546, 2002.

  13. B. M.E. Moret, D.A. Bader, and T. Warnow, `` High-Performance Algorithm Engineering for Computational Phylogeny,'' The Journal of Supercomputing, 22:99-111, 2002.

  14. D.A. Bader, B.M.E. Moret, and P. Sanders, `` Algorithm Engineering for Parallel Computation,'' Experimental Algorithmics, Lecture Notes in Computer Science, 2547:1-23, 2002.

  15. D.A. Bader and M. Yan, ``Fast Character Optimization in Parsimony Phylogeny Reconstruction,'' 2003. (Submitted)

  16. D.A. Bader, ``An Improved, Randomized Algorithm for Parallel Selection With an Experimental Study,'' 2003. (Submitted)

  17. D.A. Bader and G. Cong, ``Parallel Spanning Tree Algorithms for Symmetric Multiprocessors (SMPs),'' 2003. (Submitted)

  18. D.A. Bader and G. Cong, ``Fast Shared-Memory Algorithms for Computing the Minimum Spanning Forest of Sparse Graphs,'' 2003. (Submitted)

  19. D.A. Bader and S. Sreshta, ``A New Parallel Algorithm for Planarity Testing,'' 2003. (Submitted)

 

Peer-Reviewed Conference Tutorials

  1. Robert Pennington, David A. Bader, and Arthur B. Maccabe, ``Design and Analysis of NT and Linux Superclusters for Computational Grids,'' Supercomputing 1999 (SC99) Tutorial, Portland, OR, November 15, 1999.

  2. Robert Pennington, Patricia Kovatch, Arthur B. Maccabe, and David A. Bader, ``Design and Analysis of High Performance Clusters,'' Supercomputing 2000 (SC2000) Tutorial, Dallas, TX, November 5, 2000.

  3. David A. Bader, Bruce Hendrickson, and Steve Plimpton, ``Parallel Programming for Cluster Computers,'' Supercomputing 2000 (SC2000) Tutorial, Dallas, TX, November 6, 2000.

  4. S. Aluru and D.A. Bader, ``Opportunities and Challenges in Computational Biology,'' The IEEE and ACM Supercomputing Conference 2002 (SC2002) Tutorial, Baltimore, MD, November 17, 2002.

 

Peer-Reviewed Conference Publications

  1. D. A. Bader and J. JáJá . `` Parallel Algorithms for Image Histogramming and Connected Components with an Experimental Study,'' Fifth ACM SIGPLAN Symposium of Principles and Practice of Parallel Programming, Santa Barbara, CA, July 19-21, 1995.

  2. D. A. Bader and J. JáJá. `` Practical Parallel Algorithms for Dynamic Data Redistribution, Median Finding, and Selection,'' 10th International Parallel Processing Symposium (IPPS 96) Conference, Honolulu, HI, pp. 292-301, April 15-19, 1996.

  3. D. A. Bader, J. JáJá , D. Harwood, and L.S. Davis. `` Parallel Algorithms for Image Enhancement and Segmentation by Region Growing with an Experimental Study,'' 10th International Parallel Processing Symposium (IPPS 96) Conference, Honolulu, HI, pp. 414-423, April 15-19, 1996.

  4. D. R. Helman, D. A. Bader, and J. JáJá . `` Parallel Algorithms for Personalized Communication and Sorting with an Experimental Study,'' Eighth Annual ACM Symposium on Parallel Algorithms and Architectures, Padua, Italy, pp. 211-220, June 1996.

  5. S.N.V. Kalluri, Z. Zhang, J. JáJá, D.A. Bader, H. Song, N. El Saleous, E. Vermote, and J.R.G. Townshend `` A Hierarchical Data Archiving and Processing System to Generate Custom Tailored Products from AVHRR Data,'' IEEE 1999 International Geoscience and Remote Sensing Symposium (IGARSS'99), Hamburg, Germany, pp. 2374-2376, Vol. 5, June/July 1999.

  6. D.A. Bader, A.B. Maccabe, J.R. Mastaler, J.K. McIver III, and P.A. Kovatch, `` Design and Analysis of the Alliance / University of New Mexico Roadrunner Linux SMP SuperCluster,'' First IEEE Computer Society International Workshop on Cluster Computing (IWCC99), Melbourne, Australia, December 1999.

  7. D.A. Bader, ``High-Performance Algorithms and Applications for SMP Clusters,'' NASA High Performance Computing and Communications Computational Aerosciences Workshop (CAS 2000), NASA Ames Research Center, February 15-17, 2000.

  8. D.A. Bader, `` An Improved Randomized Selection Algorithm With an Experimental Study,'' Second Workshop on Algorithm Engineering and Experiments (ALENEX00), (sponsored by DIMACS, ACM SIGACT, and SIAM), San Francisco, CA, January 7-8, 2000.

  9. B.M.E. Moret, S. Wyman, D.A. Bader, T. Warnow, M. Yan, `` A New Implementation and Detailed Study of Breakpoint Analysis,'' Sixth Pacific Symposium on Biocomputing 2001 (PSB2001), pp. 583-594, Big Island, Hawaii, January 3-7, 2001.

  10. D.A. Bader, B. M.E. Moret, T. Warnow, S.K. Wyman, and M. Yan, ``High-Performance Algorithm Engineering for Gene-Order Phylogenies,'' DIMACS Workshop on Whole Genome Comparison, DIMACS Center, Rutgers University, Piscataway, NJ, March 1, 2001.

  11. C. Restrepo, B.T. Milne, D. Bader, W. Pockman, and A. Kerkhoff, ``Variation in vegetation growth rates: Implications for the evolution of semi-arid landscapes,'' 16th Annual Symposium of the US-International Association of Landscape Ecology, Arizona State University, Tempe, April 25-29, 2001.

  12. B. M.E. Moret, D.A. Bader, and T. Warnow, `` High-Performance Algorithm Engineering for Computational Phylogeny,'' The 2001 International Conference on Computational Science (ICCS 2001), V. Alexandrov and J. Dongarra and C.J.K. Tan (eds.), Springer-Verlag LNCS 2074, 1012-1021, San Francisco, CA, May 29, 2001.

  13. D.A. Bader, B. M.E. Moret, and M. Yan, `` A Linear-Time Algorithm for Computing Inversion Distance Between Two Signed Permutations with an Experimental Study,'' Seventh International Workshop on Algorithms and Data Structures (WADS 2001), F. Dehne, J.-R. Sack, and R. Tamassia (eds.), Springer-Verlag LNCS 2125, 365-376, Brown University, Providence, RI, August 8-10, 2001.

  14. R.K. Jansen, D.A. Bader, B. M. E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman, ``New approaches for using gene order data in phylogeny reconstruction,'' Botany 2001, Albuquerque, NM, August 12-16, 2001.

  15. B. M.E. Moret, D.A. Bader, T. Warnow, S.K. Wyman, and M. Yan, ``GRAPPA: a high-performance computational tool for phylogeny reconstruction from gene-order data,'' Botany 2001, Albuquerque, NM, August 12-16, 2001.

  16. L.A. Raubeson, D.A. Bader, B. M.E. Moret, L.-S. Wang, T. Warnow, and S.K. Wyman, ``Inferring phylogenies of photosynthetic organisms from chloroplast gene orders,'' Botany 2001, Albuquerque, NM, August 12-16, 2001.

  17. D.A. Bader, B. M.E. Moret, and L. Vawter, `` Industrial Applications of High-Performance Computing for Phylogeny Reconstruction,'' SPIE ITCom: Commercial Applications for High-Performance Computing (SPIE ITCom2001), Denver, CO, SPIE Vol. 4528, pp. 159-168, August 21-22, 2001.

  18. D.A. Bader, A. Illendula, B. M.E. Moret, and N.R. Weisse-Bernstein, `` Using PRAM Algorithms on a Uniform-Memory-Access Shared-Memory Architecture,'' Fifth Workshop on Algorithm Engineering (WAE 2001), G.S. Brodal, D. Frigioni, and A. Marchetti-Spaccamela, (eds.), Springer-Verlag LNCS 2141, 129-144, University of Aarhus, Denmark, August 28-31, 2001.

  19. Y. Sun, D.A. Bader, X. Lin, and Y. Ling, `` Broadcast on Clusters of SMPs with Optimal Concurrency,'' The 2002 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'02), Las Vegas, NV, June 2002.

  20. D.A. Bader, S. Sreshta, and N.R. Weisse-Bernstein, `` Evaluating Arithmetic Expressions using Tree Contraction: A Fast and Scalable Parallel Implementation for Symmetric Multiprocessors (SMPs),'' 9th International Conference on High Performance Computing (HiPC 2002), Bangalore, India, Lecture Notes in Computer Science, 2552:63-75, December 2002.

 

Edited Collections

  1. David A. Bader and Srinivas Aluru, Editors, Proceedings of the First IEEE International Workshop on High Performance Computational Biology (HiCOMB 2002), Fort Lauderdale, FL, April 15, 2002.

  2. David A. Bader and Srinivas Aluru, Editors, Proceedings of the Second IEEE International Workshop on High Performance Computational Biology (HiCOMB 2003), IEEE Computer Society Press, Nice, France, April 22, 2003.

  3. David A. Bader and Srinivas Aluru, Guest Editors, Journal of Parallel and Distributed Computing Special Issue on High-Performance Computational Biology, Elsevier, to appear Fall 2003.

  4. David A. Bader and Srinivas Aluru, Guest Editors, Concurrency and Computation: Practice and Experience Special Issue on Extended Papers from the Second IEEE International Workshop on High Performance Computational Biology, John Wiley \& Sons, to appear Winter 2003/4.

  5. David A. Bader, Albert Y. Zomaya, et al., Editors, Handbook of Innovative Computing, Springer-Verlag USA, to appear 2004.

 

Invited Papers

  1. D. A. Bader, `` Editorial: A New, Architectural Paradigm for High-performance Computing,'' Parallel and Distributed Computing Practices Journal, 2(2), 1999.

 

Additional Technical Reports

  1. D. A. Bader. ``Object Oriented Simulation of Systems With Examples in Structural Design And Parallel Processing,'' Master's Thesis, Department of Computer Science and Electrical Engineering, Lehigh University, January 1992.

  2. D. A. Bader. ``PARSIM: A Simulator for Designing Parallel Algorithms and Architectures,'' Lehigh University Research Report CSEE-TR-90-07, Department of Computer Science and Electrical Engineering, Lehigh University, 1990.

  3. D. A. Bader and P. J. Stinson. ``Table of Lower Bounds on the Minimum Distance of Cyclic and BCH Codes,'' NSF Research Experience for Undergraduates (REU) Program Summer Project Report, Lehigh University Research Report CSEE-TR-90-06, Department of Computer Science and Electrical Engineering, Lehigh University, 1989.