The Best Paper Awards Committee has chosen Andrzej Brodzik's study of
a new approach to DNA sequence alignment as the winner of the 2006 Ronald
Fante Best Paper Award. His paper, "Phase-Only
Filtering for the Masses (of DNA Data): A New Approach to Sequence Alignment,"
appeared in the June 2006 issue of IEEE Transactions on Signal Processing,
Special Edition on Genomic Signal Processing.
The award came as a surprise to Andy, who says "The Ronald Fante Best
Paper Award is a great honor. I would like to thank the Engineering Council
for recognizing my work, especially as the award came truly unexpectedly.
I would also like to acknowledge the generous advice I received from Marvin
Drake, Ed Hanfling, Ann Jones, and Marnie Salisbury (and many research colleagues
from academia and government labs). Last but not least, I could not have
completed the work without the unwavering support of Olivia Peters, whose
project supported this investigation."
Andy's paper explores an innovative application of the symmetric phase-only matched filter (SPOMF),
traditionally used in optical signal processing, image registration, watermarking,
and sonar, to DNA sequence alignment. In describing his work, Andy notes,
"Both DNA sequence analysis and decryption of arbitrary codes rely,
in part, on comparing an unfamiliar sequence to one that is already known, thus establishing islands of similarity, and then
forming a hypothesis about the function/meaning of the new sequence. The
full sequence of human DNA contains 3 billion letters, and an effective
investigation of biological phenomena requires the comparison of many
genomes. The dimensionality of the problem greatly complicates the task
of sequence alignment. Prior approaches mediate this problem by employing
various heuristic techniques. This has the undesirable effect of making
the algorithms' performance depend on many parameters, including
the data itself. The SPOMF approach removes both the parameterization
and the dependence on the data, and injects into the computation the fastest
mathematical construction available—the Fast Fourier Transform
algorithm. This speeds up the computation of similar sequences and increases
the predictability of results."
"Future progress in molecular biology and the rate of that progress
will ultimately depend on an effective merger of mathematical and life
sciences," Andy continues. "This creates a great opportunity
for MITRE, whose traditional strength has always been in information technology.
Most relevant to the MITRE mission is that research in this area will
bear directly on the future development of effective strategies for mitigating
bio-terrorist and bio-warfare threats."
"This year's Best Paper contest received a large number of
high-quality papers, making the selection process difficult," says
Vice President and Chief Technology Officer Steve Huffman. "However,
the winning paper stood out for both its technical quality and innovative
application of signal processing techniques to DNA sequence alignment.
It's an excellent example of applying one of MITRE's traditional
areas of technical expertise to a new problem space by recognizing that
there are analogous problems in both domains."
Forty other papers received Incentive awards in the 2006 competition.
A complete list of the winners follows.
Bayer, Samuel, John Burger, Lisa Ferro, John Henderson, Lynette Hirschman,
and Alex Yeh, 2006, "Evaluating Semantic Evaluations: How RTE Measures Up," in Lecture
Notes in Computer Science—Machine Learning Challenges, Joaquin
Quinonero-Candela, Ido Dagan, Bernardo Magnini, and Florence d'Alché-Buc,
eds. (Berlin and Heidelberg: Springer Verlag), 309–331.
Bhadra, Dipasis, Brendan Hogan, and Roger Schaufele, April–June
2006, "Improving Aviation Forecasts for FAA's En Route Facilities,"
Journal of Air Traffic Control, Vol. 48, No. 2, 42–47.
Bhadra, Dipasis, and Frederick Morser (F050), 2006, "Analysis
of System-wide Investment in the National Airspace System: A Portfolio
Analytical Framework and an Example," Journal of Air Transportation,
Vol. 11, No. 1, 3–26.
Box, Frank, Philip I. Long, and Richard E. Snow, September 2006, "Capacity
of the Nationwide VHF Air/Ground Radio System for Air Traffic Services,"
IEEE Transactions on Vehicular Technology, Vol. 55, No. 5,
1457–1466.
Brodzik, Andrzej K., June 2006, "Phase-Only Filtering for the
Masses (of DNA Data): A New Approach to Sequence Alignment," IEEE
Transactions on Signal Processing, Special Edition on Genomic Signal
Processing, Vol. 54, No. 6, 2456–2466.
Burns, Kevin J., 2006, "Atoms
of EVE': A Bayesian Basis for Esthetic Analysis of Style in Sketching,"
Artificial Intelligence for Engineering Design, Analysis, and Manufacturing,
Vol. 20, 185–199.
Burns, Kevin J., 2006, "Bayesian
Inference in Disputed Authorship: A Case Study of Cognitive Errors and
a New System for Decision Support," Information Sciences,
Vol. 176, No. 11, 1570–1589.
Channakeshava, Karthik, Binoy Ravindran, and E. Douglas Jensen, April
2006, "Utility Accrual Channel Establishment in Multihop Networks,"
IEEE Transactions on Computers, Vol. 55, No. 4, 428–442.
DeArmon, James S., Gerald A. Dorfman, George H. Solomos, Michelle
J. Blucher, David A. Knorr, and Ho Y. Yi, 2006, "Excess Flying
Time in the National Airspace System," Air Traffic Control
Quarterly, Vol. 14, No. 4, 283–309.
Ellenbogen, James C., 2006, "Neutral Atoms Behave Much Like Classical
Spherical Capacitors," Physical Review A, Vol. 74, 34501-1–34501-4.
Flournoy, R. Douglas, Elizabeth Lee, and Robert Mikula, June/July
2006, "Testing Net-centric Systems-of-Systems: Applying Lessons Learned
from Distributed Simulation Testing," ITEA Journal of Test and Evaluation,
Vol. 27, No. 2, 47–55.
Grabowski, Robert, Richard Weatherly, Robert Bolling, David Seidel,
Michael Shahid, and Ann Jones, October 2006, "MITRE
Meteor: An Off-Road Autonomous Vehicle for DARPA's Grand Challenge,"
Journal of Field Robotics, Vol. 23, No. 9, 811–835.
Higgs, Brandon W., John Dileo, Wenling E. Chang, Haley B. Smith, Olivia
J. Peters, Rasha Hammamieh, Marti Jett, and Jordan C. Feidler, May 31,
2006, "Modeling
the Effects of a Staphylococcal Enterotoxin B (SEB) on the Apoptosis
Pathway," BMC Microbiology, Vol. 6, No. 48.
Hirschman, Lynette, and Laurie Damianos, 2006, "Mining
Online Media for Global Disease Outbreak Monitoring,” in Discrete
Methods in Epidemiology, J. Abello and G. Cormode, eds., Providence,
RI: American Mathematical Society, 131–150.
Hirschman, Lynette, William S. Hayes, and Alfonso Valencia, December
2006, "Knowledge
Acquisition from the Biomedical Literature," in Semantic
Web: Revolutionizing Knowledge Discovery in the Life Sciences,
Christopher J.O. Baker and Kei-Hoi Cheung, eds., New York: Springer-Verlag,
53-81.
Hwang, Seunghyeon, Santana Burintramart, Tapan K. Sarkar, and Steven
R. Best, November 2006, "Direction of Arrival (DOA) Estimation
Using Electrically Small Tuned Dipole Antennas," IEEE Transactions
on Antennas and Propagation, Vol. 54, No. 11, 3292–3301.
Kerchner, Marcia D., June 2006, A
Dynamic Methodology for Improving the Search Experience,"
Information Technology and Libraries, Vol. 25, No. 2, 78–87.
Leamy, Michael J., February 2007, "Bulk Dynamic Response Modeling
of Carbon Nanotubes Using an Intrinsic Finite Element Formulation Incorporating
Interatomic Potentials," International Journal of Solids and
Structures, Vol. 44, No. 3–4, 874–894.
Li, Peng, Haisang Wu, Binoy Ravindran, and E. Douglas Jensen, April
2006, "A Utility Accrual Scheduling Algorithm for Real-Time Activities
with Mutual Exclusion Resource Constraints," IEEE Transactions
on Computers, Vol. 55, No. 4, 454–469.
Maybury, Mark T., 2006, "New Directions in Question Answering," in Advances in Open
Domain Question Answering, Tomek Strzalkowski and Sanda Harbagiu,
eds. (Dordrecht, the Netherlands: Springer), 533–558.
Maybury, Mark T., Oliviero Stock, and Wolfgang Wahlster, September/October
2006, "Intelligent Interactive Entertainment Grand Challenges,"
IEEE Intelligent Systems, Vol. 21, No. 5, 14–18.
Maybury, Mark T., Penny Chase, Brant Cheikes, Richard Pietravalle,
Jeffrey Sebring, Mick Costa, D. Brackney, P. Lehtola, S. Matzner, T.
Hetherington, B. Wood, C. Sibley, J. Marin, T. Longstaff, L. Spitzner,
J. Haile, J. Copeland, and S. Lewandowski, November 29, 2006, "(U)
Detection of Malicious Insider Activity Using Models of Insider Behavior,"
Journal of Intelligence Community Research and Development.
Mitola, Joseph III, 2006, Cognitive Radio Architecture—The Engineering Foundations of Radio XML,
Hoboken, NJ: John Wiley & Sons.
Mitola, Joseph III, 2006, "Cognitive
Radio Architecture," in Cognitive Radio Technology,
Bruce Fette, ed., New York: Newnes.
Mitola, Joseph III, 2006, "Cognitive
Radio Architecture—Organizing Computational Intelligence for Peer
and Network Collaboration," in Cooperation in Wireless
Networks: Principles and Applications, Frank H.P. Fitzek and Marcos
D. Katz, eds., New York: Springer-Verlag.
Mohtashemi, Mojdeh, Brandon W. Higgs, and Richard Levins, 2006, "Infection
and Atherosclerosis: Is There an Association?" Complex
Systems, Vol. 16, 259–276.
Mohtashemi, Mojdeh, Peter Szolovits, James Dunyak, and Kenneth D.
Mandl, 2006, "A
Susceptible-Infected Model of Early Detection of Respiratory Infection
outbreaks on a Background of Influenza," Journal of Theoretical
Biology, Vol. 241, 954–963.
Moore, James W., 2006, "The
Role of Process Standards in Process Definition," in CMMI®:
Guidelines for Process Integration and Product Improvement, Mary
Beth Chrissis, Mike Konrad, and Sandy Shrum, eds., 2nd ed. (Boston:
Addison-Wesley).
Mui, Lik, Mojdeh Mohtashemi, and Sameer Verma, 2005/2006, "Multi-agents
Model of the Open Source Development Process," International
Journal of Technology, Knowledge and Society, Vol. 1, No. 6, 43–60.
Obrst, Leo, Werner Ceusters, Inderjeet Mani, Steve Ray, and Barry
Smith, 2006, "The
Evaluation of Ontologies: Toward Improved Semantic Interoperability,"
in Semantic Web: Revolutionizing Knowledge Discovery in the Life
Sciences, Christopher J.O. Baker and Kei-Hoi Cheung, eds., New
York: Springer-Verlag.
Shively, Curtis, Rick Niles, and Thomas T. Hsiao, Summer 2006, "Performance
and Availability Analysis of a Simple Local Airport Position Domain
Monitor for WAAS," Navigation, Vol. 53, No. 2, 97–108.
Shyy, Dong Jye, and James Dunyak, July 2006, "Capacity Enhancement
of CDMA Networks Using Interference Cancellation Techniques,"
IEEE Communications, Vol. 44, No. 7, 86–92.
Shyy, Dong Jye, Jin Yu, and Yu-Dong Yao, 2006, "Modeling
and Performance Evaluation of 3G CDMA Networks with Beamforming,"
Wireless Personal Communications, Vol. 39, 1–13.
Stankosky, Michael, and Ellen F. MacGarrigle, 2006, "Validating
Enterprise Management Engineering Through the Use of Knowledge Capital
Assessments," Journal of Information and Knowledge Management,
Vol. 5, No. 2, 129–142.
Stine, John A., April 2006, "Enabling
Secondary Spectrum Markets Using Ad Hoc and Mesh Networking Protocols [PDF],"
Journal of Communications, Vol. 1, No. 1, 26–37.
Wellner, Ben, Lisa Ferro, Warren Greiff, and Lynette Hirschman, December
2006, "Reading
Comprehension Tests for Computer-based Understanding Evaluation,"
Natural Language Engineering, Vol. 12, No. 4, 305–334.
Woodard, Jeffrey P., and Monica Carley-Spencer, Fall 2006, "No-Reference
Image Quality Metrics for Structural MRI," Neuroinformatics,
Vol. 4, No. 3, 243–262.
Wright, Kenneth, December 15, 2006, "Aviation System Performance
During the Summer Convective Weather Season," Journal of the
Transportation Research Forum, Vol. 45, No. 3, 77–92.
Wu, Haisang, Binoy Ravindran, E. Douglas Jensen, and Peng Li, August
2006, "Energy-Efficient, Utlity Accrual scheduling under Resource
Constraints for Mobile Embedded Systems," ACM Transactions
on Embedded Computing Systems, Vol. 5, No. 3, 513–542.
Yanco, Holly A., and Jill L. Drury, September 2006, "Rescuing
Interfaces: A Multi-Year Study of Human-Robot Interaction at the AAAI
Robot Rescue Competition," Autonomous Robots, Vol.,
Vol. 22, No. 1, published online December 27, 2006.
