DEPARTMENT OF COMPUTER SCIENCE
July 1, 2005 - June 30, 2006
I. Publications, Performances, Exhibits
II. Papers and Presentations Presented at
Professional Meetings
III. Editorships, Offices, and Consultancies
V. Awards for Distinguished Teaching, Research,
or Professional Activities
I. Publications, Performances, Exhibits
Burg,
Jennifer J.
None
Cañas,
Daniel A.
None
Fetrow,
Jacquelyn S.
“Active site profiling to identify protein functional sites in sequences and structures.” Current Protocols in Bioinformatics. 2006 In press.
(with Creamer, T. P.) “Rose is a Rose is a Rose. Especially if you're a George.” A Perspectives article in Proteins: Struct. Funct. Bioinformatics. 2006 In press.
(with Allen, E. E., Pecorella, A., John, D. J., and Turkett, W.) “Reconstructing Networks Using Co-temporal Functions.” Proceedings of the 2006 ACM Southeast Conference, 417-422.
(with John, D. J.) “Bioinformatics and Computing Curriculum: A New Model for Interdisciplinary Courses.” SIGCSE Bulletin, 38(1), 2006, 185-189.
(with Knutson, S. T., and Edgell, M. H.) “Mutations in α-helical solvent exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations.” Proteins: Struct. Funct. Bioinformatics. 2005 December 9 (Epub ahead of print).
(with Huff, R. G., Bayram, E., Tan, H., Knutson, S. T., Knaggs, M. H., Richon, A. B., and Santago II, P.) “Chemical and Structural Diversity in Cyclooxygenase Protein Active Sites.” Chemistry and Biodiversity. 2005. 2:1533-1552.
(with Allen, E. E., Daniel, L. W., Thomas, S. J., and John, D. J.) “Algebraic dependency models of protein signal transduction networks from time-series data.” J. Theor. Biol. 2006 Jan 21; 238(2):317-30. (Epub 2005 July 5)
Fulp,
Errin W.
"Parallel Firewall Designs for High-Speed Networks.” IEEE INFOCOM, High Speed Networking Workshop,
2006.
(with Tarsa,
Stephen J.) "Balancing Trie-Based Policy Representations for Network
Firewalls." Proceedings of the
IEEE International Symposium on Computer Communications, 2006.
(with Farley,
Ryan J.) "A Function-Parallel Architecture for High-Speed Firewalls."
Proceedings of the IEEE International
Conference on Communications, 2006.
(with Farley,
Ryan J.) "The Effect of Processing Delay on Function-Parallel Network
Firewalls." Proceedings of the
IASTED International Conference on Parallel and Distributed Computing and
Networks, 2006.
John,
David J.
(with Allen, E. E., Daniel, L. W., Fetrow, J. S., and Thomas, S. J.) “Algebraic
dependency models of protein signal transduction networks from time-series
data.” J. Theor. Biol. 2006 Jan 21; 238(2):317-330.
(Epub 2005 July 5)
(with Allen, Edward E., Fetrow,
Jacquelyn S., Pecorella, Anthony, and Turkett, William) “Reconstructing
Networks using Co-temporal Functions.” Proceedings of the 2006 ACM
Southeast Conference, 417-422.
(with Fetrow, Jacquelyn S.) “Bioinformatics and Computing Curriculum: A New Model for Interdisciplinary Courses.” SIGCSE Bulletin, 38(1), 2006, 185-189.
Pauca,
V. Paúl
(with Plemmons, R., and Piper, J.) “Nonnegative Matrix Factorization for
Spectral Data Analysis,”
Linear Algebra and Its Applications, Vol. 416, pp.29-47, 2006.
(with Shahnaz, F.,
Plemmons,
Robert J.
(with Pauca, P., and Piper, J.) “Nonnegative Matrix Factorization for Spectral
Data Analysis,”
Linear Algebra and Its Applications, Vol. 416, pp.29-47, 2006.
(with Shahnaz, F.,
(with Bardsley, J., Jefferies, S., and Nagy, J.) “A Computational Method for the Restoration of Images with an Unknown, Spatially-Varying Blur.” Optics Express, Vol. 14, No. 5, pp. 1767-1782, March 2006.
(with Mu, Z., and Santago, P.) “Iterative Ultrasonic Signal and Image Deconvolution for Estimation of the Complex Medium Response.” International Journal of Imaging Systems and Technology, Vol. 15, No. 6, pp. 266-266, April 2006.
Thomas,
Stan J.
(with
Allen, E. E., Daniel, L. W., Fetrow, J. S., and John, D. J.) “Algebraic
dependency models of protein signal transduction networks from time-series
data.” J. Theor. Biol. 2006 Jan 21; 238(2):317-330.
(Epub 2005 July 5)
Torgersen,
Todd C.
None
Turkett,
William H.
(with Allen, Edward E., Pecorella, Anthony, Fetrow, Jacquelyn S., and John, David J.) “Reconstructing Networks Using Co-temporal Functions.” Proceedings of the 2006 ACM Southeast Conference, 417-422.
“Static Bayesian Modeling of Biological Time Series Data.” To appear in Proceedings of Probabilistic Modeling and Machine Learning in Structural and Systems Biology Workshop (held June 17-18, 2006).
Wong,
Yue-Ling
None
II. Papers and Presentations Presented at
Professional Meetings
Burg,
Jennifer J.
Presentations:
"Digital Media: Why Do We Need It, and How Do We Teach It As
REAL Computer Science," tutorial/workshop at SIGCSE 2006, March 3, 2006,
"Curriculum Material for Teaching Digital
Media as Computer Science," poster session at SIGCSE 2006, March 2, 2006,
"How to Teach Digital Media as
Science and Integrate It Into the Computer Science Curriculum," tutorial/workshop
at the ACM Southeast Conference, March
10, 2006,
Cañas,
Daniel A.
None
Fetrow, Jacquelyn S.
Paper: (with John, D. J.) “Bioinformatics
and Computing Curriculum: A New Model for Interdisciplinary Courses.” SIGSCE
2006,
Invited Conference Presentations:
21st Annual Perspectives
in Biology Symposium, Nov. 11-12, 2005,
The Protein Society 19th
Symposium. Systems Biology Workshop for Educators, July 30-August 3, 2005,
Invited Seminars:
Fulp,
Errin W.
Papers:
“Improving the Performance of
Firewalls and Intrusion Protection Systems for High-Speed Networks.” Department of Computer Science Colloquium,
“Security Issues for the Next
Generation of Network.” Department of Computer Science Seminar,
"Parallel Firewall Designs for High-Speed Networks." IEEE INFOCOM, High-Speed Networking Workshop, 2006.
Invited Presentations:
“Firewall and Intrusion Detection Systems for
High-Speed Networks.” DOE Pacific Northwest National Laboratory, Cyber Security
Group Seminar, 2005.
“Firewall Architectures for High-Speed Networks.” DOE PI Meeting, DOE Brookhaven National Laboratory, 2005.
“Firewall Optimization Techniques and Architectures for
High-Speed Networks.” DOE Pacific
Northwest National Laboratories (Cyber Security Group),
John,
David J.
Paper: (with Fetrow, Jacquelyn S.)
“Bioinformatics and Computing Curriculum:
A New Model for Interdisciplinary Courses.” SIGCSE 2006,
Pauca, V. Paúl
Paper: (with Cai, Y., and Kraft, B.) “Truncated Singular Value Decomposition of
Point Spread Function Mapping for Correction of Image Distortion in Echo Planar
Imaging (EPI).” 5th Annual
Graduate Student Research Symposium, Virginia Tech –
Presentations:
“Advancements in the Reconstruction of
PERIODIC Iris Imagery.” Fourth 2005 ARDA/DTO Advanced Imaging Workshop
“Spectral Unmixing Methods for the
Characterization of Non-Resolved Space Objects.” PRET Annual Review Maui
High Performance Computing Center,
“Periodic: Simulation Software and its Application to Iris Recognition.” Third 2005 ARDA Advanced Imaging Workshop, Oak Ridge National Lab, Oak Ridge, TN, October 2005.
“Optimal Restoration Strategies for Iris
Recognition of Blurred Imagery.” Optical Society of
Plemmons,
Robert J.
Presentations:
“Array Imaging
for Superresolution.” International Conference on Superresolution Imaging,
August 2005.
“The PERIODIC
System for High Resolution and Low Profile Imaging.” Optical Society of
GA, October 2005.
“Nonnegative Matrix Factorization
and Applications.” Technion Workshop on Data Mining,
“Some Computational Issues in
Spectral Imaging.”
“Low-Rank Nonnegative Factorizations
for Spectral Imaging Applications.” Stanford Workshop on Algorithms for Modern
Massive Data Sets,
Papers
and Presentations:
“Optimizing Phase
Masks for Iris Recognition.” Optical Society of
“Algorithms and Theory for
Nonnegative Matrix Factorizations in Data Mining.” International Conference on
Computational Statistics,
Thomas,
Stan J.
None
Torgersen,
Todd C.
Presentation: “A Proposed Alternative to Seeding for Source
Separation using Non-negative Matrix
Factorization,”
given at 2006 PRET Program Review, Jan. 16-18, 2006,
Workshops:
Participant
in the PERIODIC project’s Third Workshop on Advanced Imaging, held October
11-13, 2005, at Oak Ridge National Labs (ORNL).
The PERIODIC project includes a series of funded workshops held at
ORNL. Participation is by invitation
only.
Participant
in the PERIODIC project’s Fourth Workshop on Advanced Imaging, held February
22-24, 2006, at Oak Ridge National Labs (ORNL).
Participant
in the PERIODIC project’s Fifth Workshop on Advanced Imaging, held June 28-30,
2006, at Oak Ridge National Labs (ORNL).
Turkett,
William H.
None
Wong,
Yue-Ling
Presentation: "Designing Digital Media Curriculum
- Challenges and Learning Principles.” AACE SITE Conference,
III. Editorships, Offices, and Consultancies
Burg,
Jennifer J.
The IMEJ of Computer-Enhanced Learning, which ceased publication in January 2006
Member
of the Board of the International Digital Media and Arts Association
Cañas,
Daniel A.
Editorial
Board, International Journal of Information and Computer Security.
Refereed
papers for International Journal of Information and Computer Security.
Fetrow, Jacquelyn S.
Editorial
Board Service for journal: Proteins: Structure, Function and Bioinformatics,
manuscript
manager and editor.
Guest
editor for special issue of Proteins:
Structure, Function and Bioinformatics in honor
of
George Rose (with Professor Trevor Creamer,
Board of Advisors, Aqualutions,
Board of Directors, Quantum Bio,
Responsibilities: Participate in monthly Board meetings with senior management and other Board
members (several hours per month)
Fulp,
Errin W.
Research and Development Advisor for GreatWall Systems, consulted one day each week from September to current.
Computer Security Researcher (responsible for research group consisting of 1 graduate and 2 undergraduate students), Cyber-Security Group, Department of Energy Pacific Northwest National Laboratories, Richland, Washington, May 31 – August 10, 2005.
John,
David J.
None
Pauca, V. Paúl
Co-Chair, Advanced
Signal Processing Algorithms, Architectures, and Implementations XVI
Conference, International Symposium on Optical Science and Technology, the SPIE
51th Annual Meeting, to be held in San Diego, CA, August, 2006.
Program Co-Chair, ACMSE 2007, 45th ACM
Southeast Conference, to be held in
Program Committee Member, V Jornadas Peruanas de Computation 2006 – V JPC 2006, to be held in
Consultant, Disruptive Technologies Office, for research work for the PERIODIC Advanced Imaging Project, during May through August of 2006.
Consultant, Army Research Laboratory / University of New Mexico (UNM), for research work with Dr. S. Prasad (UNM) for the Army's Advanced Sensors Collaborative Technology Alliance.
Plemmons,
Robert J.
Advisory
Editor, Linear Algebra and Applications
Editorial
Board, Electronic Transactions on Numerical Analysis
Editorial
Board, Applied and Computational Control, Signals, and Circuits
Section
Committee Chair, Society for Industrial and Applied Mathematics
Referee for OSA,
Consultant, Army Research Laboratory, Adelphi, MD, “Sparse Representation and Compressed Sensing of Image Date,” 16 days per year
Thomas,
Stan J.
Independent Expert –
Torgersen,
Todd C.
U. T. Battelle, LLC for the Department of Energy,
194.4 hours, April 1, 2006, to Sept. 30, 2006
Turkett, William H.
None
Wong,
Yue-Ling
None
Burg,
Jennifer J.
None
Cañas, Daniel A.
None
Fetrow,
Jacquelyn S.
$1,073,242 for 4 years Algebraic and Statistical Models of Redox Signaling (PI),
NIH-NIGMS 1R01
($268,179 for year 1) GM075304
$242,320 for 2 years Profiling
of Redox-Sensitive Signaling Proteins (co-Investigator), NIH-NCI ($121,458 for
year 1) 1R21 CA112145
$507,157 for 3 years Integrated
process for functional site feature analysis (PI), NSF MCB-0517343
($168,390 for year 1)
Fulp,
Errin W.
$26,609 Managing the CyberCIEGE Internship
Program at
Laboratory
$99,731 Integrated Scalable Parallel Firewall and Intrusion Detection System for High-Speed Networks, Department of Energy
John,
David J.
$1,073,242 for 4 years Algebraic and Statistical Models of Redox Signaling (co-Investigator),
NIH-
$268,179 for year 1 NIGMS
1R01 GM075304
Pauca, V. Paúl
$80,000 Enhanced
Iris Recognition Systems for Personal Identification, Army Research Office
$82,743 Innovative
Methods for High Resolution Imaging and Feature Extraction (co-PI), Army
Research Office
Plemmons,
Robert J.
$65,000 Space
Situational Awareness – Research at
$80,000 Novel
Integrated Optical Systems for Iris Recognition (co-PI), CIA funding through
DynCorp, Inc., February 2006
$82,743 Innovative
Methods for High Resolution Imaging and Feature Extraction (co-PI), Army
Research Office
Thomas,
Stan J.
$1,073,245 for 4 years Algebraic and Statistical Models of
Redox Signaling, (co-Investigator), NIH-
$268,179 for year 1 NIGMS 1R01 GM075304
$11,250 A Consortium
to Promote Computational Science and High Performance
Computing,
Subcontract to Appalachian
Torgersen,
Todd C.
$82,743 Innovative
Methods for High Resolution Imaging and Feature Extraction (PI), Army Research
Office
Turkett, William H.
None
Wong,
Yue-Ling
None
V. Awards
for Distinguished Teaching, Research, or Professional Activities
Burg, Jennifer J.
None
Cañas,
Daniel A.
None
Fetrow,
Jacquelyn S.
Innovative Teaching Award (for Bioinformatics course, developed with David John), Center for Teaching
and Learning,
Fulp,
Errin W.
Nominated for the Reid-Doyle Prize for excellence in teaching, 2006
John,
David J.
Innovative Teaching Award (for Bioinformatics course, developed with Jacquelyn Fetrow), Center for Teaching
and Learning,
Pauca,
V. Paúl
The AT&T Faculty Fund Fellowship for the Spring semester 2006, by the Department of Computer Science
Plemmons,
Robert J.
None
Thomas,
Stan J.
None
Torgersen,
Todd C.
None
Turkett,
William H.
None
Wong,
Yue-Ling
None