David A. Bader

Professor
College of Computing
Georgia Tech
Atlanta, GA
30332

 
 

 

09 July 2014

Curriculum Vitae for David A. Bader

Computational Science and Engineering
College of Computing
Georgia Institute of Technology
Atlanta, GA 30332

Office phone: (404)385-0004
FAX number: (404)506-9492

EDUCATIONAL BACKGROUND

EMPLOYMENT HISTORY

CURRENT FIELDS OF INTEREST

David A. Bader is a Full Professor and Chair of the School of Computational Science and Engineering, College of Computing, at Georgia Institute of Technology, and Executive Director of High Performance Computing. He received his Ph.D. in 1996 from The University of Maryland, and his research is supported through highly-competitive research awards, primarily from NSF, NIH, DARPA, and DOE. Dr. Bader serves as a board member of the Computing Research Association (CRA), on the NSF Advisory Committee on Cyberinfrastructure, on the Council on Competitiveness High Performance Computing Advisory Committee, on the IEEE Computer Society Board of Governors, and on the Steering Committees of the IPDPS and HiPC conferences. He is the editor-in-chief of IEEE Transactions on Parallel and Distributed Systems (TPDS) and Program Chair for IPDPS 2014. Bader also serves as an associate editor for several high impact publications including IEEE Transactions on Computers (TC), ACM Transactions on Parallel Computing (TOPC), and ACM Journal of Experimental Algorithmics (JEA). Dr. Bader's interests are at the intersection of high-performance computing and real-world applications, including computational biology and genomics and massive-scale data analytics. He has co-chaired a series of meetings, the IEEE International Workshop on High-Performance Computational Biology (HiCOMB), co-organized the NSF Workshop on Petascale Computing in the Biological Sciences, written several book chapters, and co-edited special issues of the Journal of Parallel and Distributed Computing (JPDC) and IEEE TPDS on high-performance computational biology. He is also a leading expert on multicore, manycore, and multithreaded computing for data-intensive applications such as those in massive-scale graph analytics. He has co-authored over 130 articles in peer-reviewed journals and conferences, and his main areas of research are in parallel algorithms, combinatorial optimization, massive-scale social networks, and computational biology and genomics. Prof. Bader is a Fellow of the IEEE and AAAS, a National Science Foundation CAREER Award recipient, and has received numerous industrial awards from IBM, NVIDIA, Intel, Cray, Oracle/Sun Microsystems, and Microsoft Research. Dr. Bader has served as a lead scientist in several DARPA programs including High Productivity Computing Systems (HPCS) with IBM PERCS, Ubiquitous High Performance Computing (UHPC) with NVIDIA ECHELON, Anomaly Detection at Multiple Scales (ADAMS) and Power Efficiency Revolution For Embedded Computing Technologies (PERFECT). He has also served as Director of the Sony-Toshiba-IBM Center of Competence for the Cell Broadband Engine Processor. Bader is a co-founder of the Graph500 List for benchmarking ``Big Data'' computing platforms. Bader is recognized as a ``RockStar'' of High Performance Computing by InsideHPC and as HPCwire's People to Watch in 2012 and 2014.

TEACHING

Continuing Education

  • 1998 NSF Engineering Education Scholars Program, University of Wisconsin-Madison.
  • 1998 Teaching-Wise Educational Workshop, University of New Mexico.
  • 2000 American with Disabilities Act Training, "Access to Education," University of New Mexico.
  • Scholarly Communication and the Common Good: A Symposium for the University of New Mexico's Academic Community, February 27, 2003.
  • Faculty Scholarly Communication Symposium: Stewardship of the University Community's Knowledge-Base, March 12, 2004.
  • 3rd Annual Scholarly Communication Symposium: Cultural Transformation of the University's Knowledge Base, March 3, 2005.

Individual Student Guidance

Postdoctoral Fellows Supervised

  • Tanya (Yonit) Berger-Wolf (PhD, University of Illinois, Urbana-Champaign), NSF Postdoctoral Research Associateship in Experimental Computer Science. Computational methods for controlled breeding programs and evolutionary trees reconstruction. 2002-2004. (joined Univ. of Illinois - Chicago).
  • Henning Meyerhenke (PhD, University of Paderborn, Germany), 2010-2011.
  • Yuzhong Sun (PhD, Chinese Academy of Sciences). Hybrid parallel algorithms for routing collective communications on SMP clusters. 1999-2000.
  • Tiffani L. Williams (PhD, Central Florida). Alfred P. Sloan Postdoctoral Fellowship in Computational Molecular Biology. 2001-2004. (joined Texas A&M Univ.).

Postdoctoral Students Supervised

  • James A. McCoy, Sandia National Laboratories Computational Science Retraining Program, "Porting a parallel VHDL simulation environment to Sandia National Labs parallel computing platforms," 1998.
  • Michael Keenan, "Multivariate Image Analysis Tools for Chemical Characterization," Sandia National Laboratories Computational Science Retraining Program, 1999.
  • Doug Wall, Sandia National Laboratories Computational Science Retraining Program, "Improving the Performance of a Crevice Corrosion Code Using Space Iterative Methods and Parallelization," 2000.
  • David Beck, Sandia National Laboratories Computational Science Retraining Program, "Evaluation and Characterization of Secure File Storage in Client Parallel I/O," 2000.

Ph.D. Students Supervised

  • Mi Yan. Thesis Title: ``High Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony,'' January 2004. (Future Technologies Solution Design Center, IBM Corp.)
  • Guojing Cong, with distinction. Thesis Title: ``On the Design and Implementation of Parallel Algorithms for Graph Problems on Shared-Memory Machines,'' October 2004. (IBM T.J. Watson Research Center)
  • Jinyang Liu. Thesis Title: ``Control and Noise Immunity of High Resolution Experiments on Earth Orbit,'' October 2005. (Janelia Farms Research Center, Howard Hughes Medical Institute)
  • Matthew J. Sottile. Thesis Title: ``A Measurement and Simulation Methodology for Parallel Computing Performance Studies,'' April 2006. (University of Oregon)
  • Xuefei Wang. Thesis Title: ``Hybrid Neuro-Fuzzy Inference Models for Outcome Prediction in Acute Leukemia Using Gene Expression and Covariate Data,'' October 2007. (co-advised with S. Atlas)
  • Kamesh Madduri. Thesis Title: ``A High-Performance Framework for Analyzing Massive Complex Networks,'' July 2008. Recipient of the College of Computing's 2008 Outstanding Graduate Research Assistant Award. (Luis W. Alvarez Postdoctoral Fellowship in Computational Science, Lawrence Berkeley National Laboratory)
  • Virat Agarwal. Thesis Title: ``A High-Performance Framework for Analyzing Massive Complex Networks,'' June 2010. (IBM T.J. Watson Research Center, Yorktown Heights, NY)
  • Seunghwa Kang. Thesis Title: ``On The Design of Architecture-Aware Algorithms For Emerging Applications,'' January 2011. (Pacific Northwest National Laboratory)
  • David Ediger. Thesis Title: ``Analyzing Hybrid Architectures for Massively Parallel Graph Analysis,'' May 2013.
  • Vipin Sachdeva, (B.Tech, IIT Guwahati; M.S., U New Mexico, entered Fall 2009)
  • Zhaoming Yin. Thesis Title: ``Enhance the Understanding of Whole-Genome Evolution by Designing, Accelerating and Parallelizing Phylogenetic Algorithms,'' May 2014.
  • Emily Rogers, (B.S., University of California, Berkeley; M.S., Georgia Tech, entered Fall 2010), co-advised with Dr. Christine Heitsch.
  • Robert McColl, (B.S., Vanderbilt University, entered Fall 2010)
  • Oded Green. Thesis Title: ``High Performance Computing for Irregular Algorithms and Applications with a Focus on Big Data Analytics,'' May 2014.
  • Anita Zakrzewska, (B.S., Brandeis University, entered Fall 2011)
  • James Fairbanks, (B.S., University of Florida, entered Fall 2012)
  • Lluis Miquel Munguia, (B.S., Univ Politécnica de Catalunya (UPC), Barcelona, entered Fall 2012)
  • JiaJia Li, (Ph.D., Chinese Academy of Sciences, entered Fall 2013)

M.S. Thesis Students Supervised

  • Mr. Ajith Kumar Illendula, June 2000, Thesis: "Efficient and Practical Parallel Algorithms for Ear Decomposition with Experimental Studies." (joined Intel Corp., Rio Rancho, NM).
  • Mr. Niranjan Prabhu, December 2000, Thesis: "Practical Parallel Algorithms for Cycle Detection in Planar Partitioned Digraphs." (joined Intel Corp., Chandler, AZ)
  • Ms. Vinila Yarlagadda, December 2000, Thesis: "Design of Practical Parallel Algorithms for Uniform-Memory Access Symmetric Multiprocessors." (joined Intel Corp., Chandler, AZ).
  • Ms. Bei Wang, Summer 2002, Thesis: "Modeling and Simulation of Optimization Problems in Landscape Ecology." (joined Ph.D. program at University of Southern California).
  • Ms. Min Zhu, September 2002, Thesis: "Parallel Branch and Bound Algorithms with Experimental Studies on Shared Memory Multiprocessors." (joined Ph.D. program in Mathematics)
  • Mr. Bhaskar Subramanian, with distinction, December 2002, Thesis: "Automated Synthesis of Pass Transistor Asynchronous Sequential Circuits," (joined Sun Microsystems)
  • Ms. Zhan Li, December 2002, Thesis: ``Parallel Algorithms for Uniform-Memory-Access Shared Memory Multiprocessors,'' (co-advised with B. Moret). (joined Bioinformatics Lab, Penn State University).
  • Ms. Sukanya Sreshta, with distinction, December 2003, Thesis: "Designing Parallel Graph Algorithms for Symmetric Multiprocessors." (joined OpNet Technologies, Bethesda, MD)
  • Ms. Meenakshi Balasubramanian, July 2005, Thesis: ``Design and Implementation of Scalable Synthetic Compact Application (SSCA) Graph Theoretic Benchmark using Unified Parallel C (UPC).'' (joined Merrill Lynch, New York).
  • Mr. Eswaramoorthi Nallusamy, October 2005, Thesis: ``A Framework for Using Processor Cache as RAM in LinuxBIOS on x86 Cluster,'' (joined Intel Corp., DuPont, WA)
  • Mr. Vipin Sachdeva, with distinction, December 2005, Thesis: ``High Performance Computing for Computational Biology and Graph Theory.'' (joined IBM Research, Austin Research Laboratory)
  • Ms. Sirisha Muppavarapu, January 2006, Thesis: ``Analysis of A Sequence Alignment Problem Using Unified Parallel C (UPC),'' (joined Intel Corp., Rio Rancho, NM)
  • Midhun Kumar Allu, Summer 2006, Thesis. (co-advised with E. Ritchie). (joined AT&T, New Jersey)
  • Rick Quax, July 2008, Thesis: ``Modeling and Simulating the Propagation of Infectious Diseases using Complex Networks.''
  • Amrita Mathuriya, December 2008. (joined Intel Corp., Beaverton, OR)
  • Prashant Gaurav, December 2011. (joined Groupon, Mountain View, CA)
  • Pushkar Pande, December 2011. (joined Risk Management Solutions, Newark, CA)

M.S. Non-Thesis Students Supervised

  • Ms. Kavita Balakavi, Spring 1999. (joined Intel Corp., Beaverton, OR).
  • Ms. Sireesha Sankuratripati, with distinction, Summer 2001. (joined Intel Corp., Chandler, AZ)
  • Mr. Charan Donepudi, Summer 2001. (joined Intel Corp., Chandler, AZ).
  • Mr. Raghuram Mandiga, Summer 2001.
  • Mr. Ram Saran Attaluri, Spring 2002.
  • Mr. JingYi Dong, January 2003. (joined PhD program, Georgia Tech).
  • Mr. Tu-Thach Ong, Fall 2003. (Sandia National Laboratories)
  • Ms. Prishanthy Wilson, Fall 2003. (joined Isochron Data Corporation, Austin, TX).
  • Mr. Susheel Kumar Puthana, Spring 2004. (joined Xilinx Corp., Colorado)
  • Vikas Chaudhary, Spring 2004. (entered PhD Program, Arizona State University).
  • Shruti Krishnamurthy, Spring 2004.
  • Glenn Harper, Fall 2004.
  • Arun Illendula, Fall 2004.
  • Mallikarjun Komma, Fall 2004.
  • Mr. Mehmet Fatih Su, Fall 2005.
  • Sangeetha Illendula, Fall 2006. (joined Lumidigm Inc.)
  • Sulabh Patel, Summer 2007. (joined Electronic Arts, Inc.)
  • Manisha Gajbe, Fall 2009.
  • Sainath Mallidi, December 2010.

Undergraduate Researchers

  • Virat Agarwal (IIT-Delhi, 2004)
  • Nitesh Agrawal (IIT-Roorkee, 2008)
  • Diana Aranda (NSF REU, 2002-2003)
  • Troy Brant (Georgia Tech, 2006-2007)
  • Warren Chancellor (Morehouse College, 2008)
  • Gaurav Goel (IIT-Delhi, 2004)
  • Sonny Hernandez (NSF REU, University of Southern California, 2007)
  • Neha Jatav (IIT-Bombay, 2010)
  • Letisha Kaskaske (NSF REU, 2002-2003)
  • Michael Lee (Univ Maryland, Baltimore County, 2008)
  • Angeline Madrid-Ritchey (NSF REU, 2002-2003)
  • Kamesh Madduri (NSF REU, IIT-Madras, 2003-2004)
  • Nicholas Merryman (Georgia Tech, 2006)
  • Danny Miller (Georgia Tech, 2006-2007), 2010 UROP Thesis
  • Milan Kumar Mohapatra (IIT-Roorkee, 2010)
  • Emeline Picart (INSA, France, 2003)
  • Abhishek Narain Singh (IIT-Delhi, 2004)
  • Manoj Soni (IIT-Roorkee, 2008)
  • Yamini Sridharan (IIT-Kharagpur, 2005)
  • Laura Waymire (NSF REU, 2001-2003)

Teaching Honors and Awards

  • Thank a Teach Certificate ``in recognition for excellence in teaching,'' Center for the Enhancement of Teaching and Learning, Georgia Tech, 2008, 2009.

RESEARCH AND CREATIVE SCHOLARSHIP

Thesis

Published Journal Papers (refereed)

  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 an Experimental Study,'' 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, 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. M. Snir and D.A. Bader, `` A Framework for Measuring Supercomputer Productivity,'' The International Journal of High Performance Computing Applications, 18(4): 417-432, 2004.

  15. D.A. Bader, `` An Improved, Randomized Algorithm for Parallel Selection With an Experimental Study,'' Journal of Parallel and Distributed Computing, 64(9):1051-1059, 2004.

  16. D.A. Bader, `` Computational Biology and High-Performance Computing,'' Special Issue on Bioinformatics, C. Stewart (ed.), Communications of the ACM, 47(11):34-41, 2004.

  17. D.A. Bader and G. Cong, ``A Fast, Parallel Spanning Tree Algorithm for Symmetric Multiprocessors (SMPs),'' Journal of Parallel and Distributed Computing, 65(9):994-1006, 2005.

  18. G. Cong and D.A. Bader, ``Designing Irregular Parallel Algorithms With Mutual Exclusion and Lock-free Protocols,'' Journal of Parallel and Distributed Computing, 66(6):854-866, 2006.

  19. D.A. Bader and G. Cong, ``Fast Shared-Memory Algorithms for Computing the Minimum Spanning Forest of Sparse Graphs,'' Journal of Parallel and Distributed Computing, 66(11):1366--1378, 2006.

  20. D.A. Bader and S. Sreshta, ``A New Parallel Algorithm for Planarity Testing,'' Parallel Processing Letters, 2006. (to appear)

  21. S. Dhakal, M.M. Hayat, J.E. Pezoa, C. Yang, and D.A. Bader, ``Dynamic Load Balancing in Distributed Systems in the Presence of Delays: A Regeneration-Theory Approach,'' IEEE Transactions on Parallel & Distributed Systems, 18(4):485-497, 2007.

  22. D.H.P. Low, B. Veeravalli, and D.A. Bader, ``On the Design of High-Performance Algorithms for Aligning Multiple Protein Sequences on Mesh-Based Multiprocessor Architectures,'' Journal of Parallel and Distributed Computing, 67(9):1007-1017, 2007.

  23. D.A. Bader, V. Agarwal, K. Madduri, and S. Kang, ``High Performance Combinatorial Algorithm Design on the Cell Broadband Engine Processor,'' Parallel Computing, 33(10-11):720-740, 2007.

  24. D.A. Bader and K. Madduri, ``A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multi-core Parallel Algorithms,'' Parallel Computing, 34(11):627-639, 2008.

  25. D.A. Bader, V. Agarwal, and S. Kang, ``Computing Discrete Transforms on the Cell Broadband Engine,'' Parallel Computing, 35(3):119-137, 2009.

  26. V. Agarwal, D.A. Bader, L. Dan, L.-K. Liu, D. Pasetto, M. Perrone, and F. Petrini, ``Faster FAST : Multicore Acceleration of Streaming Financial Data,'' Computer Science - Research and Development, Springer, 23(3):249-257, 2009.

  27. Y. Ye, Z. Du, D.A. Bader, Q. Yang, and W. Huo, ``GPUMemSort: A High Performance Graphic Co-processors Sorting Algorithm for Large Scale In-Memory Data,'' GSTF International Journal on Computing, 1(2):23-28, 2011.

  28. S. Kang, J. Tang, S.W. Schaeffer, and D.A. Bader, ``Rec-DCM-Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time,'' PLoS ONE, 6(8):e22483, 2011.

  29. Y. Chai, Z. Du, D.A. Bader, and X. Qin, ``Efficient Data Migration to Conserve Energy in Streaming Media Storage Systems,'' IEEE Transactions on Parallel & Distributed Systems, 2012.

  30. X. Liu, P. Pande, H. Meyerhenke, and D.A. Bader, ``PASQUAL: Parallel Techniques for Next Generation Genome Sequence Assembly,'' IEEE Transactions on Parallel & Distributed Systems, 24(5):977-986, 2013.

  31. M. Shel Swenson, Joshua Anderson, Andrew Ash, Prashant Gaurav, Zsuzsanna Sükösd, David A. Bader, Stephen C. Harvey and Christine E Heitsch, ``GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops,'' BMC Research Notes, 5:341, 2012.

  32. D. Ediger, K. Jiang, E.J. Riedy, and D.A. Bader, ``GraphCT: Multithreaded Algorithms for Massive Graph Analysis,'' IEEE Transactions on Parallel & Distributed Systems, 2012.

Papers in Special Volumes

  1. 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.

  2. D.A. Bader, K. Madduri, J.R. Gilbert, V. Shah, J. Kepner, T. Meuse, and A. Krishnamurthy, `` Designing Scalable Synthetic Compact Applications for Benchmarking High Productivity Computing Systems,'' CTWatch Quarterly, 2(4B):41-51, November 2006.

  3. D.A. Bader, ``Petascale Computing for Large-Scale Graph Problems,'' 7th International Conference on Parallel Processing and Applied Mathematics (PPAM 2007), Lecture Notes in Computer Science, 4967:166-169, 2008.

  4. D.A. Bader, ``Analyzing Massive Social Networks using Multicore and Multithreaded Architectures,'' Facing the Multicore-Challenge: Aspects of New Paradigms and Technologies in Parallel Computing, Lecture Notes in Computer Science, 6310:1, 2010.

Published Books and Parts of Books

  1. David A. Bader, William E. Hart, and Cynthia A. Phillips, ``Parallel Algorithm Design for Branch and Bound,'' in H.J. Greenberg, editor, Tutorials on Emerging Methodologies and Applications in Operations Research, Kluwer Academic Press, Chapter 5, pp. 1-44, 2004.

  2. David A. Bader and Mi Yan, ``High Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony,'' in S. Aluru, editor, Handbook of Computational Molecular Biology, Chapman & Hall / CRC Computer and Information Science Series, Chapter 22, pp. 1-19, 2006.

  3. David A. Bader, Bernard M.E. Moret, Tiffani L. Williams, and Mi Yan, ``High-Performance Phylogeny Reconstruction Under Maximum Parsimony,'' in A.Y. Zomaya, editor, Parallel Computing for Bioinformatics and Computational Biology, Wiley, Chapter 16, 2006.

  4. Srinivas Aluru, Nancy Amato, David A. Bader, Suchendra Bhandarkar, Laxmikant Kale, and Dan Marinescu, ``Parallel Computational Biology,'' in M.H. Heroux, P. Raghavan, and H.D. Simon, editors, Frontiers of Scientific Computing, SIAM Series on Software, Environments, and Tools, 2006.

  5. David A. Bader, Usman Roshan, and Alexandros Stamatakis, ``Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions,'' in C.-W. Tseng, editor, Advances in Computing, 68: Computational Biology and Bioinformatics, Elsevier, Chapter 4, pages 127--176, 2006.

  6. David A. Bader, Kamesh Madduri, Guojing Cong, and John Feo, ``Design of Multithreaded Algorithms for Combinatorial Problems,'' in S. Rajasekaran and J. Reif, editors, Handbook of Parallel Computing: Models, Algorithms, and Applications, CRC Press, Chapter 31, 2007.

  7. David A. Bader and Guojing Cong, ``Efficient Parallel Graph Algorithms for Shared-memory Multiprocessors,'' in S. Rajasekaran and J. Reif, editors, Handbook of Parallel Computing: Models, Algorithms, and Applications, CRC Press, Chapter 26, 2007.

  8. Kamesh Madduri, David A. Bader, Jonathan W. Berry, Joseph R. Crobak, and Bruce A. Hendrickson, ``Multithreaded Algorithms for Processing Massive Graphs,'' in D.A. Bader, editor, Petascale Computing: Algorithms and Applications, Chapman & Hall / CRC Press, Chapter 12, 2007.

  9. David A. Bader (ed.), Petascale Computing: Algorithms and Applications, Chapman & Hall / CRC Press, 2007.

  10. Kamesh Madduri, David A. Bader, Jonathan W. Berry, Joe R. Crobak, ``Parallel Shortest Path Algorithms for Solving Large-Scale Instances,'' in C. Demetrescu, A.V. Goldberg, and D. Johnson, editors, The Shortest Path Problem: Ninth DIMACS Implementation Challenge, DIMACS Series in Discrete Mathematical and Theoretical Computer Science, American Mathematical Society, vol. 74, pp. 249-190, 2009.

  11. Virat Agarwal, Lin Duan, Lurng-Kuo Liu, Michael Perrone, Fabrizio Petrini, Davide Pasetto, and David A. Bader, ``The Case of the Fast Financial Feed,'' in A. Gavrilovska, editor, Attaining High Performance Communications: A Vertical Approach, Chapman & Hall / CRC Press, Chapter 13, pages 305-328, 2009.

  12. Jakub Kurzak, David A. Bader, and Jack Dongarra (eds.), Scientific Computing with Multicore and Accelerators, Chapman & Hall / CRC Press, 2010.

  13. David A. Bader, Christine Heitsch, and Kamesh Madduri, ``Large-Scale Network Analysis,'' in J. Kepner and J. Gilbert, editor, Graph Algorithms in the Language of Linear Algebra, SIAM Press, Chapter 12, pages 253-285, 2011.

  14. Jeremy Kepner, David A. Bader, Robert Bond, Nadya Bliss, Christos Faloutsos, Bruce Hendrickson, John Gilbert, and Eric Robinson, ``Fundamental Questions in the Analysis of Large Graphs,'' in J. Kepner and J. Gilbert, editor, Graph Algorithms in the Language of Linear Algebra, SIAM Press, Chapter 16, pages 353-357, 2011.

  15. David A. Bader and Kamesh Madduri, ``Computational Challenges in Emerging Combinatorial Scientific Computing Applications,'' in O. Schenk, editor, Combinatorial Scientific Computing, Chapman \& Hall / CRC Press, Chapter 17, pages 471-494, 2012.

  16. David A. Bader, Henning Meyerhenke, Peter Sanders, and Dorothea Wagner (eds.), Graph Partitioning and Graph Clustering, American Mathematical Society, 2013.

  17. E. Jason Riedy, Henning Meyerhenke, David Ediger and David A. Bader, ``Parallel Community Detection for Massive Graphs,'' in David A. Bader, Henning Meyerhenke, Peter Sanders, and Dorothea Wagner (eds.), Graph Partitioning and Graph Clustering, American Mathematical Society, Chapter 14, pages 207-222, 2013.

Edited Special Issues of Journals

  1. David A. Bader and Srinivas Aluru, Guest Editors, Special Issue on High-Performance Computational Biology, Journal of Parallel and Distributed Computing 63(7-8):671-673 (issue: 671-773), 2003.

  2. David A. Bader and Srinivas Aluru, Guest Editors, Concurrency and Computation: Practice and Experience Special Issue: High Performance Computational Biology, John Wiley & Sons, 16(9):817-821 (issue: 817-988), 2004.

  3. David A. Bader, Srinivas Aluru, and Nancy Amato, Guest Editors, Special Issue on High-Performance Computational Biology, IEEE Transactions on Parallel and Distributed Systems 17(8):737-739 (issue: 737-807), 2006.

  4. David A. Bader and Srinivas Aluru, Guest Editors, Special Issue on High-Performance Computational Biology, Parallel Computing 34(11):613-615 (issue: 613-692), 2008.

  5. David A. Bader, David Kaeli, Volodymyr Kindratenko, Guest Editors, Special Issue on High-Performance Computing with Accelerators, IEEE Transactions on Parallel and Distributed Systems 22(1):3-6 (issue: 3-162), 2010.

  6. David A. Bader and Philippas Tsigas, Guest Editors, Special Issue on Multicore Algorithms, ACM Journal on Experimental Algorithmics 17(1), 2012.

Edited Proceedings

  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 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 2003.

  3. Dan C. Marinescu, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), IEEE Computer Society Press, Santa Fe, NM, April 2004.

  4. Mohammed J. Zaki, David A. Bader, Johan Montagnat and Concettina Guerra, Topic Editors, ``High Performance Bioinformatics,'' Proceedings of the 10th International Euro-Par Conference, Pisa, Italy, August 31 - September 3, 2004. Springer-Verlag LNCS, 3149:988, 2004.

  5. David A. Bader and Ashfaq A. Khokhar, Editors, Proceedings of the 17th ISCA International Conference on Parallel and Distributed Computing Systems (PDCS 2004), San Francisco, CA, September 15-17, 2004.

  6. Nancy Amato, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), IEEE Computer Society Press, Denver, CO, April 2005.

  7. David A. Bader, Manish Parashar, Varadarajan Sridhar, and Viktor K. Prasanna, Editors, Proceedings of the 12th International Conference on High Performance Computing (HiPC 2005), Goa, India, Lecture Notes in Computer Science, 3769, December 2005.

  8. Chau-Wen Tseng, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Fifth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2006), IEEE Computer Society Press, Rhodes Island, Greece, April 2006.

  9. Ananth Grama, Shankar Subramaniam, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Sixth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2007), IEEE Computer Society Press, Long Beach, CA, April 2007.

  10. Bertil Schmidt, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Seventh IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), IEEE Computer Society Press, Miami, FL, April 2008.

  11. Michela Taufer, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Eighth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009), IEEE Computer Society Press, Rome, Italy, May 2009.

  12. George Karypis, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Ninth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2010), IEEE Computer Society Press, Atlanta, GA, April 2010.

  13. Anantharaman Kalyanaraman, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Tenth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2011), IEEE Computer Society Press, Anchorage, AK, May 2011.

  14. Mark Clement, Quinn Snell, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Eleventh IEEE International Workshop on High Performance Computational Biology (HiCOMB 2012), IEEE Computer Society Press, Shanghai, China, May 2012.

  15. Jaroslaw Zola, David A. Bader, and Srinivas Aluru, Editors, Proceedings of the Twelfth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2013), IEEE Computer Society Press, Boston, MA, May 2013.

  16. Alba Cristina Magalhaes Alves de Melo, Srinivas Aluru, and David A. Bader, Editors, Proceedings of the Thirteenth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2014), IEEE Computer Society Press, Phoenix, AZ, May 2014.

Conference Presentations

Invited Keynote Addresses

  1. ``Using PRAM Algorithms on a Uniform Memory Access Shared-Memory Architecture,'' The Sixth International Workshop on High-Level Parallel Programming Models and Supportive Environments (HIPS'01), San Francisco, CA, April 23, 2001.

  2. ``Massively Parallel Processing for Computational Genomics: Reconstructing Evolutionary Trees from Gene-Order Data,'' Second Workshop on Massively Parallel Processing (WMPP 2002), held in conjunction with The International Parallel and Distributed Processing Symposium (IPDPS 2002), Fort Lauderdale, FL, April 19, 2002.

  3. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' Workshop on Bioinformatics and Computational Biology (BCB 2002), Bangalore, India, December 18, 2002.

  4. `` High-Performance Algorithm Engineering for Large-Scale Graph Problems and Computational Biology,'' D.A. Bader, Proc. 4th International Workshop on Efficient and Experimental Algorithms (WEA), Lecture Notes in Computer Science, 3503:16-21, May 2005.

  5. `` An Open Benchmark Suite for Evaluating Computer Architecture on Bioinformatics and Life Science Applications,'' D.A. Bader, Proc. SPEC Benchmark Workshop 2006, Austin, TX, January 2006.

  6. ``Petascale Computing for Large-Scale Graph Problems,'' Second International Conference on High Performance Computing and Communications (HPCC-06), Munich, Germany, September 13-15, 2006.

  7. ``Solving Massive Graph Problems using Petascale Computing,'' The Ninth DIMACS Implementation Challenge: The Shortest Path Problem, DIMACS Center, Rutgers University, Piscataway, NJ, November 14, 2006.

  8. ``Solving Massive Graph Problems using Petascale Computing,'' DIMACS-Georgia Tech Workshop on Complex Networks and their Applications, Atlanta, GA, January 22-24, 2007.

  9. ``Petascale Computing for Large-Scale Graph Problems,'' Eighth IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-07), Long Beach, CA, March 30, 2007.

  10. ``Petascale Computing for Large-Scale Graph Problems,'' Seventh International Conference on Parallel Processing and Applied Mathematics (PPAM), Gdansk, Poland, September 11, 2007.

  11. ``Petascale Computing for Large-Scale Graph Problems,'' The 2008 International Workshop on Multi-Core Computing Systems (MuCoCoS'08), Barcelona, Spain, March 7, 2008.

  12. ``Petascale Phylogenetic Reconstruction of Evolutionary Histories,'' 3rd Annual High Performance Computing Day at Lehigh Lehigh University, Bethlehem, PA, April 4, 2008.

  13. ``Accelerators, Cell Broadband Engine, Graphics Processors, and FPGAs,'' Los Alamos Computer Science Symposium (LACSS), Santa Fe, NM, October 14, 2008.

  14. ``Petascale Phylogenetic Reconstruction of Evolutionary Histories,'' Symposium on Biomedical High Performance Computing CDC Biotechnology Core Facility, Atlanta, GA, October 23, 2008.

  15. ``Accelerating Applications with Cell Broadband Engine, Graphics, and Multithreaded, Processors,'' SC08 Workshop on Bridging Multicore's Programmability Gap Austin, TX, November 11, 2008.

  16. ``Emerging Applications in Combinatorial Scientific Computing,'' Combinatorial Scientific Computing, Seminar No. 09061, Schloss Dagstuhl International Conference and Research Center for Computer Science, Wadern, Germany, February 5, 2009.

  17. ``Accelerating Scientific Applications with Cell Broadband Engine Processor,'' Carleton Cell BE Programming Workshop, Ottawa, Canada, May 13-15, 2009.

  18. ``Massive-Scale Graph Analytics,'' Graph Search Engineering, Seminar No. 09491, Schloss Dagstuhl International Conference and Research Center for Computer Science, Wadern, Germany, December 1, 2009.

  19. ``Analyzing Massive Social Networks using Multicore and Multithreaded Architectures,'' presented at Facing the Multicore Challenge, Heidelberg Academy of Sciences, Heidelberg, Germany, March 17, 2010.

  20. ``Massive Scale Analytics of Streaming Social Networks,'' 6th Erlangen International High-End-Computing Symposium, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany, June 4, 2010.

  21. ``Multicore and Manycore Computing for Algorithm Engineers,'' Algorithm Engineering, Seminar No. 10261, Schloss Dagstuhl International Conference and Research Center for Computer Science, Wadern, Germany, June 29, 2010.

  22. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' IBM Thomas J. Watson Research Center, IBM Research Spring Strategy Meeting, Yorktown Heights, NY, April 28, 2011.

  23. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' The NSF Workshop on Data Intensive Computing, Graphs, and Combinatorics in Bio-Informatics, Finance, and National Security, The City University of New York, Staten Island, NY, July 26-27, 2011.

  24. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' The 9th International Conference on Parallel Processing and Applied Mathematics (PPAM 2011), Torun, Poland, September 11-14, 2011.

  25. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' Workshop on Parallel Algorithms and Software for Analysis of Massive Graphs (ParGraph), Bengaluru, India, December 18, 2011.

  26. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' 4th Georgia Scientific Computing Symposium, Athens, GA, February 25, 2012.

  27. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' Distinguished Lecture, University of Delaware, May 3, 2012.

  28. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' From Data to Knowledge: Machine-Learning with Real-time and Streaming Applications, Berkeley, CA, May 8, 2012.

  29. ``Massive Data Analytics Using Heterogeneous Computing,'' 21st International Heterogeneity in Computing Workshop (HCW 2012), held in conjunction with The International Parallel and Distributed Processing Symposium (IPDPS 2012), Shanghai, China, May 21, 2012.

  30. ``Massive-scale Graph Analytics,'' Conference on Scientific Computing (ALGORITMY 2012), Vysoke Tatry, Podbanske, Slovakia, September 14, 2012.

  31. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' Boos-Allen-Hamilton Distinguished Colloquium in Electrical and Computer Engineering, University of Maryland, September 28, 2012.

  32. ``Gathering Intelligence with Massive Graphs,'' Invited Talk, The 25th IEEE and ACM Supercomputing Conference (SC13), Denver, CO, November 19, 2013.

Conference Presentations with Proceedings (refereed)

  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 (PPoPP), Santa Barbara, CA, July 19-21, 1995. (22 papers accepted)

  2. D. A. Bader and J. JáJá. `` Practical Parallel Algorithms for Dynamic Data Redistribution, Median Finding, and Selection,'' 10th International Parallel Processing Symposium (IPPS), Honolulu, HI, pp. 292-301, April 15-19, 1996. (126 papers accepted out of 353 papers submitted: 35.7% acceptance rate)

  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) Conference, Honolulu, HI, pp. 414-423, April 15-19, 1996. (126 papers accepted out of 353 papers submitted: 35.7% acceptance rate)

  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 (SPAA), Padua, Italy, pp. 211-220, June 1996. (39 papers accepted out of 106 papers submitted: 36.8% acceptance rate)

  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), 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 (IWCC), Melbourne, Australia, December 1999. (37 papers accepted)

  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. (15 papers accepted out of 35 papers submitted: 42.8% acceptance rate)

  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. (230 accepted and invited papers)

  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. (40 papers accepted out of 89 papers submitted: 44.9% acceptance rate)

  14. 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. (21 papers accepted)

  15. 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. (15 papers accepted out of 25 papers submitted: 60% acceptance rate)

  16. 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), Las Vegas, NV, June 2002.

  17. 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. (57 papers accepted out of 145 papers submitted: 39.3% acceptance rate)

  18. D.A. Bader and G. Cong, ``A Fast, Parallel Spanning Tree Algorithm for Symmetric Multiprocessors (SMPs),'' 18th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Santa Fe, NM, April 26-30, 2004. (142 papers accepted out of 447 papers submitted: 31.8% acceptance rate)

  19. D.A. Bader and G. Cong, ``Fast Shared-Memory Algorithms for Computing the Minimum Spanning Forest of Sparse Graphs,'' 18th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Santa Fe, NM, April 26-30, 2004. (142 papers accepted out of 447 papers submitted: 31.8% acceptance rate)

  20. G. Cong and D.A. Bader, ``The Euler Tour Technique and Parallel Rooted Spanning Tree,'' 33rd International Conference on Parallel Processing (ICPP), Montreal, Canada, pages 448-457, August 15-18, 2004. (65 papers accepted out of 190 papers submitted: 34.2% acceptance rate)

  21. M. F. Su, I. El-Kady, D. A. Bader, and S.-Y. Lin, ``A Novel FDTD Application Featuring OpenMP-MPI Hybrid Parallelization,'' 33rd International Conference on Parallel Processing (ICPP), Montreal, Canada, pages 373-379, August 15-18, 2004. (65 papers accepted out of 190 papers submitted: 34.2% acceptance rate)

  22. D.A. Bader and K. Madduri, ``A Parallel State Assignment Algorithm for Finite State Machines,'' The 11th International Conference on High Performance Computing (HiPC 2004), L. Bougé and V.K. Prasanna, (eds.), Springer-Verlag LNCS 3296, 297-308, Bangalore, India, December 2004. (48 papers accepted out of 214 papers submitted: 22.4% acceptance rate)

  23. G. Cong and D.A. Bader, ``Lock-free Parallel Algorithms: An Experimental Study,'' The 11th International Conference on High Performance Computing (HiPC 2004), L. Bougé and V.K. Prasanna, (eds.), Springer-Verlag LNCS 3296, 516-527, Bangalore, India, December 2004. (48 papers accepted out of 214 papers submitted: 22.4% acceptance rate)

  24. G. Cong and D.A. Bader, ``An Experimental Study of Parallel Biconnected Components Algorithms on Symmetric Multiprocessors (SMPs),'' 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Denver, CO, April 4-8, 2005. (115 papers accepted out of 343 papers submitted: 33.5% acceptance rate)

  25. D.A. Bader, G. Cong, and J. Feo, ``On the Architectural Requirements for Efficient Execution of Graph Algorithms,'' The 34th International Conference on Parallel Processing (ICPP 2005), pp. 547-556, Georg Sverdrups House, University of Oslo, Norway, June 14-17, 2005. (69 papers accepted out of 241 papers submitted: 28.6% acceptance rate)

  26. D.A. Bader, V. Sachdeva, A. Trehan, V. Agarwal, G. Gupta, and A.N. Singh, ``BioSPLASH: A sample workload from bioinformatics and computational biology for optimizing next-generation high-performance computer systems,'' (Poster Session), 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005), Detroit, MI, June 25-29, 2005.

  27. D.A. Bader, V. Sachdeva, ``BioSPLASH: Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system,'' (Poster Session), The 4th IEEE Computational Systems Bioinformatics Conference (CSB 2005), Stanford University, CA, August 8-11, 2005.

  28. D.A. Bader, V. Sachdeva, ``A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic,'' The 18th ISCA International Conference on Parallel and Distributed Computing Systems (PDCS 2005), Las Vegas, NV, September 12-14, 2005.

  29. G. Cong, D.A. Bader, ``An Empirical Analysis of Parallel Random Permutation Algorithms on SMPs,'' The 18th ISCA International Conference on Parallel and Distributed Computing Systems (PDCS 2005), Las Vegas, NV, September 12-14, 2005.

  30. D.A. Bader, Y. Li, T. Li, V. Sachdeva, ``BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications,'' The IEEE International Symposium on Workload Characterization (IISWC 2005), Austin, TX, October 6-8, 2005. (17 papers accepted out of 52 papers submitted: 32.6% acceptance rate)

  31. D.A. Bader and K. Madduri, ``Design and Implementation of the HPCS Graph Analysis Benchmark on Symmetric Multiprocessors,'' The 12th International Conference on High Performance Computing (HiPC 2005), D.A. Bader et al., (eds.), Springer-Verlag LNCS 3769, 465-476, Goa, India, December 2005. (50 papers accepted out of 362 papers submitted: 13.8% acceptance rate)

  32. M. Sottile, V. Chandu, and D.A. Bader, ``Performance analysis of parallel programs via message-passing graph traversal,'' 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rhodes Island, Greece, April 25-29, 2006. (125 papers accepted out of 531 papers submitted: 23.5% acceptance rate)

  33. D.A. Bader, V. Chandu, and M. Yan, ``ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony,'' The 35th International Conference on Parallel Processing (ICPP 2006), Columbus, OH, August 14-18, 2006. (64 papers accepted out of 200 papers submitted: 32.0% acceptance rate)

  34. D.A. Bader and K. Madduri, ``Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2,'' The 35th International Conference on Parallel Processing (ICPP 2006), Columbus, OH, August 14-18, 2006. (64 papers accepted out of 200 papers submitted: 32.0% acceptance rate)

  35. D.A. Bader and K. Madduri, ``Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks,'' The 35th International Conference on Parallel Processing (ICPP 2006), Columbus, OH, August 14-18, 2006. (64 papers accepted out of 200 papers submitted: 32.0% acceptance rate)

  36. K. Madduri, D.A. Bader, J.W. Berry, and J.R. Crobak, ``Parallel Shortest Path Algorithms for Solving Large-Scale Instances,'' 9th DIMACS Implementation Challenge -- The Shortest Path Problem, DIMACS Center, Rutgers University, Piscataway, NJ, November 13-14, 2006.

  37. D.A. Bader, V. Agarwal, and K. Madduri, ``Efficient Implementation of Irregular Algorithms on Cell Multi-core Architecture,'' (Poster Session), Supercomputing '06 Workshop: General-Purpose GPU Computing: Practice And Experience, Tampa, FL, November 13, 2006.

  38. K. Madduri, D.A. Bader, J.W. Berry, and J.R. Crobak, ``An Experimental Study of A Parallel Shortest Path Algorithm for Solving Large-Scale Graph Instances,'' Workshop on Algorithm Engineering and Experiments (ALENEX), New Orleans, LA, January 6, 2007. (15 papers accepted out of 60 papers submitted: 25.0% acceptance rate)

  39. D.A. Bader, V. Agarwal, and K. Madduri, ``On the Design and Analysis of Irregular Algorithms on the Cell Processor: A case study on list ranking,'' 21st IEEE International Parallel and Distributed Processing Symposium (IPDPS), Long Beach, CA, March 26-30, 2007. (109 papers accepted out of 419 papers submitted: 26.0% acceptance rate)

  40. D.A. Bader and K. Madduri, ``A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multi-core Parallel Algorithms,'' Sixth IEEE International Workshop on High Performance Computational Biology (HiCOMB), Long Beach, CA, March 26, 2007.

  41. D.A. Bader, V.N. Kanade, and K. Madduri, ``SWARM: A Parallel Programming Framework for Multi-Core Processors,'' First Workshop on Multithreaded Architectures and Applications (MTAAP), Long Beach, CA, March 30, 2007.

  42. J.R. Crobak, J.W. Berry, K. Madduri, and D.A. Bader, ``Advanced Shortest Path Algorithms on a Massively-Multithreaded Architecture,'' First Workshop on Multithreaded Architectures and Applications (MTAAP), Long Beach, CA, March 30, 2007.

  43. G. Cong, D.A. Bader, ``Techniques for Designing Efficient Parallel Graph Algorithms for SMPs and Multicore Processors,'' The 5th International Symposium on Parallel and Distributed Processing and Applications (ISPA 2007), Niagara Falls, Ontario, Canada, August 29-31, 2007.

  44. D.A. Bader and K. Madduri, ``High-Performance Combinatorial Techniques for Analyzing Massive Dynamic Interaction Networks,'' DIMACS Workshop on Computational Methods for Dynamic Interaction Networks, DIMACS Center, Rutgers University, Piscataway, NJ, September 24-25, 2007.

  45. D.A. Bader, S. Kintali, K. Madduri, and M. Mihail, ``Approximating Betweenness Centrality,'' The 5th Workshop on Algorithms and Models for the Web-Graph (WAW2007), San Diego, CA, December 11-12, 2007.

  46. D.A. Bader, V. Agarwal, ``FFTC: Fastest Fourier Transform for the IBM Cell Broadband Engine,'' The 14th Annual IEEE International Conference on High Performance Computing (HiPC 2007), S. Aluru et al., (eds.), Springer-Verlag LNCS 4873, 172-184, Goa, India, December 18-21, 2007. (52 papers accepted out of 253 papers submitted: 20.5% acceptance rate)

  47. D.A. Bader and K. Madduri, ``SNAP, Small-world Network Analysis and Partitioning: an open-source parallel graph framework for the exploration of large-scale networks,'' 22nd IEEE International Parallel and Distributed Processing Symposium (IPDPS), Miami, FL, April 14-18, 2008. (105 papers accepted out of 410 papers submitted: 25.6% acceptance rate)

  48. D.A. Bader and S. Patel, ``High Performance MPEG-2 Software Decoder on the Cell Broadband Engine,'' 22nd IEEE International Parallel and Distributed Processing Symposium (IPDPS), Miami, FL, April 14-18, 2008. (105 papers accepted out of 410 papers submitted: 25.6% acceptance rate)

  49. V. Agarwal, L.-K. Liu, and D.A. Bader, ``Financial Modeling on the Cell Broadband Engine,'' 22nd IEEE International Parallel and Distributed Processing Symposium (IPDPS), Miami, FL, April 14-18, 2008. (105 papers accepted out of 410 papers submitted: 25.6% acceptance rate)

  50. S. Kang and D.A. Bader, ``Optimizing JPEG2000 Still Image Encoding on the Cell Broadband Engine,'' The 37th International Conference on Parallel Processing (ICPP 2008), Portland, OR, September 8-12, 2008. (81 papers accepted out of 263 papers submitted: 30.8% acceptance rate)

  51. D.A. Bader, A. Chandramowlishwaran, and V. Agarwal, ``On the Design of Fast Pseudo-Random Number Generators for the Cell Broadband Engine and an Application to Risk Analysis,'' The 37th International Conference on Parallel Processing (ICPP 2008), Portland, OR, September 8-12, 2008. (81 papers accepted out of 263 papers submitted: 30.8% acceptance rate)

  52. S. Hao, Z. Du, D.A. Bader, and M. Wang, ``A Prediction Based CMP Cache Migration Policy,'' 10th IEEE International Conference on High Performance Computing and Communications (HPCC), Dalian, China, September 25-27, 2008. (90 papers accepted out of 455 papers submitted: 19.7% acceptance rate)

  53. S. Kang and D.A. Bader, ``An Efficient Transactional Memory Algorithm for Computing Minimum Spanning Forest of Sparse Graphs,'' 14th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), Raleigh, NC, February 14-18, 2009. (26 papers accepted out of 109 papers submitted: 23.9% acceptance rate)

  54. A. Mathuriya, D.A. Bader, C.E. Heitsch, and S.C. Harvey, ``GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction,'' 24th Annual ACM Symposium on Applied Computing (SAC), Computational Sciences Track, Honolulu, HI, March 8-12, 2009. (30% acceptance rate)

  55. K. Madduri and D.A. Bader, ``Compact Graph Representations and Parallel Connectivity Algorithms for Massive Dynamic Network Analysis,'' 23rd IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rome, Italy, May 25-29, 2009. (100 papers accepted out of 440 papers submitted: 22.7% acceptance rate)

  56. S. Kang, D.A. Bader, and R. Vuduc, ``Understanding the Design Trade-offs among Current Multicore Systems for Numerical Computations,'' 23rd IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rome, Italy, May 25-29, 2009. (100 papers accepted out of 440 papers submitted: 22.7% acceptance rate)

  57. K. Madduri, D. Ediger, K. Jiang, D.A. Bader, and D.G. Chavarría-Miranda, ``A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets,'' Third Workshop on Multithreaded Architectures and Applications (MTAAP), Rome, Italy, May 29, 2009. (12 papers accepted out of 22 papers submitted.)

  58. R. Quax, D.A. Bader, and P.M.A. Sloot, ``Simulating Individual-Based Models of Epidemics in Hierarchical Networks,'' International Conference on Computational Science (ICCS), G. Allen, J. Nabrzyski, E. Seidel G.D. van Albada, J. Dongarra, P.M.A. Sloot, (eds.), Springer-Verlag LNCS 5544, 726-734, Baton Rouge, LA, May 25-27 2009. (57 papers accepted out of 165 papers submitted: 34.5% acceptance rate)

  59. V. Agarwal, D.A. Bader, L. Dan, L.-K. Liu, D. Pasetto, M. Perrone, and F. Petrini, ``Faster FAST : Multicore Acceleration of Streaming Financial Data,'' 24th International Supercomputing Conference (ISC), Hamburg, Germany, June 23-26, 2009. Best Paper Award. (24 papers accepted out of 54 papers submitted: 44.4% acceptance rate)

  60. S. Hao, Z. Du, D.A. Bader, and Y. Ye, ``A Partition-Merge based Cache-Conscious Parallel Sorting Algorithm for CMP with Shared Cache,'' The 38th International Conference on Parallel Processing (ICPP 2009), Vienna, Austria, September 22-25, 2009. (71 papers accepted out of 220 papers submitted: 32.2% acceptance rate)

  61. K. Jiang, D. Ediger and D.A. Bader, ``Generalizing k-Betweenness Centrality Using Short Paths and a Parallel Multithreaded Implementation,'' The 38th International Conference on Parallel Processing (ICPP 2009), Vienna, Austria, pages 542-549, September 22-25, 2009. (71 papers accepted out of 220 papers submitted: 32.2% acceptance rate)

  62. Z. Du, Z. Yin, and D.A. Bader, ``A Tile-based Parallel Viterbi Algorithm for Biological Sequence Alignment on GPU with CUDA,'' 9th IEEE International Workshop on High Performance Computational Biology (HiCOMB), Atlanta, GA, April 19, 2010. (10 papers accepted out of 17 papers submitted.)

  63. S. Kang and D.A. Bader, ``Large Scale Complex Network Analysis using the Hybrid Combination of a MapReduce cluster and a Highly Multithreaded System,'' 4th Workshop on Multithreaded Architectures and Applications (MTAAP), Atlanta, GA, April 23, 2010. (11 papers accepted out of 22 papers submitted.)

  64. D. Ediger, K. Jiang, J. Riedy, and D.A. Bader, ``Massive Streaming Data Analytics: A Case Study with Clustering Coefficients,'' 4th Workshop on Multithreaded Architectures and Applications (MTAAP), Atlanta, GA, April 23, 2010. (11 papers accepted out of 22 papers submitted.)

  65. V. Sachdeva, M. Kistler, and D.A. Bader ``Evaluating Cell/B.E. Software Cache for ClustalW,'' The IEEE International Symposium on Circuits and Systems (ISCAS 2010), Paris, France, May 31 - June 2, 2010.

  66. D. Ediger, K. Jiang, J. Riedy, D.A. Bader, C. Corley, R. Farber and W.N. Reynolds. ``Massive Social Network Analysis: Mining Twitter for Social Good,'' The 39th International Conference on Parallel Processing (ICPP 2010), San Diego, CA, September 13-16, 2010. (70 papers accepted out of 225 papers submitted: 31.1% acceptance rate)

  67. Y. Ye, Z. Du, and D.A. Bader. ``GPUMemSort: A High Performance Graphic Co-processors Sorting Algorithm for Large Scale In-Memory Data,'' Annual International Conference on Advances in Distributed and Parallel Computing (ADPC 2010), Singapore, November 1-2, 2010.

  68. V. Agarwal, F. Petrini, D. Pasetto and D.A. Bader. ``Scalable Graph Exploration on Multicore Processors,'' The 22nd IEEE and ACM Supercomputing Conference (SC10), New Orleans, LA, November 13-19, 2010. (51 papers accepted out of 253 papers submitted: 20.2% acceptance rate)

  69. Z. Du, Z. Yin, W. Liu, and D.A. Bader, ``On Accelerating Iterative Algorithms with CUDA: A Case Study on Conditional Random Fields Training Algorithm for Biological Sequence Alignment,'' IEEE International Conference on Bioinformatics & Biomedicine, Workshop on Data-Mining of Next Generation Sequencing Data (NGS2010), Hong Kong, December 20, 2010.

  70. Z. Du, W. Liu, X. Yu, D.A. Bader, and C. Xu, ``A Waterfall Model to Achieve Energy Efficient Task Mapping for Large Scale GPU Cluster,'' 20th International Heterogeneity in Computing Workshop (HCW), Anchorage, AK, May 16, 2011. (10 papers accepted out of 16 papers submitted.)

  71. D. Ediger, J. Riedy, H. Meyerhenke, and D.A. Bader, ``Tracking Structure of Streaming Social Networks,'' 5th Workshop on Multithreaded Architectures and Applications (MTAAP), Anchorage, AK, May 20, 2011. (10 papers accepted out of 17 papers submitted.)

  72. D. Mizell, D.A. Bader, E.L. Goodman, and D.J. Haglin, ``Semantic Databases and Supercomputers,'' 2011 Semantic Technology Conference (SemTech), San Francisco, CA, June 5-9, 2011.

  73. E.J. Riedy, H. Meyerhenke, D. Ediger, and D.A. Bader, ``Parallel Community Detection for Massive Graphs,'' The 9th International Conference on Parallel Processing and Applied Mathematics (PPAM 2011), Torun, Poland, September 11-14, 2011. Lecture Notes in Computer Science, 7203:286-296, 2012. (134 papers accepted out of 243 papers submitted: 55% acceptance rate)

  74. E.J. Riedy, D. Ediger, D.A. Bader, and H. Meyerhenke, ``Parallel Community Detection for Massive Graphs,'' 10th DIMACS Implementation Challenge -- Graph Partitioning and Graph Clustering, Atlanta, GA, February 13-14, 2012.

  75. E.J. Riedy, H. Meyerhenke, D.A. Bader, D. Ediger, and T. Mattson, ``Analysis of Streaming Social Networks and Graphs on Multicore Architectures,'' The 37th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Kyoto, Japan, March 25-30, 2012.

  76. J. Riedy, H. Meyerhenke, and D.A. Bader, ``Scalable Multi-threaded Community Detection in Social Networks,'' 6th Workshop on Multithreaded Architectures and Applications (MTAAP), Shanghai, China, May 25, 2012. (9 papers accepted out of 15 papers submitted.)

  77. O. Green, R. McColl, and D.A. Bader, ``GPU Merge Path -- A GPU Merging Algorithm,'' 26th ACM International Conference on Supercomputing (ICS), San Servolo Island, Venice, Italy, June 25-29, 2012. (36 papers accepted out of 161 papers submitted: 22.4% acceptance rate)

  78. O. Green, R. McColl, and D.A. Bader, ``A Fast Algorithm for Streaming Betweenness Centrality,'' 4th ASE/IEEE International Conference on Social Computing (SocialCom), Amsterdam, The Netherlands, September 3-5, 2012. (44 papers accepted out of 191 papers submitted: 23.0% acceptance rate)

  79. D. Ediger, R. McColl, J. Riedy, and D.A. Bader, ``STINGER: High Performance Data Structure for Streaming Graphs,'' The IEEE High Performance Extreme Computing Conference (HPEC), Waltham, MA, September 20-22, 2012. Best Paper Award.

  80. J. Marandola, S. Louise, L. Cudennec, J.-T. Acquaviva and D.A. Bader, ``Enhancing Cache Coherent Architecture with Access Patterns for Embedded Manycore Systems,'' 14th IEEE International Symposium on System-on-Chip (SoC), Tampere, Finland, October 11-12, 2012. (15 papers accepted out of 39 papers submitted: 38.5% acceptance rate)

  81. L.M. Munguía, E. Ayguade, and D.A. Bader, ``Task-based Parallel Breadth-First Search in Heterogeneous Environments,'' The 19th Annual IEEE International Conference on High Performance Computing (HiPC), Pune, India, December 18-21, 2012. (41 papers accepted out of 163 papers submitted: 25.1% acceptance rate)

  82. S. Kang, D.A. Bader, and R. Vuduc, ``Energy-Efficient Scheduling for Best-Effort Interactive Services to Achieve High Response Quality,'' 27th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Boston, MA, May 20-24, 2013. (108 papers accepted out of 490 papers submitted: 22.0% acceptance rate)

  83. J. Riedy and D.A. Bader, ``Multithreaded Community Monitoring for Massive Streaming Graph Data,'' 7th Workshop on Multithreaded Architectures and Applications (MTAAP), Boston, MA, May 24, 2013. (11 papers accepted out of 16 papers submitted.)

  84. D. Ediger and D.A. Bader, ``Investigating Graph Algorithms in the BSP Model on the Cray XMT,'' 7th Workshop on Multithreaded Architectures and Applications (MTAAP), Boston, MA, May 24, 2013. (11 papers accepted out of 16 papers submitted.)

  85. O. Green and D.A. Bader, ``Faster Betweenness Centrality Based on Data Structure Experimentation,'' International Conference on Computational Science (ICCS), Barcelona, Spain, June 5-7, 2013. (185 papers accepted out of 612 papers submitted: 30.0% acceptance rate)

  86. Z. Yin, J. Tang, S. Schaeffer, and D.A. Bader, ``Streaming Breakpoint Graph Analytics for Accelerating and Parallelizing the Computation of DCJ Median of Three Genomes,'' International Conference on Computational Science (ICCS), Barcelona, Spain, June 5-7, 2013. (185 papers accepted out of 612 papers submitted: 30.0% acceptance rate)

  87. T. Senator, D.A. Bader, et al., ``Detecting Insider Threats in a Real Corporate Database of Computer Usage Activities,'' 19th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), Chicago, IL, August 11-14, 2013. (126 papers accepted out of 726 papers submitted: 17.4% acceptance rate)

  88. J. Fairbanks, D. Ediger, R. McColl, D.A. Bader and E. Gilbert, ``A Statistical Framework for Streaming Graph Analysis,'' IEEE/ACM International Conference on Advances in Social Networks Analysis and Modeling (ASONAM), Niagara Falls, Canada, August 25-28, 2013.

  89. A. Zakrzewska and D.A. Bader, ``Measuring the Sensitivity of Graph Metrics to Missing Data,'' 10th International Conference on Parallel Processing and Applied Mathematics (PPAM), Warsaw, Poland, September 8-11, 2013.

  90. O. Green and D.A. Bader, ``A Fast Algorithm for Streaming Betweenness Centrality,'' 5th ASE/IEEE International Conference on Social Computing (SocialCom), Washington, DC, September 8-14, 2013. (XX papers accepted out of YYY papers submitted: 9.9% acceptance rate)

  91. R. McColl, O. Green, and D.A. Bader, ``A New Parallel Algorithm for Connected Components in Dynamic Graphs,'' The 20th Annual IEEE International Conference on High Performance Computing (HiPC), Bangalore, India, December 18-21, 2013. (49 papers accepted out of 196 papers submitted: 25.0% acceptance rate)

  92. R. McColl, D. Ediger, J. Poovey, D. Campbell, and D.A. Bader, ``A Performance Evaluation of Open Source Graph Databases,'' The 1st Workshop on Parallel Programming for Analytics Applications (PPAA 2014) held in conjunction with the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 2014), Orlando, Florida, February 16, 2014.

  93. O. Green, L.M. Munguia, and D.A. Bader, ``Load Balanced Clustering Coefficients,'' The 1st Workshop on Parallel Programming for Analytics Applications (PPAA 2014) held in conjunction with the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP 2014), Orlando, Florida, February 16, 2014.

  94. A. McLaughlin and D.A. Bader, ``Revisiting Edge and Node Parallelism for Dynamic GPU Graph Analytics,'' 8th Workshop on Multithreaded Architectures and Applications (MTAAP), held in conjuntion with The IEEE International Parallel and Distributed Processing Symposium (IPDPS 2014), Phoenix, AZ, May 23, 2014.

  95. Z. Yin, J. Tang, S. Schaeffer, D.A. Bader, ``A Lin-Kernighan Heuristic for the DCJ Median Problem of Genomes with Unequal Contents,'' 20th International Computing and Combinatorics Conference (COCOON), Atlanta, GA, August 4-6, 2014.

  96. Y. You, D.A. Bader and M.M. Dehnavi, ``Designing an Adaptive Cross-Architecture Combination for Graph Traversal,'' The 43rd International Conference on Parallel Processing (ICPP 2014), Minneapolis, MN, September 9-12, 2014. (54 papers accepted out of 150 papers submitted: 36.0% acceptance rate)

  97. A. McLaughlin, J. Riedy, and D.A. Bader, ``Optimizing Energy Consumption and Parallel Performance for Betweenness Centrality using GPUs,'' The 18th Annual IEEE High Performance Extreme Computing Conference (HPEC), Waltham, MA, September 9-11, 2014.

  98. A. McLaughlin and D.A. Bader, ``Scalable and High Performance Betweenness Centrality on the GPU,'' The 26th IEEE and ACM Supercomputing Conference (SC14), New Orleans, LA, November 16-21, 2014. Best Student Paper Finalist. (82 papers accepted out of 394 papers submitted: 20.8% acceptance rate)

Conference Presentations with Proceedings (non-refereed)

  1. D.A. Bader and V.K. Prasanna, ``DOSA: Design Optimizer for Scientific Applications,'' NSF Next Generation Workshop, Long Beach, CA, March 25-26, 2007.

  2. C.A. Stewart, M. Lingwall, and D.A. Bader, ``Lecture on Progress Toward Petascale Applications in Bioinformatics and Computational Biology,'' p. 1458, 7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE), p. 1458, Harvard Medical School, Boston, MA, October 14-17, 2007.

  3. D.A. Bader and V.K. Prasanna, ``DOSA: Design Optimizer for Scientific Applications,'' NSF Next Generation Workshop, Miami, FL, April 13-14, 2008.

Conference Presentations without Proceedings

  1. 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.

  2. 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.

  3. 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.

  4. T.J. Warnow, J.L. Boore, H.M. Fourcade, R.K. Jansen, R. Haberle, T.W. Chumley, L. Raubeson, S. Wyman, C. dePamphilis, B. Moret, D. Bader, W. Miller, ``Comparative chloroplast genomics of seed plants: integrating computational methods, phylogeny, and molecular evolution,'' (Poster Session), Evolution 2003, Chico, CA, June 20-24, 2003.

  5. D.A. Bader, `` Scalable Graph Algorithms for Shared Memory,'' 11th SIAM Conference on Parallel Processing for Scientific Computing (PP04), San Francisco, CA, February 25-27, 2004.

  6. D.A. Bader, `` High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' Minisymposium on Parallel Computational Biology, 11th SIAM Conference on Parallel Processing for Scientific Computing (PP04), San Francisco, CA, February 25-27, 2004.

  7. D.A. Bader, `` Fast, Sparse Graph Algorithms using Symmetric Multiprocessors,'' Minisymposium on Combinatorial Algorithms and Parallel Computing, 11th SIAM Conference on Parallel Processing for Scientific Computing (PP04), San Francisco, CA, February 25-27, 2004.

  8. D.A. Bader, ``Dynamic Computations in Large-Scale Graphs,'' Minisymposium on Data-Aware Parallel Computing, 12th SIAM Conference on Parallel Processing for Scientific Computing (PP06), San Francisco, CA, February 22-24, 2006.

  9. D.A. Bader and K. Madduri, ``Efficient Shared-memory Algorithms and Implementations for Solving Large-scale Graph Problems,'' Minisymposium on High-Performance Computing with Large Graphs, 2006 SIAM Annual Meeting (AN06), Boston, MA, July 10-14, 2006.

  10. D.A. Bader, V. Agarwal, ``FFTC: Fastest Fourier Transform for the IBM Cell Broadband Engine,'' The 11th Annual High Performance Embedded Computing Workshop (HPEC), Lexington, MA, September 18-20, 2007.

  11. D.A. Bader, ``Irregular Algorithms on the Cell Broadband Engine,'' Minisymposium on High Performance Computing on the Cell Processor, 13th SIAM Conference on Parallel Processing for Scientific Computing (PP08), Atlanta, GA, March 12, 2008.

  12. D.A. Bader, ``Accelerators, Cell Broadband Engine, Graphics Processors, and FPGAs,'' Minisymposium on Future Challenges in High Performance Computing for Algorithm and Tool Developers, 13th SIAM Conference on Parallel Processing for Scientific Computing (PP08), Atlanta, GA, March 13, 2008.

  13. D.A. Bader, ``Parallel Algorithms for Small-world Network Analysis and Partitioning,'' Minisymposium on HPC on Large Graphs, 13th SIAM Conference on Parallel Processing for Scientific Computing (PP08), Atlanta, GA, March 13, 2008.

  14. D.A. Bader, ``Accelerating Combinatorial Scientific Computing with the Cell Broadband Engine Processor,'' Minisymposium on Revolutionary Technologies for Acceleration of Emerging Petascale Applications, 13th SIAM Conference on Parallel Processing for Scientific Computing (PP08), Atlanta, GA, March 13, 2008.

  15. S. Kang and D.A. Bader, ``Optimizing Discrete Wavelet Transform on the Cell Broadband Engine,'' The 12th Annual High Performance Embedded Computing Workshop (HPEC), Lexington, MA, September 23-25, 2008.

  16. D. Pekurovsky, P.K. Yeung, D.A. Bader, R.D. Moser, J.J. Riley, A. Majumdar, D.A. Donzis, ``High Reynolds Number Turbulence at Petascale,'' Pathways to Blue Waters: Communication Intensive Algorithms and Applications, Urbana, IL, October 15-17, 2008. (invitation-only)

  17. D.A. Bader, ``Exascale Analytics for Massive Social Networks,'' Minisymposium on High-Performance Computing on Massive Real-World Graphs, 2009 SIAM Annual Meeting (AN09), Denver, CO, July 6-10, 2009.

  18. D.A. Bader, ``Parallel Algorithms for Social Network Analysis,'' Minisymposium on Parallel Algorithms and Software for Massive Graphs, 14th SIAM Conference on Parallel Processing for Scientific Computing (PP10), Seattle, WA, February 25, 2010.

  19. J.P. McCloskey and D.A. Bader, ``Modularity and Graph Algorithms,'' Minisymposium on Analyzing Massive Real-World Graphs, 2010 SIAM Annual Meeting (AN10), Pittsburgh, PA, July 12-16, 2010.

  20. S. Kang and D.A. Bader, ``Large Scale Complex Network Analysis Using the Hybrid Combination of a MapReduce Cluster and a Highly Multithreaded System,'' The 14th Annual High Performance Embedded Computing Workshop (HPEC), Lexington, MA, September 15-16, 2010.

  21. P. Pande and D.A. Bader, ``Computing Betweenness Centrality for Small World Networks on a GPU,'' The 15th Annual High Performance Embedded Computing Workshop (HPEC), Lexington, MA, September 21-22, 2011.

  22. H. Meyerhenke, E.J. Riedy, and D.A. Bader, ``Parallel Community Detection in Streaming Graphs,'' Minisymposium on Parallel Analysis of Massive Social Networks, 15th SIAM Conference on Parallel Processing for Scientific Computing (PP12), Savannah, GA, February 15-17, 2012.

  23. D. Ediger, E.J. Riedy, H. Meyerhenke, and D.A. Bader, ``Analyzing Massive Networks with GraphCT,'' Poster Session, 15th SIAM Conference on Parallel Processing for Scientific Computing (PP12), Savannah, GA, February 15-17, 2012.

  24. R.C. McColl, D. Ediger, and D.A. Bader, ``Many-Core Memory Hierarchies and Parallel Graph Analysis,'' Poster Session, 15th SIAM Conference on Parallel Processing for Scientific Computing (PP12), Savannah, GA, February 15-17, 2012.

  25. E.J. Riedy, D. Ediger, H. Meyerhenke, and D.A. Bader, ``STING: Software for Analysis of Spatio-Temporal Interaction Networks and Graphs,'' Poster Session, 15th SIAM Conference on Parallel Processing for Scientific Computing (PP12), Savannah, GA, February 15-17, 2012.

  26. D.A. Bader, H. Meyerhenke, and E.J. Riedy, ``Applications and Challenges in Large-scale Graph Analysis,'' Minisymposium on Frontiers in Large-Scale Graph Analysis, 2013 SIAM Conference on Computational Science and Engineering (CSE13), Boston, MA, February 25 - March 1, 2013.

  27. R.C. McColl, D. Ediger, D.A. Bader, and E.J. Riedy, ``Analyzing Graph Structure in Streaming Data with STINGER,'' Minisymposium on Frontiers in Large-Scale Graph Analysis, 2013 SIAM Conference on Computational Science and Engineering (CSE13), Boston, MA, February 25 - March 1, 2013.

  28. X. Liu, P. Pande, H. Meyerhenke, and D.A. Bader, ``PASQUAL: Parallel Techniques for Next Generation Genome Sequence Assembly,'' Minisymposium on Scalable Graph-theoretic Models for Computational Biology, 2013 SIAM Conference on Computational Science and Engineering (CSE13), Boston, MA, February 25 - March 1, 2013.

  29. D.A. Bader, A. Buluç, J. Gilbert, J. Gonzalez, J. Kepner and T. Mattson, ``The Graph BLAS effort and its implications for Exascale,'' SIAM Workshop on Exascale Applied Mathematics Challenges and Opportunities (EX14), Chicago, IL, July 6, 2014.

Conference Tutorials (peer-reviewed)

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

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

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

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

  5. David A. Bader, Usman Roshan, and Alexandros Stamatakis, ``Computational Grand Challenges in Assembling the Tree of Life: Problems & Solutions,'' The IEEE and ACM Supercomputing Conference 2005 (SC2005), Seattle, WA, November 13, 2005.

  6. Srinivas Aluru, David A. Bader, and Ananth Kalyanaraman, ``High-Performance Computing Methods for Computational Genomics,'' The IEEE and ACM Supercomputing Conference 2006 (SC2006), Tampa, FL, November 13, 2006.

  7. Srinivas Aluru, David A. Bader, and Ananth Kalyanaraman, ``High-Performance Computing Methods for Computational Genomics,'' The 21st IEEE International Parallel and Distributed Processing Symposium (IPDPS 2007), Long Beach, CA, March 27, 2007.

  8. David A. Bader, David Ediger, E. Jason Riedy, ``Parallel Programming for Graph Analysis,'' The 16th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming (PPoPP 2011), San Antonio, TX, February 12, 2011.

  9. David A. Bader, David Ediger, E. Jason Riedy, ``Parallel Programming for Graph Analysis,'' full-day tutorial, Columbia, MD, September 28, 2011.

  10. David A. Bader, David Ediger, E. Jason Riedy, ``Parallel Programming for Graph Analysis,'' The 17th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming (PPoPP 2012), New Orleans, LA, February 25, 2012.

  11. David A. Bader, ``Fundamentals of Super Computing,'' The IEEE and The Optical Society's OFC/NFOEC 2013 Technical Conference, Anaheim, CA, March 17, 2013.

Other

Published Papers (non-refereed)

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

  2. D. A. Bader, `` Book Reviews: A Guide to Experimental Algorithmics, by Catherine C. McGeoch,'' INFORMS Journal on Computing, 25(3), 2013.

Additional Technical Reports

  1. 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.

  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. ``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.

Research Proposals and Grants (Principal Investigator)

  1. NASA NGT-50951, Graduate Student Researcher Fellowship, $88,000, 1992-1996.
  2. Research Associate, NSF CISE 96-25668, CISE Postdoctoral Research Associate in Computational Science & Engineering Science: High Performance Computing for Remote Sensing Applications with the Institute for Advanced Computer Studies (UMIACS), University of Maryland, College Park. NSF 96-25668.
  3. NRC 9601610, Research Associateship Award, $42,500, 1996-1997. (award declined)
  4. DOE Sandia National Laboratories, Sandia University New Assistant Professorship Program (SUNAPP) Award, PI: D.A. Bader, Collaborative research with the Algorithms & Discrete Math Department at SNL developing methodologies for high performance computing on clusters of symmetric multiprocessors. Contract Number AX-3006, $30,000, 9/01/1998 - 8/31/1999.
  5. DOE Sandia National Laboratories, Sandia University New Assistant Professorship Program (SUNAPP) Award, PI: D.A. Bader, Collaborative research with the Algorithms & Discrete Math Department at SNL developing methodologies for high performance computing on clusters of symmetric multiprocessors. Contract Number AX-3006, $30,000, 10/01/1999 - 9/30/2000.
  6. NSF DEB 99-10123, ``Ecosystem Studies: Self-Organization of Semi-Arid Landscapes: Test of Optimality Principles,'' PIs: B.T. Milne, D.A. Bader, W.T. Pockman, C. Restrepo, National Science Foundation, Division of Environmental Biology, $674,911, 1/1/2000 - 2/29/2004.
  7. NSF ITR 00-81404, ``ITR/ACS: Algorithms for Irregular Discrete Computations on SMPs,'' PIs: B.M. Moret and D.A. Bader, National Science Foundation, Information Technology Research Program, $452,052, 9/1/2000 - 1/31/2004.
  8. DOE Sandia National Laboratories, Computer Science Research Institute Award. "High Performance Computing Algorithms and Applications," PI: D.A. Bader, Contract Number 14968, $35,000, 11/28/2000 - 7/14/2001.
  9. NSF CAREER 00-93039, ``CAREER: High-Performance Algorithms for Scientific Applications,'' PI: D.A. Bader, National Science Foundation, Faculty Early Career Development (CAREER) Program, $635,641 (NSF portion: $385,641, UNM cost share: $250,000), 9/1/2001 - 1/31/2006. Research Experiences for Undergraduate (REU) supplement: $12,000.
  10. NSF EIA 01-21377, ``Collaborative Research: ITR/AP Reconstructing Complex Evolutionary Histories,'' PIs: B.M.E. Moret and D.A. Bader (New Mexico); T. Warnow, R. Jansen, and R. Linder (Texas-Austin); National Science Foundation, Information Technology Research (ITR) Program, $792,540 (UNM portion), 9/15/2001 - 9/30/2006.
  11. NSF DEB 01-20709, ``Comparative Chloroplast Genomics: Integrating Computational Methods, Molecular Evolution, and Phylogeny,'' PIs: R. Jansen, T. Warnow (Texas-Austin); L. Raubeson (Central Wash.); B.M.E. Moret, D.A. Bader (New Mexico); C. dePamphilis, W. Miller (Penn State); and J. Boore (DOE Joint Genome Inst.); National Science Foundation, Biocomplexity in the Environment (BE): Genome-Enabled Environmental Science and Engineering (GEN-EN) Program; $1.35M (total); $192,599 (UNM subcontract), 10/1/2001 - 9/30/2006.
  12. DOE Sandia National Laboratories, Computer Science Research Fund, "Enabling PetaFLOPs Computing Applications," PI: D.A. Bader, Contract Number 27983, $100,000, 2/1/2002 - 1/31/2003.
  13. IBM / DARPA, "PERCS Productive, Easy-to-Use, Reliable Computing Systems," UNM PIs: D.A. Bader and B.M.E. Moret, High Productivity Computing Systems (Phase 1) Program, $3M (total); $65,000 (UNM portion), 7/15/2002 - 9/16/2003.
  14. NSF EIA 02-03584, "Postdoc: A Hierarchical Methodology for SMP Clusters," PIs: B.M.E. Moret and D.A. Bader, National Science Foundation, CISE Postdoctoral Research Associate in Experimental Computer Science, $138,072 (NSF portion: $66,000, UNM cost share: $72,072), 8/1/2002 - 7/31/2004.
  15. Alfred P. Sloan Foundation, "Postdoctoral Fellowship in Computational Molecular Biology for Dr. Tiffani L. Williams," PIs: B.M.E. Moret and D.A. Bader, Sloan Foundation and Department of Energy, $152,072 (Sloan/DOE portion: $120,000, UNM cost share: $32,072), 8/1/2002 - 7/31/2004.
  16. DOE Sandia National Laboratories, Combinatorial Algorithms for Homeland Defense, PI: D.A. Bader, Contract Number 55856, $29,735, 8/26/2002 - 5/30/2003.
  17. IBM / DARPA, "PERCS Productive, Easy-to-Use, Reliable Computing Systems," UNM PIs: D.A. Bader, B.M.E. Moret, A.B. Maccabe, P.G. Bridges, High Productivity Computing Systems (Phase 2) Program, $53.3M (total); $900,000 (UNM portion, from DARPA: $600K, and UNM cost share: $300K), 7/15/2003 - 9/16/2006.
  18. DOE Sandia National Laboratories, Parallel Algorithms for Computational Electromagnetics, PI: D.A. Bader, Contract Number 161449, $13,000, 8/1/2003 - 7/31/2004.
  19. NSF Emerging Frontiers / BIO 03-31654, ``ITR Collaborative Research: Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics,'' PI: B.M.E. Moret (U New Mexico); coPI's: D.A. Bader (U New Mexico), F. Berman (UC San Diego), P. Bourne (UC San Diego), M. Donoghue (Yale), D.M. Hillis (U Texas-Austin), W. Hunt (U Texas-Austin), J. Kim (U Pennsylvania), P. Lewis (U Connecticut), D. Maddison (U Arizona), W. Maddison (U Arizona), D. Miranker (U Texas-Austin), B. Mischler (UC Berkeley), L. Meyers (U Texas-Austin), E. Myers (UC Berkeley), S. Rao (UC Berkeley), S. Russell (UC Berkeley), D. Swofford (Florida State U), T. Warnow (U Texas-Austin), W. Wheeler (American Museum of Natural History), T. Williams (U New Mexico); National Science Foundation, Information Technology Research Program, $11.6M Total, (UNM: $3,540,907), 10/1/2003 -- 9/30/2008.
  20. DOE Sandia National Laboratories, Innovative Parallel Algorithms for Computational Electromagnetics, PI: D.A. Bader, Contract Number 305103, $29,640, 6/1/2004 - 5/31/2005.
  21. NSF DBI 04-20513, "Acquisition of a High Performance Shared-Memory Computer for Computational Science and Engineering at the University of New Mexico," PIs: H. Guo, D.A. Bader, S.R. Atlas, M.S. Ingber, and T. Oprea. National Science Foundation, Major Research Instrumentation Program, $350,378 (NSF), $150,162 (UNM cost share), 9/1/2004 - 8/31/2007.
  22. DOE Sandia National Laboratories, Designing Parallel Graph Algorithms for Multi-Threaded Architectures, PI: D.A. Bader, $73,000, 1/1/2005 -- 12/31/2005.
  23. Los Alamos National Laboratory, LinuxBIOS support on advanced 64-bit systems, PI: D.A. Bader, $40,000, 1/1/2005 -- 12/31/2005.
  24. NSF 05-29795, ``CAREER: High-Performance Algorithms for Scientific Applications, Research Experience for Undergraduate (REU) Supplement'' PI: D.A. Bader, National Science Foundation, Faculty Early Career Development (CAREER) Program, 5/27/2005 - 5/31/2006. $15,000.
  25. Los Alamos National Laboratory, Performance Evaluation of Large-Scale Parallel Programs, PI: D.A. Bader, $75,000, 9/1/2005 -- 6/30/2006.
  26. NSF CCF 06-11589, ``CAREER: High-Performance Algorithms for Scientific Applications,'' PI: D.A. Bader, National Science Foundation, Faculty Early Career Development (CAREER) Program, $96,037 (NSF portion, transfered from NSF 00-93039), $12,000 (new NSF Research Experience for Undergraduates supplement), $42,109 (Georgia Tech cost share), 12/1/2005 -- 12/31/2006.
  27. NSF CSR 06-14915, ``Collaborative Research: CSR---AES: A Framework for Optimizing Scientific Applications,'' Lead PI: David A. Bader, and USC PI: Viktor Prasanna (U Southern California), National Science Foundation, Computer Systems Research, $200,000 Total (Georgia Tech portion: $100,000), 6/15/06 - 6/15/08.
  28. NSF DBI 06-32517, ``Workshop Proposal: Petascale Computing in the Biosciences is Being Held on August 29-30, 2006 in Arlington, VA.,'' PIs: Allan Snavely (University of California, San Diego), David A. Bader, and Gwen A. Jacobs (Montana State University), Biological Sciences Directorate National Science Foundation, $54,488, 8/15/06 - 7/31/07.
  29. IBM Faculty Fellowship Award, ``Optimizing Data-Intensive Applications for Cell BE,'' $40,000, 7/1/2006.
  30. NASA ARC 5119/NNA06CN37H, ``Performance Analysis and Optimization of NASA Scientific Applications on the NAS Supercomputers,'' NASA Graduate Student Researcher Program (GSRP) Fellowship for Kamesh Madduri, NASA NP-2005-07-375-HQ, $24,000, 10/1/2006-9/30/2007.
  31. Sony-Toshiba-IBM Cell Center of Competence, Director: D.A. Bader; Associate Directors: Santosh Pande, Karsten Schwan, and Irfan Essa, Supported by an award from IBM Corp. and Sony Corp., $320,000, 11/1/2006.
  32. Microsoft Research, ``Enabling MS Visual Studio Programmers to Design Efficient Parallel Algorithms for Multi-Core Processors,'' External Research & Programs ``Parallel and Concurrent Programming 2006-2007'' Program, $75,000, 10/24/2006.
  33. NASA ARC, ``Performance Analysis and Optimization of NASA Scientific Applications on the NAS Supercomputers,'' NASA Graduate Student Researcher Program (GSRP) Fellowship for Kamesh Madduri (Second Year Renewal), $30,000, 10/1/2007-9/30/2008.
  34. NIH R01 GM083621, ``Combinatorial and Computational Methods for the Analysis, Prediction, and Design of Viral RNA Structures,'' PIs: Christine Heitsch, David A. Bader, Steve Harvey. NSF-NIH Joint DMS/NIGMS Initiative to Support Research in the Area of Mathematical Biology, National Institutes of Health, $720,000, 9/1/07 - 8/31/12.
  35. NSF CNS-0708307, ``Collaborative Research: CRI: IAD: Development of a Research Infrastructure,'' PIs: Jay Brockman (University of Notre Dame), David A. Bader, Guang Gao (University of Delaware), John Gilbert (University of California, Santa Barbara), Ed Upchurch (California Institute of Technology), Kathy Yelick (University of California, Berkeley), Computing Research Infrastructure (CRI) Program, National Science Foundation, $787,150, 8/1/07 - 7/31/12.
  36. ``Focused Research Program in High-Performance Computing,'' Coordinator: David A. Bader, and 29 other Engineering, Sciences, and Computing faculty, Georgia Institute of Technology, 8/1/07 - 7/30/08, $30,000 May 30, 2007. (Georgia Tech selects five FRP proposals for award each year.)
  37. NSF OCI-0749223, ``Collaborative Research: Enabling Discovery in High Reynolds Number Turbulence via Advanced Tools for Petascale Simulation and Analysis,'' Lead PI: Pui-Kuen Yeung, coPIs: David A. Bader; Amitava Majumdar, Dmitry Pekurovsky (University of California, San Diego), James J. Riley (University of Washington), Robert D. Moser (University of Texas at Austin) ; National Science Foundation, Accelerating Discovery in Science and Engineering Through Petascale Simulations and Analysis (PetaApps), $1.6M, 10/1/07 - 9/30/12.
  38. MIT Lincoln Laboratory, ``High Performance Computing for Massive Graph Analysis,'' $50,000, 4/1/2008-10/31/2008.
  39. Department of Defense, ``DoD HPCMP JEOM Summer Intern Program at Georgia Tech,'' $143,070 5/17/2008-7/31/2009.
  40. NVIDIA Professor Partnership Award, D.A. Bader, $25,000, 8/1/2008.
  41. ``Focused Research Program in High-Performance Computing,'' Coordinator: David A. Bader, and 50 other Engineering, Sciences, and Computing faculty, Georgia Institute of Technology, 8/1/08 - 7/30/09, $30,000 May 30, 2008. (Georgia Tech selects five FRP proposals for award each year.)
  42. NSF IIP-0831110, ``Collaborative Research: Establishing an I/UCRC Center for Multicore Productivity Research (CMPR),'' Georgia Tech PI: David A. Bader; CoPIs: Rich Vuduc, Ada Gavrilovska, and Nathan Clark. University of Maryland, Baltimore County PI: Milton Halem; CoPI: Yelena Yesha. University of California, San Diego PI: Sheldon Brown. Industry/University Cooperative Research Centers (I/UCRC) Program, National Science Foundation, $30,000, ($10,000 Georgia Tech portion) 8/15/08 - 7/31/09.
  43. ``High-Performance Computing for Massive Graph Analysis,'' Georgia Tech PI: David A. Bader, Pacific Northwest National Laboratory, $180,000, (of DoD $4.0M award for the Center for Adaptive Supercomputing Software (CASS)), 8/1/08 - 7/7/09.
  44. MIT Lincoln Laboratory, ``Exascale Analytics for Massive Spatio-Temporal Graphs,'' $100,000, 11/1/2008-9/30/2009.
  45. IBM Faculty Award, $40,000, 7/23/2009.
  46. ``Center for Adaptive Supercomputing Software for Multithreaded Architectures (CASS-MT): Analyzing Massive Social Networks,'' Georgia Tech PI: David A. Bader, Pacific Northwest National Laboratory, $1,269,533, 8/1/09 - 3/30/13.
  47. NSF IIP-0934114, ``Collaborative Research: Establishing a Center for Hybrid Multicore Productivity Research (CHMPR),'' Georgia Tech PI: David A. Bader; CoPIs: Tom Conte, Rich Vuduc, Hyesoon Kim, and Nathan Clark. University of Maryland, Baltimore County PI: Milton Halem; CoPI: Yelena Yesha. University of California, San Diego PI: Sheldon Brown. Industry/University Cooperative Research Centers (I/UCRC) Program, National Science Foundation, $275,000, 8/15/09 - 7/31/14.
  48. NSF OCI-0904461, ``Collaborative Research: Understanding Whole-genome Evolution through Petascale Simulation,'' Georgia Tech Lead PI: David A. Bader; University of South Carolina PI: Jijun Tang; Pennsylvania State University PI: Stephen W. Schaeffer. Accelerating Discovery in Science and Engineering Through Petascale Simulations and Analysis (PetaApps) Program, National Science Foundation, $1,000,000, ($400,000 GA Tech portion), 9/1/09 - 8/31/13.
  49. NIH RC2 HG005542, ``Dynamically Scalable Accessible Analysis for Next Generation Sequence Data,'' PIs: James Taylor, Anton Nekrutenko (Emory University); David A. Bader. Research and Research Infrastructure "Grand Opportunities" (RC2), National Institutes of Health, $1,546,190, ($179,368 GA Tech portion), 9/25/09 - 7/31/11.
  50. Air Force Research Laboratory / General Dynamics Information Technology, ``Georgia Tech/AFRL Workshop on Computational Science and Engineering,'' $4,000, 8/1/2009-11/30/2009.
  51. IBM X10 Innovation Award, ``Dynamic Graph Data Structures in X10,'' $20,000, 12/14/2009.
  52. DOE Sandia National Laboratories, Exploration of Shared Memory Graph Benchmarks, PI: D.A. Bader, $49,962, 2/1/2010 -- 9/30/2010.
  53. Northrop Grumman, ``Membership, NSF Center for Hybrid Multicore Productivity Research (CHMPR),'' PIs: David A. Bader and Tom Conte, $40,000, 5/20/10 - 5/19/11.
  54. Intel, Parallel Algorithms in Non-Numeric Computing Award, ``STING: Spatio-Temporal Interaction Networks and Graphs: An open-source dynamic graph package for Intel platforms,'' PIs: D.A. Bader and E.J. Riedy, $375,000, 6/2010 -- 5/2013.
  55. DARPA, "Challenge Applications and Scalable Metrics (CHASM) for Ubiquitous High Performance Computing," PIs: D.P. Campbell, M.A. Richards, D.A. Bader, M. Gokhale, J.S. Vetter, T. Sterling, Ubiquitous High Performance Computing (UHPC) Program, $7.5M (total), 6/25/2010 -- 6/24/2014.
  56. DARPA, "Echelon: Extreme-scale Compute Hierarchies with Efficient Locality-Optimized Nodes," Leadership Team: W.J. Dally, S. Keckler (NVIDIA), S. Scott (Cray), K. Yelick (Berkeley), M. Erez (UT-Austin), D.A. Bader (Georgia Tech); Ubiquitous High Performance Computing (UHPC) Program, $25M (total), (GT Portion: $878K); 6/25/2010 -- 6/24/2014.
  57. NSF OCI-1051537, ``Accelerators for Data Intensive Applications; A Workshop to Engage the Science and Engineering Community,'' PI: Viktor Prasanna (University of Southern California), co-PI: David A. Bader; Software Institutes Program, National Science Foundation, $37,837, 8/15/10 - 8/14/11.
  58. Oracle, ``Membership, NSF Center for Hybrid Multicore Productivity Research (CHMPR),'' PIs: David A. Bader and Tom Conte, $40,000, 3/2/11 - 3/1/12.
  59. DARPA, "Benchmarking the IBM PERCS and Cray CASCADE architectures," High Productivity Computing Systems (HPCS) Program, PIs: D.A. Bader and J. Riedy, $287,994, 6/1/2011 -- 3/31/2014.
  60. DARPA, "Proactive Detection of Insider Threats with Graph Analysis at Multiple Scales," PIs: T. Senator (SAIC) and D.A. Bader (GTRI), Anomaly Detection at Multiple Scales (ADAMS) Program, $2,927,976 (GT portion), 5/1/2011 -- 4/30/2013.
  61. DARPA, "Ground Truthing Social Media Data," PIs: L. Weiss and D.A. Bader, $614,000, 8/15/2011 -- 8/14/2012.
  62. ExxonMobil Research & Engineering, "High Performance Computing Based Algorithms for Mixed Integer Programming," PIs: George Nemhauser, David A. Bader, and Shabbir Ahmed, $209,253, 1/1/2012 -- 12/31/2013.
  63. Intel Corp., ``In support of the 10th DIMACS Implementation Challenge on Graph Partitioning and Graph Clustering,'' PI: D.A. Bader, $5,000, 1/2012.
  64. Sandia National Laboratories, ``In support of the 10th DIMACS Implementation Challenge on Graph Partitioning and Graph Clustering,'' PI: D.A. Bader, $4,000, 1/2012.
  65. DARPA, "SOCINT: Social Signals for Identifying & Using Influential Subnetworks," PI: E. Gilbert, coPIs: D.A. Bader, I. Essa, C. Dovrolis, L. Weiss, and E. Briscoe, Social Media in Strategic Communication (SMISC) Program, $3,217,920, 2/1/2012 -- 1/31/2015.
  66. NSF OCI-1216504, ``Software Infrastructure for Accelerating Grand Challenge Science with Future Computing Platforms,'' PI: D.A. Bader, co-PIs: R. Vuduc and E.J. Riedy; Software Institutes Program, National Science Foundation, $104,386 10/1/12 - 9/30/13.
  67. DARPA, "GRATEFUL: GRaph Analysis Tackling power EFficiency, Uncertainty, and Locality," PI: D.A. Bader, coPI: E.J. Riedy, Power Efficiency Revolution for Embedded Computing Technologies (PERFECT) Program, $2,929,819 10/19/2012 -- 10/18/2017.
  68. NSF ACI-1265434, ``EAGER: Collaborative Research: Using PDE Descriptions to Generate Code Precisely Tailored to Energy-Constrained Systems Including Large GPU Accelerated Clusters,'' Georgia Tech PI: David A. Bader; University of Illinois at Urbana-Champaign PI: Gengbin Zheng; Louisiana State University PI: Steven Brandt, and coPIs: Peter Diener, Frank Löffler, and David Koppelman. EArly-concept Grants for Exploratory Research (EAGER) Program, National Science Foundation, $294,914, ($100,000 GA Tech portion), 9/1/13 - 8/31/15.
  69. NSF ACI-1339745, ``SI2-SSI: Collaborative: The XScala Project: A Community Repository for Model-Driven Design and Tuning of Data-Intensive Applications for Extreme-Scale Accelerator-Based Systems,'' Georgia Tech PI: David A. Bader, and coPIs: Jason Riedy and Rich Vuduc; University of Southern California PI: Viktor Prasanna. Software Infrastructure for Sustained Innovation Program, National Science Foundation, $1,937,624, ($1,188,710 GA Tech portion), 10/1/13 - 9/30/15.
  70. NSF ACI-1362300, ``Collaborative Research: IEEE IPDPS Conference Student Participation Support,'' David A. Bader; National Science Foundation, $13,000, 1/1/14 - 6/30/15.

Research Proposals and Grants (Contributor)

  1. NSF DEB 00-80529, ``Sevilleta LTER III: Long Term Ecological Research in a Biome Transition Zone,'' National Science Foundation, Division of Environmental Biology, PIs: C.N. Dahm (current), J.R. Gosz (former), J.W. Brunt, T.K. Lowrey, W.T. Pockman, D. Pennington, R.R. Parmenter, $1,400,000, 10/15/2000 - 10/14/2002. (Senior Personnel)
  2. NSF EIA 01-13095, ``ITR/AP(DEB): Collaborative Research `Computing Optimal Phylogenetic Trees under Genome Rearrangement Metrics','' PIs: R. Jansen and B.M.E. Moret), National Science Foundation, Information Technology Research (ITR) Program, $450,000 (total); $161,903 (UNM portion), 10/1/2001 - 9/30/2004. (Senior Personnel)
  3. NSF INT 01-29062, ``Time-Delay Systems: Analysis, Computer Aided Design and Applications,'' PI: K. Gu, (Southern Illinois), National Science Foundation, U.S.-France Cooperative Research International Program, $10,000 (total); $1,000 (UNM portion), 3/15/2002 - 2/28/2003.

Equipment Grants

  1. NSF PACI/NCSA, ``Linux Based Clusters for the Alliance: A Proposal to Establish a Linux Based Cluster (LBC) at the University of New Mexico,'' PIs: D.A. Bader, A.B. Maccabe, F. Gilfeather, approx. $200,000, March 1999.
  2. IBM, "Development and Investigation of an Interoperable, Hybrid Technology System for Local/Remote Scientific and Visual Computing," PIs: S.R. Atlas, D.A. Bader, R.A. Ballance, T.P. Caudell, B.T. Smith, J. Sobolewski, IBM Shared University Research (SUR) Program, approx. $3M, 1/1/2000.
  3. Sun Microsystems, ``Sun StorEdge Array for Computational Science,'' PIs: D.A. Bader, K. Schwan, M. Wolf, Academic Equipment Grant (AEG) Program, approx. $42,800, 6/13/2005.
  4. Xilinx Corp., ``Reconfigurable Computing with FPGA Devices,'' (two Digilent Spartan 3 development boards), PI: D.A. Bader, Xilinx University Program (XUP), 2/28/2006.
  5. IBM Corp., ``Optimizing Scientific Libraries for IBM Cell,'' PI: D.A. Bader; Additional Researchers: Santosh Pande, Karsten Schwan, and Irfan Essa, Shared University Research (SUR) Program, approx. $55K, 7/1/2006.
  6. Sun Microsystems, ``Optimizing Computational Science Applications on Sun Multithreaded Processors,'' (two Sun T2000 blades with UltraSPARC ``Niagara'' T1 processors), PI: D.A. Bader, Academic Excellence Grant (AEG) Program, approx. $34K, 7/5/2006.
  7. NVIDIA Research, (two Tesla C870 HPC compute boards), PI: D.A. Bader, Professor Partnership Program, approx. $2,500, 3/26/2008.
  8. IBM Corp., ``Optimizing R Libraries for IBM Cell Broadband Engine,'' PI: D.A. Bader; Additional Researcher: Richard Vuduc, Shared University Research (SUR) Program, $40K, 7/29/2008.
  9. Sun Microsystems, ``Multithreaded Algorithms,'' (Sun SPARC Enterprise T5240 Server, ``Maramba''), PI: D.A. Bader, approx. $36,500, 3/30/2009.
  10. Intel Corp., Single-Chip Cloud (SCC) Research, Lead PI: D.A. Bader (``Evaluating the SCC for Dynamic Streaming Graphs''); PI: R. Vuduc (``Models and autotuning for generalized n-body algorithms''); PI: A. Gavrilovska and co-PI K. Schwan, (``Scalable Systems Software for SCC Platforms''); 6/11/2010.
  11. Oracle, ``Multithreaded Algorithms,'' (two (2) Oracle Servers, each with two X4470's with four processes each and 1.5TB memory), PIs: D.A. Bader and E.J. Riedy, $118,000, 4/16/2012.
  12. NVIDIA Research, (GeForce Titan), PI: D.A. Bader, and Adam McLaughlin, Professor Partnership Program, 10/4/2013.

SERVICE

Professional Activities

Memberships and Activities in Professional Societies

Conference Committee Activities

Invitational Meetings Attended

Professional Meetings Attended

On-Campus Georgia Tech Committees

  • Member, Strategic Planning Committee, School of Computational Science & Engineering, College of Computing, 2012-2013.
  • Member, Space/Building Planning Committee, School of Computational Science & Engineering, College of Computing, 2012-2013.
  • Member, Faculty Recruiting Committee, School of Computational Science & Engineering, College of Computing, 2012-2013.
  • Representative for College of Computing, Academic Senate (AS) and General Faculty Assembly (GFA), 2011-2014, elected 2011.
  • Chair, Faculty Recruiting Committee, School of Computational Science & Engineering, College of Computing, 2011-2012.
  • Member, School Chair Advisory Committee, School of Computational Science & Engineering, College of Computing, (elected), 2011-2012, 2012-2013.
  • Member, CSE Seminar and Distinguished Lecture Series Committee, School of Computational Science & Engineering, College of Computing, 2011-2012.
  • Chair, School Chair Advisory Committee, School of Computational Science & Engineering, College of Computing, (elected), 2010-2011.
  • Chair, Retention, Promotion, Tenure (RPT) Committee, School of Computational Science & Engineering, College of Computing, 2009-2010, 2010-2011, 2012-2013.
  • Member, Faculty Recruiting Committee, School of Computational Science & Engineering, College of Computing, 2010-2011.
  • Chair, Faculty Recruiting Committee, School of Computational Science & Engineering, College of Computing, 2009-2010.
  • Chair, Critical Review Committee, School of Computational Science and Engineering, College of Computing, 2010.
  • Chair, Periodic Peer Review Committee for Full Professor in School of Computational Science and Engineering, College of Computing, 2009-2010.
  • Member, Periodic Peer Review Committee for Full Proessor in School of Computational Science and Engineering, College of Computing, 2009-2010.
  • Member, Retention, Promotion, Tenure (RPT) Committee, College of Computing, 2008-2009, 2012-2014.
  • Member, Dean's Advisory Committee, College of Computing, 2009-2010, elected 2009.
  • Chair, Chair Advisory Committee, School of Computational Science & Engineering, College of Computing, 2009-2010, elected 2009.
  • Member, Integrative BioSystems Institute (IBSI) Advisory Committee, 2008-present.
  • Coordinator, Faculty Recruiting Committee / High-Performance Computing, Computational Science & Engineering Division, College of Computing, 2007-2008.
  • Member, Computational Biology Faculty Search Committee, School of Biology, 2007-2008.
  • Chair, Provost's Bioinformatics Review Committee, Fall 2007.
  • Chair, Faculty Recruiting Committee, Computational Science & Engineering Division, College of Computing, 2006-2007.
  • Member, Provost's HPC Task Force, 2006-2007.
  • Member, Technology Services Advisory Committee (TSAC), College of Computing, 2006.
  • Representative, Undergraduate Research Opportunities in Computing (UROC) Program, Computational Science & Engineering Division, College of Computing, 2006-present.
  • Member, Faculty Recruiting Committee, Computational Science & Engineering Division, College of Computing, 2005-2006.
  • Member, Graduate Admissions Committee, College of Computing, 2005-2006.
  • Member, Graduate Committee, College of Computing, 2005-2006.

Special Assignments at Georgia Tech

  • Chair, Oak Ridge - Georgia Tech Linkage Task Force, Georgia Institute of Technology, 2006.
  • Director of Graduate Studies, Computational Science & Engineering Division, College of Computing, Georgia Institute of Technology, 2005-2006.

Other University Service

  • Member, Tenure & Promotion Committee, Electrical and Computer Engineering Department, University of New Mexico, 2004-2005.
  • Member, ECE Chair Search Committee, University of New Mexico, 2004-2005.
  • Member, Tenure & Promotion Committee, Electrical and Computer Engineering Department, University of New Mexico, 2003-2004.
  • Member, Committee on Studies, Dean Paul Roth, School of Medicine, University of New Mexico, Summer 2003.
  • Member, Awards Committee, Electrical and Computer Engineering Department, University of New Mexico, 2002-2003.
  • Coordinator, High-Performance Computing Track of Computer Engineering and Graduate Committee Member, Electrical and Computer Engineering Department, University of New Mexico, 2002-2003.
  • Member, Office of Research High-Performance Computing Center Committee, Fall 2001 - Spring 2002.
  • Member, Graduate Committee, Electrical and Computer Engineering Department, University of New Mexico, 2001-2002.
  • Member, SOE Research Excellence Awards Committee, Spring 2001.
  • Member, Awards Committee, Electrical and Computer Engineering Department, University of New Mexico, Spring 2001.
  • Area Chair for Computer Engineering, Graduate Committee, Electrical and Computer Engineering Department, University of New Mexico, Fall 2000 - Summer 2001.
  • Attendee, U.S. Senator Bingaman's roundtable meeting of Biotechnology, Sante Fe, September 21, 2000.
  • Faculty Liaison, University of New Mexico (UNM) Centennial Science and Engineering Library, Fall 2000 - Spring 2005.
  • Member, Strategic Planning, University of New Mexico, Fall 2000.
  • Host, ECE and IEEE Distinguished Guest Dr. Bruce Eisenstein, 2000 IEEE President, May 26-27, 2000.
  • Coordinator, SOE/ECE Executive Meeting and Tour with the National Radio Astronomy Observatory (NRAO), April 13, 2000.
  • Member, Awards Committee, Electrical and Computer Engineering Department, University of New Mexico, Spring 2000.
  • Member, NSF/Alliance $1.5M Linux Supercluster Panel Review, Spring 2000.
  • Member, School of Engineering Math Task Force, University of New Mexico, 1999 - 2000.
  • Chairperson, Computer Use Committee, Electrical and Computer Engineering Department, University of New Mexico, 1999.
  • Member, Search Committee for Systems Analyst III, Electrical and Computer Engineering Department, University of New Mexico, 1999.
  • Member, Search Committee for Computer Engineering Faculty Position, Electrical and Computer Engineering Department, University of New Mexico, 1998.
  • Outside Member, Search Committee for Computer Science Faculty Position, Computer Science Department, University of New Mexico, 1998.
  • Faculty Advisor, ECE Web Page Designer Staff Position, University of New Mexico (UNM) ECE Department, 1998.
  • Member, Research Allocation Committee, University of New Mexico (UNM) Faculty Senate, 1998-2000.
  • Member, Search Committee for Manager of Systems and Programming, University of New Mexico (UNM) ECE Department, 1998.
  • Represented the University of New Mexico at Sandia National Laboratories' ``Adventures in Supercomputing'' EXPO '98.
  • Member, Computer Use Committee, Electrical and Computer Engineering Department, University of New Mexico, 1998.
  • Associate Faculty, Albuquerque High Performance Computing Center.
  • Associated Faculty & Program Committee, Science & Engineering Computation (SEC) Program, Albuquerque High Performance Computing Center, 1998-2002.
  • College of Engineering Graduate Student Senator, UMCP College Park Senate, 1995-96.
  • UMCP Electrical Engineering Graduate Student Association, Founder and President 1994-95
  • Graduate student representative to the UMCP-EE's Department Council, 1994-95
  • Graduate student representative to the UMCP-EE's Graduate Studies and Research Committee, 1993-94

Ph.D. Examining Committees --- Georgia Tech

  • Nova Ahmed (advisor: Umakishore Ramachandran), 2010.
  • Senyo Apewokin (advisor: Scott Wills), 2008.
  • Michael Ryan Bales (advisor: Scott Wills), 2011.
  • Rocky Dunlap (advisor: Leo Mark), 2013.
  • Jared Gossett (advisor: Steve Harvey), 2013.
  • Yan Gu (advisor: Richard Fujimoto), 2007.
  • Cory Hawkins (advisor: Scott Wills), 2007.
  • Zhengyu He (advisor: Bo Hong), 2012.
  • Andrey Kislyuk (advisor: Joshua Weitz), 2010.
  • Alfred Park (advisor: Richard Fujimoto), 2008.
  • Reza Haji Aghaee Khiabani (co-advisors: Cyrus Aidun and Yogendra Joshi), 2010.
  • Daniel A. Reasor Jr. (advisor: Cyrus Aidun), 2011.
  • Srikanth Yoginath (advisor: Kalyan Perumalla), 2014.

Ph.D. Examining Committees --- University of New Mexico

  • Jose Salazar, 1998.
  • Saeid Taheri, 2004.
  • Jijun Tang, 2004.
  • Yan Zhu, 2004.
  • Michael Collins, 2005.
  • Zhaoxian Zhou, 2005.
  • Shibin Qiu, 2006.
  • Monique Morin, 2007.

Ph.D. Examining Committees --- Other Universities

  • Jaroslaw Zola, Institut National Polytechnique de Grenoble, France, 2005.
  • Weiguo Liu, Nanyang Technological University, Singapore, 2006.
  • David Kunzman, University of Illinois at Urbana-Champaign, 2011.

M.S. Thesis Committees --- University of New Mexico

  • Ihsan Demir, 2000.
  • Adam Siepel, 2001.
  • Todd Underwood, 2001.
  • Yan Xu, 2001.
  • William F. Lawry, 2002.
  • Mahin Mahmoodi, 2002.
  • Jingkun Yu, 2002.
  • Shu Zhou, 2002.
  • Sean Brennan, 2003.
  • G. Matthew Fricke, 2003.
  • Edgar A. León, 2003.
  • Anna Tholse, 2003.
  • Zak Betz, 2004.
  • Joel V. Earnest-DeYoung, 2004.
  • Tao Liu, 2004.
  • Sung-hee Lee, 2005.
  • Sushant Sharma, 2005.
  • M. Leigh Fanning, 2007.

Consulting and Advisory Appointments

NATIONAL AND INTERNATIONAL PROFESSIONAL RECOGNITION

Honors and Awards

Editorial Service

OTHER CONTRIBUTIONS

Seminar Presentations (Invited Papers and Talks at Meetings and Symposia)

  1. ``Eighth Graph500 List,'' Birds-of-a-Feather, 29th International Supercomputing Conference (ISC), Leipzig, Germany, June 23, 2014.

  2. ``Mono-Site (centralized) Large Scale Data Mining: Hadoop, HPC, GPU,'' at the Parallel and Distributed Data Analytics (PDDA) CEA/EDF/INRIA Summer School, CEA Cadarache, France, June 16-20, 2014.

  3. Co-Organizer, held in conjuntion with The IEEE International Parallel and Distributed Processing Symposium (IPDPS 2014), Phoenix, AZ, May 19, 2014.
  4. ``Multi-threaded Graph Streaming,'' at the Graph Algorithms Building Blocks (GABB 2014), held in conjunction with the 28th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2014), Phoenix, AZ, May 23, 2014.

  5. ``Heterogeneity in Large-Scale Data Analytics,'' Panelist, at the 23rd International Heterogeneity in Computing Workshop (HCW 2014), held in conjunction with the 28th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2014), Phoenix, AZ, May 19, 2014.

  6. ``Big Data Analytics,'' Inspur HPC Connections Workshop, co-located with The 25th IEEE and ACM Supercomputing Conference (SC13), Denver, CO, November 20, 2013.

  7. ``Massive-Scale Graph Analytics,'' Panelist, At the Intersection of Big Data and Extreme Computing Birds-of-a-Feather, The 25th IEEE and ACM Supercomputing Conference (SC13), Denver, CO, November 20, 2013.

  8. ``Seventh Graph500 List,'' Birds-of-a-Feather, The 25th IEEE and ACM Supercomputing Conference (SC13), Denver, CO, November 19, 2013.

  9. ``Sixth Graph500 List,'' Birds-of-a-Feather, 28th International Supercomputing Conference (ISC), Leipzig, Germany, June 18, 2013.

  10. ``Making Connections in Big Data: Exascale Graph Analytics & the Graph500,'' Panelist, Latest Advances in Scalable Algorithms for Large Scale Systems, 28th International Supercomputing Conference (ISC), Leipzig, Germany, June 18, 2013.
  11. ``Massive-scale Graph Analytics,'' Czech Academy of Sciences, Prague, Czech Republic, June 11, 2013.

  12. ``The Future of Big Data,'' Panelist, Big Data in 10 Years, The IEEE International Parallel and Distributed Processing Symposium (IPDPS 2013), Boston, MA, May 22, 2013.
  13. ``Massive-scale Graph Analytics,'' Panelist, Big Data Meets Big Models, 2013 SIAM Conference on Computational Science and Engineering (CSE13), Boston, MA, February 25 - March 1, 2013.

  14. ``Massive-scale Graph Analytics,'' Workshop on Massive Data Analytics on Scalable Systems (DataMASS), The 19th IEEE International Conference on High Performance Computing (HiPC 2012), Pune, India, December 18, 2012.

  15. ``Massive-scale Streaming Graph Analytics,'' Panelist, Graph Analytics in Big Data, The 24th IEEE/ACM Supercomputing Conference (SC12), Salt Lake City, UT, November 15, 2012.

  16. ``Fifth Graph500 List,'' Birds-of-a-Feather, The 24th IEEE/ACM Supercomputing Conference (SC12), Salt Lake City, UT, November 13, 2012.

  17. ``Massive-scale Streaming Graph Analytics,'' Panelist, Cyber Security's Big Data, Graphs, and Signatures, The 24th IEEE/ACM Supercomputing Conference (SC12), Salt Lake City, UT, November 13, 2012.

  18. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' Booz Allen Hamilton Distinguished Colloquium Series in Electrical and Computer Engineering, University of Maryland, College Park, September 28, 2012.
  19. ``Massive-scale Graph Analytics,'' AGH University of Science and Technology, Krakow, Poland, September 17, 2012.

  20. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' NSF Workshop on Research Directions in the Principles of Parallel Computation, Pittsburgh, PA, June 28, 2012.
  21. ``Fourth Graph500 List,'' Birds-of-a-Feather, 27th International Supercomputing Conference (ISC), Hamburg, Germany, June 19, 2012.

  22. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' Student Research Symposium, The 18th IEEE International Conference on High Performance Computing (HiPC 2011), Bengaluru, India, December 18, 2011.
  23. ``Opportunities and Challenges in Massive Data-Intensive Computing,'' Big Data, Analytics, & HPC workshop, Georgia Tech Research Institute Technical Series, Atlanta, GA, December 9, 2011.

  24. ``STING: Spatio-Temporal Interaction Networks and Graphs for Intel Systems,'' Intel Workshop on Parallel Algorithms for Non-Numeric Computing, San Jose, CA, August 29, 2011.

  25. ``Graph 500 Benchmark for Data Intensive HPC Applications,'' Birds-of-a-Feather, 26th International Supercomputing Conference (ISC), Hamburg, Germany, June 19-23, 2011.

  26. ``Accelerating Real-World Applications,'' presented at the AMD Fusion Developer Summit 11, Bellevue, WA, June 14, 2011.

  27. ``Graph Based Approaches to Scientific Data,'' presented at the Climate Knowledge Discovery Workshop, Deutsches Klimarechenzentrum GmbH (DKRZ), Hamburg, Germany, March 30 - April 1, 2011.

  28. ``Broader Engagements and Workforce Development in High Performance Computing,'' Panelist, presented at the NSF Future of High Performance Computing workshop, Arlington, VA, December 3, 2010.

  29. ``Unveiling the First Graph 500 List,'' Birds-of-a-Feather, The 22nd IEEE and ACM Supercomputing Conference (SC10), New Orleans, LA, November 13-19, 2010.

  30. ``Petascale Computing for Computational Biology and Genomics,'' Information Science and Technology Center (ISTeC) distinguished lecture series, Colorado State University, Fort Collins, CO, October 4, 2010.

  31. ``Massive-Scale Analysis of Streaming Social Networks,'' joint Electrical and Computer Engineering Department and Computer Science Department Special Seminar, Colorado State University, Fort Collins, CO, October 1, 2010.

  32. ``Massive-Scale Analysis of Streaming Social Networks,'' Clusters, Clouds, and Grids for Scientific Computing (CCGSC 2010), Flat Rock, NC, September 10, 2010.

  33. ``Massive-Scale Analysis of Streaming Social Networks,'' ACM Chapter of Georgia State University, Atlanta, GA, September 1, 2010.

  34. ``Architectural and Programming Support for Massive Streaming Analytics,'' Workshop on Programming and Runtime Models for Heavily Threaded Systems (PRMHTS), Annapolis, MD, July 27, 2010.

  35. ``Massive Scale Analytics of Streaming Social Networks,'' Workshop on Algorithms for Massive Modern Data Sets (MMDS), Stanford University, Stanford, CA, June 15, 2010.

  36. ``Graph 500 Benchmark for Data Intensive HPC Applications,'' Birds-of-a-Feather, 25th International Supercomputing Conference (ISC), Hamburg, Germany, May 30 - June 3, 2010.

  37. ``Memory Driven Applications,'' and ``Executive Panel Feedback,'' Panelist, 2009 Advanced Computing Systems (ACS) Research Program Workshop, Annapolis, MD, September 16-17, 2009.

  38. ``Accelerating Data-Intensive Scientific Applications,'' Georgia Tech/AFRL Computational Science Workshop on Computational Science Challenges Using Emerging & Massively Parallel Computer Architectures, Atlanta, GA, August 17, 2009.

  39. ``Petascale Computing for Computational Biology and Genomics,'' Computational Life Sciences lecture series, Emory University, Atlanta, GA, December 10, 2008.

  40. ``High Performance Computing for the Analysis of Massive Graphs,'' Knowledge Discovery and Dissemination (KDD) Conference 2008, Oak Ridge, TN, December 3, 2008.

  41. ``Accelerating Applications on Heterogeneous Multicore Platforms,'' Panelist, Can Developing Applications for Massively Parallel Systems with Heterogeneous Processors Be Made Easy(er)?, The IEEE and ACM Supercomputing Conference 2008 (SC08), Austin, TX, November 18, 2008.

  42. ``Petascale Computing for Computational Biology and Genomics,'' Frontiers in Multi-Scale Systems Biology, An International Launch Conference Introducing Georgia Tech's New Integrative BioSystems Institute, Atlanta, GA, October 18-21, 2008.

  43. ``Fast Transforms Using the Cell Broadband Engine Processor,'' Workshop on Programming Models for Modern Architectures, Los Alamos Computer Science Symposium (LACSS), Santa Fe, NM, October 15, 2008.

  44. ``Exascale Analytics for Large-Scale Graph Problems and Computational Biology,'' Computational Science and Engineering Symposium, Georgia Institute of Technology, September 26, 2008.

  45. ``Petascale Computing for Large-Scale Graph Problems and Computational Biology,'' North Carolina State University, September 22, 2008.

  46. ``Petascale Computing for Large-Scale Graph Problems and Computational Biology,'' University of Basel, Switzerland, September 11, 2008.

  47. ``Petascale Computing for Large-Scale Graph Problems and Computational Biology,'' 37th SPEEDUP Workshop on High-Performance Computing, ETH Zürich, Switzerland, September 8, 2008.

  48. ``Fast Transforms Using the Cell Broadband Engine Processor,'' presented at the Frontiers of Multicore Computing Workshop, University of Maryland, Baltimore County (UMBC), Baltimore, MD, August 24, 2008.

  49. ``Exascale Analytics in Biology, Social Networks, and Security,'' DARPA Exascale Study, Atlanta, GA, July 9, 2008. (by invitation)

  50. ``Petascale Phylogenetic Reconstruction of Evolutionary Histories,'' Emerson Center Lectureship Symposium, Emory University, Atlanta, GA, March 31, 2008.

  51. ``Petascale Computing for Large-Scale Graph Problems,'' Barcelona Supercomputing Center, Universitat Politécnica de Catalunya, Barcelona, Spain, March 5, 2008.

  52. ``Petascale Computing for Large-Scale Graph Problems,'' Computer Science Department, University of Georgia, Athens, GA, January 18, 2008.

  53. ``Petascale Phylogenetic Reconstruction of Evolutionary Histories,'' Distinguished Lecture Series in Systems Biology, Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA, December 11, 2007.

  54. ``Petascale Phylogenetic Reconstruction of Evolutionary Histories,'' George Washington University, Washington, DC, November 28, 2007.

  55. ``Petascale Computing for Large-Scale Graph Problems,'' Electrical and Computer Engineering Department, University of New Mexico, Albuquerque, NM, October 26, 2007.

  56. ``Petascale Computing for Large-Scale Graph Problems,'' Lawrence Livermore National Laboratory, Livermore, CA, July 26, 2007.

  57. ``Manycore Algorithms,'' Panelist, Manycore Computing Workshop, Seattle, WA, June 21, 2007.

  58. ``Petascale Science and Engineering: Georgia Tech's Leadership in the ManyscaleTM Transformation,'' SOS11 Conference: Challenges of Sustained Petascale Computation, Key West, FL, June 12, 2007.

  59. ``Petascale Computing for Large-Scale Graph Problems,'' presented at the Georgia Tech Summer Undergraduate Research Experience (SURE) Program for Minorities Seminar Series, June 7, 2007.

  60. ``Achieving sustainability through exascale analysis of complex biological networks,'' Simulation and Modeling at the Exascale for Energy, Ecological Sustainability and Global Security (E3SGS) Town Hall Meeting, Oak Ridge National Laboratory, Oak Ridge, TN, May 17, 2007.

  61. ``Building a Cell Ecosystem,'' Summit on Software and Algorithms for the Cell Processor, Knoxville, TN, October 25, 2006.

  62. ``DARPA HPCS Scalable Synthetic Compact Application #2: Graph Analysis, Version 2.0,'' High Productivity Computing Systems (HPCS) Productivity Team Meeting, Denver, CO, June 22, 2006.

  63. ``Whole Genome Phylogenetic Reconstruction,'' presented at the High Throughput Biology Center, Johns Hopkins University, June 14, 2006.

  64. ``Efficient Shared Memory Algorithms and Implementations for solving large-scale graph problems,'' with Kamesh Madduri, presented at National Security Agency, May 25, 2006.

  65. ``Petascale Computing for Large-Scale Graph Problems,'' presented at Architectures and Algorithms for Petascale Computing, Seminar No. 06071, Schloss Dagstuhl International Conference and Research Center for Computer Science, Wadern, Germany, February 14, 2006.

  66. ``Discrete Sciences: High-Performance Computing,'' Oak Ridge -- Georgia Tech Discrete Sciences Workshop, Atlanta, GA, January 20, 2006.

  67. ``DARPA HPCS Scalable Synthetic Compact Application #2: Graph Analysis,'' High Productivity Computing Systems (HPCS) Productivity Meeting, Marina del Rey, CA, January 11, 2006.

  68. ``High-Performance Computing for Large-Scale Graph Problems and Computational Biology,'' presented at Oak Ridge National Laboratory, September 19, 2005.

  69. ``High-Performance Algorithm Engineering for Large-Scale Graph Problems and Computational Biology,'' presented at the The 4th International Workshop on Efficient and Experimental Algorithms (WEA 2005), Santorini Island, Greece, May 11, 2005.

  70. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Computer Science Department, Kent State University, May 4, 2005.

  71. ``On the Architectural Requirements for Efficient Execution of Graph Algorithms,'' presented at Sandia National Laboratories, Albuquerque, NM, March 24, 2005.

  72. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the College of Computing, Georgia Institute of Technology, March 17, 2005.

  73. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Department of Computer Science, College of William & Mary, March 14, 2005.

  74. ``High-Performance Computing for Large-Scale Graph Problems and Computational Biology,'' presented at the Department of Electrical and Computer Engineering, University of Delaware, February 25, 2005.

  75. ``Life Science Applications,'' IBM / DARPA High Productivity Computing Systems (HPCS) Project Meeting, Austin, TX, February 8, 2005.

  76. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Department of Electrical and Computer Engineering, Drexel University, January 21, 2005.

  77. ``An Implementation of the DARPA HPCS Scalable Synthetic Compact Application #2: Graph Analysis,'' High Productivity Computing Systems (HPCS) Productivity Meeting, Marina del Rey, CA, January 12, 2005.

  78. ``Fast, Sparse Graph Algorithms using Symmetric Multiprocessors,'' Pacific Northwest National Laboratory, December 14, 2004.

  79. ``The Productive Use of High-End Computing Systems for Applications in Computational Biology,'' Workshop on Building Scalable Simulations of Complex Socio-Technical Systems, The 5th Los Alamos Computer Science Institute (LACSI) Symposium, Santa Fe, NM, October 12, 2004.

  80. ``DARPA Scalable Synthetic Compact Application #1: Optimal Pattern Matching,'' High Productivity Computing Systems (HPCS) Program and Productivity Summit, Fairfax, VA, June 29, 2004.

  81. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Thomas Jefferson University Computational Biology Seminar Series, University of Delaware, June 7, 2004.

  82. ``The Productive Use of High-End Computers,'' presented at the Advanced Computing Laboratory of Los Alamos National Laboratory, May 27, 2004.

  83. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Biomedical Computing Center Colloquium Series, Georgia State University, May 14, 2004.

  84. ``High Performance Computational Biology,'' Panel Moderator, presented at the 18th IEEE International Parallel and Distributed Processing Symp. (IPDPS), Santa Fe, NM, April 28, 2004.

  85. Panelist, Scalable Synthetic Compact Applications, HPCS Micro and Scalable Benchmarking Technical Meeting, DARPA High Productivity Computing Systems (HPCS) Productivity Team Workshop, USC/ISI, Marina Del Ray, CA, January 15, 2004.

  86. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Computational Biology Seminar Series, Johns Hopkins University, December 23, 2003.

  87. ``High-Performance Algorithm Engineering and Computational Biology,'' presented at the DARPA HPCS / IBM PERCS Phase 2 Project Meeting, IBM T.J. Watson Research Center, Yorktown Heights, NY, September 11, 2003.

  88. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at University Visvesvaraya College of Engineering, Bangalore University, India, December 16, 2002.

  89. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at PES Institute of Technology, Bangalore, India, December 16, 2002.

  90. ``Computational Biology and High Performance Computing,'' Panelist, The IEEE and ACM Supercomputing Conference 2002 (SC2002), Baltimore, MD, November 19, 2002.

  91. ``High-Performance Computing for Reconstructing Evolutionary Trees from Gene-Order Data,'' presented at the Department of Computer Science & Engineering, The University of Texas at Arlington, October 11, 2002.

  92. ``High-Performance Algorithm Engineering and Computational Biology,'' presented at the DARPA PERCS Project Meeting, IBM T.J. Watson Research Center, Yorktown Heights, NY, July 16, 2002.

  93. ``High-Performance Computing for Reconstructing Phylogenies from Gene-Order Data,'' presented at the IDC HPC User Forum, Santa Fe, NM, April 23, 2002.

  94. ``High-Performance Computing for Reconstructing Phylogenies from Gene-Order Data,'' presented at the Sun Microsystems HPC Consortium 2001, Denver, CO, November 10-11, 2001.

  95. ``A Linear-Time Algorithm for Computing Inversion Distance Between Signed Permutations with an Experimental Study,'' presented at the Computer Science Department Colloquium of The University of New Mexico, October 16, 2001.

  96. ``High-Performance Algorithm Engineering for Computational Phylogeny,'' with Bernard Moret, presented at the UNM Medical School, September 19, 2001.

  97. ``High-Performance Algorithm Engineering for Gene-Order Phylogenies,'' Computer Science Research Institute (CSRI) seminar, Sandia National Laboratories, Albuquerque, NM, March 8, 2001.

  98. ``Open-Source Parallel Algorithms Library (OPAL): Efficient algorithms for symmetric multiprocessors,'' Extreme Linux Developer's Forum (ELDF), Santa Fe, NM, February 22, 2001.

  99. ``Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms,'' presented at the Packard Workshop on Large-Scale Phylogenetic Reconstruction, Volcano, HI, December 29, 2000.

  100. ``Using PRAM Algorithms on a Uniform Memory Access Shared-Memory Architecture,'' presented at the Advanced Computing Laboratory of Los Alamos National Laboratory, November 2, 2000.

  101. ``Using PRAM Algorithms on a Uniform Memory Access Shared-Memory Architecture,'' presented at Yale University, New Haven, CT, October 20, 2000.

  102. ``Bridging the Gap Between the Theory and Practice of Parallel Computing,'' presented at the University of New Mexico Chapter of Sigma Xi, Albuquerque, NM, October 18, 2000.

  103. ``Using PRAM Algorithms on a Uniform Memory Access Shared-Memory Architecture,'' presented at Sun Microsystems High-End Technical Users Performance Group (SUPerG) meeting, Vancouver, Canada, October 11, 2000.

  104. ``Using PRAM Algorithms on a Uniform Memory Access Shared-Memory Architecture,'' presented at Experimental Algorithmics, Seminar No. 00371, Schloss Dagstuhl International Conference and Research Center for Computer Science, Wadern, Germany, September 13, 2000.

  105. ``Designing High-Performance Algorithms for SMP Clusters,'' presented at the IBM SP Scientific Computing User Group (SCICOMP2000), San Diego Supercomputer Center, University of California, San Diego, August 15, 2000.

  106. ``Grid Forum `Advanced Programming Models' Working Group Progress Report,'' presented at the Fourth Grid Forum Meeting, Microsoft Corp., Redmond, WA, July 10-12, 2000.

  107. ``OPAL: Open Source Parallel Algorithm Library for Designing Efficient PRAM-Like Algorithms for Symmetric Multiprocessors,'' National Center for Genome Resources, Santa Fe, NM, May 22, 2000.

  108. ``Designing High-Performance Algorithms for SMP Clusters,'' presented at the IBM Hyper Cluster Computing Workshop Albuquerque High Performance Computing Center, The University of New Mexico, April 19, 2000.

  109. ``Grid Forum `Advanced Programming Models' Working Group Progress Report,'' presented at the Third Grid Forum Meeting, University of California, San Diego, CA, March 22-24, 2000.

  110. ``An Improved Randomized Selection Algorithm With an Experimental Study,'' presented at the Albuquerque High Performance Computing Center, The University of New Mexico, February 4, 2000.

  111. ``Grid Forum 'Advanced Programming Models' Working Group Progress Report,'' presented at the Second Grid Forum Meeting, Northwestern University, Chicago, IL, October 19-21, 1999.

  112. ``Tutorial: Supercomputing in the Alliance,'' with A.B. Maccabe and R. Pennington, presented at the NSF / Alliance Chautauqua, Boston University, Boston, MA, September 16, 1999.

  113. ``SuperClusters: A New Approach for High-Performance Computing,'' presented to the NSF / Alliance Chautauqua, Boston University, Boston, MA, September 14, 1999.

  114. ``SuperClusters: A New Approach for High-Performance Computing,'' presented at the NSF / Alliance Chautauqua, University of Kentucky, Lexington, KY, August 24, 1999.

  115. ``Tutorial: Supercomputing in the Alliance,'' with A.B. Maccabe and R. Pennington, presented at the NSF / Alliance Chautauqua, University of New Mexico, Albuquerque, NM, August 11, 1999.

  116. ``SuperClusters: A New Approach for High-Performance Computing,'' presented at the NSF / Alliance Chautauqua, University of New Mexico, Albuquerque, NM, August 10, 1999.

  117. ``The Grid Forum Advanced Programming Models Working Group,'' presented at the Grid Forum Birds-of-a-Feather, Eighth IEEE International Symposium on High Performance Distributed Computing (HPDC-8), Redondo Beach, CA, August 4, 1999.

  118. ``Grid Forum 'Advanced Programming Models' Working Group Report,'' presented at the First Grid Forum Workshop, NASA Ames Research Center, Moffett Field, CA, June 17, 1999.

  119. ``Analysis of the Alliance/UNM Roadrunner Linux Supercluster,'' presented at the NSF/NCSA Alliance Roadmap '99 Meeting, Chicago, IL, May 12, 1999.

  120. ``Clusters: The Next Generation,'' presented at the Albuquerque High Performance Computing Center, The University of New Mexico, March 30, 1999.

  121. ``Designing High Performance Algorithms for Clusters of SMPs,'' presented at the Computer Science Department Colloquium of The University of New Mexico, October 22, 1998.

  122. ``Designing High Performance Algorithms for Clusters of SMPs,'' presented at the Advanced Computing Laboratory of Los Alamos National Laboratory, April 13, 1998.

  123. ``Parallel Processing in Academia, National Labs, Industry,'' Panel member, Rio Grande ACM Meeting, The University of Texas, El Paso, March 27, 1998.

  124. ``Designing High Performance Algorithms for Clusters of SMPs,'' presented at New Mexico State University, Las Cruces, NM, March 26, 1998.

  125. ``Practical Parallel Algorithms for Combinatorial Problems, Data Communication, and Image Processing Applications,'' presented at Sandia National Laboratories, Albuquerque, NM, May 29, 1997.

  126. ``Practical Parallel Algorithms for Combinatorial Problems, Data Communication, and Image Processing Applications,'' presented at the Department of Electrical Engineering and Computer Engineering, The University of New Mexico, April 16, 1997.

  127. ``Practical Parallel Algorithms for Combinatorial Problems and Data Communication,'' presented at the Department of Electrical Engineering, The Catholic University of America, November 11, 1996.

  128. ``Practical Parallel Algorithms for Personalized Communication and Integer Sorting,'' presented at the NSF sponsored Capital Area Theory Seminar and UMIACS Seminar on Algorithms, February 21, 1996.

  129. ``The World's Fastest Sorting Algorithm, and Other High Performance Computing Results'' presented at the Graduate Student Interaction Day (GRID '96), University of Maryland, College Park, MD, April 11, 1996. Third Place Award.

  130. ``Parallel Algorithms for Image Processing,'' presented at the Graduate Student Interaction Day (GRID '95), University of Maryland, College Park, MD, April 6, 1995.

  131. ``Scalable and Portable Parallel Algorithms for Image Processing,'' presented at Supercomputing Research Center, Bowie, MD, March 31, 1995.

 
 

Last updated: 09 July 2014

 




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