David A. Bader is a Full Professor in the School of Computational
Science and Engineering, College of Computing, at Georgia Institute of
Technology, and Executive Director for High Performance
Computing. Dr. Bader is a lead scientist in the DARPA Ubiquitous High
Performance Computing (UHPC) program. 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 on the Research Advisory Council for
Internet2, the Steering Committees of the IPDPS and HiPC conferences,
the General Chair of IPDPS 2010 and Chair of SIAM PP12. He is an
associate editor for several high impact publications including the
Journal of Parallel and Distributed Computing (JPDC), ACM Journal of
Experimental Algorithmics (JEA), IEEE DSOnline, Parallel Computing,
and Journal of Computational Science, and has been an associate editor
for the IEEE Transactions on Parallel and Distributed Systems
(TPDS). He was elected as chair of the IEEE Computer Society Technical
Committee on Parallel Processing (TCPP) and as chair of the SIAM
Activity Group in Supercomputing (SIAG/SC).
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 100 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. He served as a member of the IBM
PERCS team for the DARPA High Productivity Computing Systems program,
was a distinguished speaker in the IEEE Computer Society Distinguished
Visitors Program, and has also served as Director of the
Sony-Toshiba-IBM Center of Competence for the Cell Broadband Engine
Processor. Bader is recognized as a ``RockStar'' of High Performance
Computing by InsideHPC and as HPCwire's People to Watch in 2012.
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, (Peking University, China, entered Fall 2010)
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, (M.S., Technion, Israel, entered Spring 2011)
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)
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).
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
David A. Bader, Henning Meyerhenke, Peter Sanders, and Dorothea Wagner (eds.),
Graph Partitioning and Graph Clustering,
American Mathematical Society,
2013.
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
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.
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.
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.
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.
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.
``Analyzing Massive Social Networks using Multicore and Multithreaded Architectures,''
presented at
Facing the Multicore Challenge,
Heidelberg Academy of Sciences,
Heidelberg, Germany, March 17, 2010.
``Massive Scale Analytics of Streaming Social Networks,''
6th Erlangen International High-End-Computing Symposium,
Friedrich-Alexander-Universität Erlangen-Nürnberg,
Germany, June 4, 2010.
``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.
``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.
``Opportunities and Challenges in Massive Data-Intensive Computing,''
Boos-Allen-Hamilton Distinguished Colloquium in Electrical and Computer Engineering,
University of Maryland, September 28, 2012.
Conference Presentations with Proceedings (refereed)
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Conference Tutorials (peer-reviewed)
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.
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.
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.
NRC 9601610, Research Associateship Award, $42,500, 1996-1997.
(award declined)
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.
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.
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.
DOE Sandia National Laboratories,
Combinatorial Algorithms for Homeland Defense,
PI: D.A. Bader,
Contract Number 55856, $29,735, 8/26/2002 - 5/30/2003.
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.
DOE Sandia National Laboratories,
Parallel Algorithms for Computational Electromagnetics,
PI: D.A. Bader,
Contract Number 161449, $13,000, 8/1/2003 - 7/31/2004.
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.
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.
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.
DOE Sandia National Laboratories,
Designing Parallel Graph Algorithms for Multi-Threaded Architectures,
PI: D.A. Bader,
$73,000, 1/1/2005 -- 12/31/2005.
Los Alamos National Laboratory,
LinuxBIOS support on advanced 64-bit systems,
PI: D.A. Bader,
$40,000, 1/1/2005 -- 12/31/2005.
IBM Faculty Fellowship Award,
``Optimizing Data-Intensive Applications for Cell BE,''
$40,000,
7/1/2006.
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.
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.
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.
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.
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.
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.
``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.)
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.
MIT Lincoln Laboratory,
``High Performance Computing for Massive Graph Analysis,''
$50,000,
4/1/2008-10/31/2008.
Department of Defense,
``DoD HPCMP JEOM Summer Intern Program at Georgia Tech,''
$143,070
5/17/2008-7/31/2009.
NVIDIA Professor Partnership Award,
D.A. Bader,
$25,000,
8/1/2008.
``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.)
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.
``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.
MIT Lincoln Laboratory,
``Exascale Analytics for Massive Spatio-Temporal Graphs,''
$100,000,
11/1/2008-9/30/2009.
``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.
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.
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.
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.
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.
IBM X10 Innovation Award,
``Dynamic Graph Data Structures in X10,''
$20,000,
12/14/2009.
DOE Sandia National Laboratories,
Exploration of Shared Memory Graph Benchmarks,
PI: D.A. Bader,
$49,962, 2/1/2010 -- 9/30/2010.
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.
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.
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.
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.
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.
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.
DARPA,
"Benchmarking the IBM PERCS architecture,"
PI: D.A. Bader,
$126,488,
6/1/2011 -- 5/31/2012.
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.
DARPA,
"Ground Truthing Social Media Data,"
PIs: L. Weiss and D.A. Bader,
$614,000,
8/15/2011 -- 8/14/2012.
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 -- 12/31/2012.
Intel Corp.,
``In support of the 10th DIMACS Implementation Challenge on Graph Partitioning and Graph Clustering,''
PI: D.A. Bader,
$5,000,
1/2012.
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.
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.
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.
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.
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.
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.
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.
Xilinx Corp., ``Reconfigurable Computing with FPGA Devices,''
(two Digilent Spartan 3 development boards),
PI: D.A. Bader,
Xilinx University Program (XUP),
2/28/2006.
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.
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.
NVIDIA Research,
(two Tesla C870 HPC compute boards),
PI: D.A. Bader,
Professor Partnership Program,
approx. $2,500,
3/26/2008.
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.
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.
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.
SERVICE
Professional Activities
Memberships and Activities in Professional Societies
CRA-NIH Workshop on Computational Challenges in Biomedicine,
Bethesda, MD,
June 15-16, 2006.
NSF Workshop on Petascale Computing in the Biological Sciences,
National Science Foundation, Arlington, VA, August 29-30, 2006.
National Academy of Engineering,
2007 U.S. Frontiers of Engineering Symposium,
Redmond, WA, September 24-26, 2007. (83 of the most creative, young engineers in the US selected to attend.)
Ethical Challenges and Practical Solutions for Managers in
Research, a conference co-sponsored by
Sigma Xi, The Scientific
Research Society and the Office of Research Integrity, Albuquerque,
NM, September 10, 1999.
Second Grid Forum
Workshop, Northwestern University, Chicago,
Illinois, October 19-21, 1999.
NSF-Sponsored Workshop on Active Services, (by invitation-only),
Northwestern University, Chicago, Illinois, October 21-22, 1999.
Supercomputing 1999 (SC99), sponsored by IEEE Computer Society
and ACM SIGARCH, Portland, OR, November 14-18, 1999.
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), 2011-2012, 2012-2013, 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.
Advisory Committee Member, Flash Gordon: A Data Intensive Computer, University of California, San Diego, NSF Office of Cyberinfrastructure award NSF-0910847, (PI: Michael Norman, co-PI: Allan Snavely), 2009-present.
``Opportunities and Challenges in Massive Data-Intensive Computing,''
Big Data, Analytics, & HPC workshop,
Georgia Tech Research Institute Technical Series,
Atlanta, GA, December 9, 2011.
``Graph Based Approaches to Scientific Data,''
presented at the
Climate Knowledge Discovery Workshop,
Deutsches Klimarechenzentrum GmbH (DKRZ),
Hamburg, Germany, March 30 - April 1, 2011.
``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.
``Massive-Scale Analysis of Streaming Social Networks,''
ACM Chapter of Georgia State University,
Atlanta, GA, September 1, 2010.
``Architectural and Programming Support for Massive Streaming Analytics,''
Workshop on Programming and Runtime Models for Heavily Threaded Systems (PRMHTS),
Annapolis, MD, July 27, 2010.
``Memory Driven Applications,'' and ``Executive Panel Feedback,'' Panelist,
2009 Advanced Computing Systems (ACS) Research Program Workshop,
Annapolis, MD, September 16-17, 2009.
``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.
``Petascale Computing for Computational Biology and Genomics,''
Computational Life Sciences lecture series, Emory University,
Atlanta, GA, December 10, 2008.
``High Performance Computing for the Analysis of Massive Graphs,''
Knowledge Discovery and Dissemination (KDD) Conference 2008,
Oak Ridge, TN, December 3, 2008.
``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.
``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.
``Exascale Analytics for Large-Scale Graph Problems and Computational Biology,''
Computational Science and Engineering Symposium,
Georgia Institute of Technology,
September 26, 2008.
``Petascale Computing for Large-Scale Graph Problems and Computational Biology,''
North Carolina State University,
September 22, 2008.
``Petascale Computing for Large-Scale Graph Problems and Computational Biology,''
University of Basel,
Switzerland, September 11, 2008.
``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.
``Exascale Analytics in Biology, Social Networks, and Security,''
DARPA Exascale Study,
Atlanta, GA, July 9, 2008. (by invitation)
``Petascale Phylogenetic Reconstruction of Evolutionary Histories,''
Emerson Center Lectureship Symposium, Emory University,
Atlanta, GA, March 31, 2008.
``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.
``Petascale Phylogenetic Reconstruction of Evolutionary Histories,''
George Washington University,
Washington, DC, November 28, 2007.
``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.
``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.
``Whole Genome Phylogenetic Reconstruction,''
presented at the
High Throughput Biology Center,
Johns Hopkins University,
June 14, 2006.
``Efficient Shared Memory Algorithms and Implementations for solving large-scale graph problems,''
with Kamesh Madduri, presented at National Security Agency, May 25, 2006.
``Discrete Sciences: High-Performance Computing,''
Oak Ridge -- Georgia Tech Discrete Sciences Workshop, Atlanta, GA, January 20, 2006.
``DARPA HPCS Scalable Synthetic Compact Application #2: Graph Analysis,''
High Productivity Computing Systems (HPCS) Productivity Meeting, Marina del Rey, CA, January 11, 2006.
``High-Performance Computing for Large-Scale Graph Problems and Computational Biology,''
presented at
Oak Ridge National Laboratory, September 19, 2005.
``On the Architectural Requirements for Efficient Execution of Graph Algorithms,''
presented at Sandia National Laboratories, Albuquerque, NM, March 24, 2005.
``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.
``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.
``DARPA Scalable Synthetic Compact Application #1: Optimal
Pattern Matching,''
High
Productivity Computing Systems (HPCS) Program and
Productivity Summit, Fairfax, VA, June 29, 2004.
``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.
``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.
``High-Performance Computing for Reconstructing Evolutionary
Trees from Gene-Order Data,''
presented at the
Computational Biology Seminar Series,
Johns Hopkins University,
December 23, 2003.
``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.
``High-Performance Computing for Reconstructing Evolutionary
Trees from Gene-Order Data,''
presented at University Visvesvaraya College of Engineering,
Bangalore University, India,
December 16, 2002.
``High-Performance Computing for Reconstructing Evolutionary
Trees from Gene-Order Data,''
presented at
PES Institute of Technology,
Bangalore, India,
December 16, 2002.
``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.
``High-Performance Computing for Reconstructing Phylogenies from
Gene-Order Data,'' presented at the IDC HPC User Forum,
Santa Fe, NM, April 23, 2002.
``High-Performance Computing for Reconstructing Phylogenies from
Gene-Order Data,'' presented at the
Sun MicrosystemsHPC
Consortium 2001, Denver, CO, November 10-11, 2001.
``High-Performance Algorithm Engineering for Computational Phylogeny,''
with Bernard Moret, presented at the UNM Medical School,
September 19, 2001.
``High-Performance Algorithm Engineering for Gene-Order Phylogenies,''
Computer Science Research
Institute (CSRI) seminar, Sandia National Laboratories,
Albuquerque, NM, March 8, 2001.
``Open-Source Parallel Algorithms Library (OPAL): Efficient algorithms for symmetric multiprocessors,''
Extreme Linux Developer's Forum (ELDF), Santa Fe, NM,
February 22, 2001.
``Genome Rearrangements Analysis under Parsimony and other
Phylogenetic Algorithms,'' presented at the Packard Workshop on
Large-Scale Phylogenetic Reconstruction, Volcano, HI, December 29,
2000.
``Using PRAM Algorithms on a Uniform Memory Access Shared-Memory
Architecture,'' presented at
Yale University,
New Haven, CT, October 20, 2000.
``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.
``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.
``Grid Forum `Advanced Programming Models' Working Group
Progress Report,''
presented at the Fourth Grid Forum Meeting, Microsoft Corp.,
Redmond, WA, July 10-12, 2000.
``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.
``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.
``Grid Forum 'Advanced Programming Models' Working Group Progress Report,''
presented at the Second Grid Forum Meeting, Northwestern University,
Chicago, IL, October 19-21, 1999.
``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.
``SuperClusters: A New Approach for High-Performance Computing,''
presented to the NSF / Alliance Chautauqua, Boston University,
Boston, MA, September 14, 1999.
``SuperClusters: A New Approach for High-Performance Computing,''
presented at the NSF / Alliance Chautauqua, University of Kentucky,
Lexington, KY, August 24, 1999.
``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.
``SuperClusters: A New Approach for High-Performance Computing,''
presented at the NSF / Alliance Chautauqua, University of New
Mexico, Albuquerque, NM, August 10, 1999.
``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.
``Analysis of the Alliance/UNM Roadrunner Linux Supercluster,''
presented at the NSF/NCSA Alliance Roadmap '99 Meeting, Chicago,
IL, May 12, 1999.
``Parallel Processing in Academia, National Labs, Industry,'' Panel
member, Rio Grande ACM Meeting, The
University of Texas, El Paso, March 27, 1998.
``Designing High Performance Algorithms for Clusters of SMPs,'' presented at
New Mexico State University,
Las Cruces, NM, March 26, 1998.
``Practical Parallel Algorithms for Combinatorial Problems, Data
Communication, and Image Processing Applications,'' presented at
Sandia National Laboratories,
Albuquerque, NM, May 29, 1997.
``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.
``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.
