Wake Forest University

Summary of Professional Activity and Publications

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

IV.  External Grants Received

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., Berry, M., and Plemmons, R. J.) “Document Clustering using Nonnegative Matrix Factorization.'' Information Processing & Management, Vol. 42, pp. 373-386, January 2006.

 

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., Berry, M., and Pauca, P.) “Document Clustering using Nonnegative Matrix Factorization.” Information Processing and Management, Vol. 42, pp. 373-386, January 2006.


 

(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, Houston, TX.

 

"Curriculum Material for Teaching Digital Media as Computer Science," poster session at SIGCSE 2006,  March 2, 2006, Houston, TX.

 

"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, Melbourne, FL.

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

Paper: (with John, D. J.) “Bioinformatics and Computing Curriculum: A New Model for Interdisciplinary Courses.” SIGSCE 2006, Houston,TX, March 2006.

 

Invited Conference Presentations:

21st Annual Perspectives in Biology Symposium, Nov. 11-12, 2005, Wake Forest University.

 

Winston-Salem Technology Council Speaker Series, Oct. 27, 2005.

 

The Protein Society 19th Symposium. Systems Biology Workshop for Educators, July 30-August 3, 2005, Boston, MA.

 

Invited Seminars:

University of Delaware, April 24, 2006.

 

Fulp, Errin W.

 

Papers:

“Improving the Performance of Firewalls and Intrusion Protection Systems for High-Speed Networks.”  Department of Computer Science Colloquium, North Carolina State University, 2006.

 

“Security Issues for the Next Generation of Network.” Department of Computer Science Seminar, Old Dominion University, 2005.

 

"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), Richland, Washington, 2005.

 

John, David J.

 

Paper: (with Fetrow, Jacquelyn S.) “Bioinformatics and Computing Curriculum:  A New Model for Interdisciplinary Courses.” SIGCSE 2006, Houston, Texas, March 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 – Wake Forest University, May 11, 2006.

 

Presentations:

“Advancements in the Reconstruction of PERIODIC Iris Imagery.” Fourth 2005 ARDA/DTO Advanced Imaging Workshop Oak Ridge National Lab, Oak Ridge, TN, February 2006.

 

“Spectral Unmixing Methods for the Characterization of Non-Resolved Space Objects.” PRET Annual Review Maui High Performance Computing Center, Maui, HI, January 2006.

 

“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 America Annual Meeting, November, 2005.

 

Plemmons, Robert J.

 

Presentations:

“Array Imaging for Superresolution.” International Conference on Superresolution Imaging, Hong Kong, China,

August 2005.

 

“The PERIODIC System for High Resolution and Low Profile Imaging.” Optical Society of America, Atlanta,

GA, October 2005.

 

“Nonnegative Matrix Factorization and Applications.” Technion Workshop on Data Mining, Haifa, Israel, December 2005.

 

“Some Computational Issues in Spectral Imaging.”  SIAM Conference on Imaging Science, Minneapolis, MN, May 2006.

 

“Low-Rank Nonnegative Factorizations for Spectral Imaging Applications.” Stanford Workshop on Algorithms for Modern Massive Data Sets, Palo Alto, CA, June 2006.


 

Papers and Presentations:

“Optimizing Phase Masks for Iris Recognition.” Optical Society of America, Charlotte, NC, July 2005.

 

“Algorithms and Theory for Nonnegative Matrix Factorizations in Data Mining.” International Conference on Computational Statistics, Limassol, Cyprus, October 2005.

 

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, Kihei, HI.

 

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, Orlando, FL, March 2006.

 

 

 


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, University of Kentucky).

 

Board of Advisors, Aqualutions, Winston-Salem, NC (student-initiated startup company; several hours per quarter).

 

Board of Directors, Quantum Bio, State College, PA

            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 Winston-Salem, NC, March 2007.

 

Program Committee Member, V Jornadas Peruanas de Computation 2006 – V JPC 2006, to be held in

Arequipa, Peru, 26-30 June 2006.

 

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, SPIE, SIAM, and IEEE journals

 

Chair, SIAM Section Committee, and Representative to Section Conferences

 

Consultant, Army Research Laboratory, Adelphi, MD, “Sparse Representation and Compressed Sensing of Image Date,” 16 days per year

 

Thomas, Stan J.

 

Independent Expert – Superior Court of North Carolina, Complex Business Case Division

 

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

 

 


IV.  External Grants Received

 

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 Pacific Northwest National

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 Air Force Maui Space Center, AFOSR – Subcontract from UNM, January 2006

 

$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 State University

 

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, Wake Forest University, February 2006

 

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, Wake Forest University, February 2006

 

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