Wake Forest University

Summary of Professional Activity and Publications

DEPARTMENT OF COMPUTER SCIENCE

July 1, 2006 - June 30, 2007

 

 

I.    Publications, Performances, Exhibits

II.   Papers and Presentations Presented at Professional Meetings

III.  Editorships, Offices, and Consultancies

IV.  External Grants Received

 

 

I.  Publications, Performances, Exhibits

 

Burg, Jennifer J.

 

None

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

(with Baxter, S. M., Day, S. W., and Reisinger, S. J.) “Scientific software development is not an oxymoron.”

PLoS Comput. Biol. 2006 Sep 8;2(9):e87.

 

“Active site profiling to identify protein functional sites in sequences and structures.” Current Protocols in Bioinformatics. [A. D. Baxevanis (chief editor); G. A. Petsko; L. D. Stein; G. D. Stormo; J. R. Yates III (guest editor); D. B. Davison (advisory editor)]; John Wiley and Sons, Inc. Unit 8.10, June 2006.

 

(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 May 1;63(2):268-72.

 

(with Budiman, M. E., Knaggs, M. H., and Alexander, R.W.) “Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.”  Proteins: Struct. Funct. Bioinform. 2007 in press.

 

(with Allen, E. E., Diao, L., John, D. J., Loeser, R. F. Jr., and Poole, L. B.) “The shuffle index and evaluation of models of signal transduction pathways.” Proceedings of the 45th ACM Southeast Regional Conference, Winston-Salem, NC.  March 2007, p. 250-255.  http://doi.acm.org/10.1145/1233341.1233386.

 

(with Olex, A. L., John, D. J., and Hiltbold, E. M.) “Additional limitations of the clustering validation method figure of merit.” Proceedings of the 45th ACM Southeast Regional Conference, Winston-Salem, NC.  March 2007.

 

(with Pryor, E. E., Jr.) “PDBSQL: A Storage Engine for Macromolecular Data.” Proceedings of the 45th ACM Southeast Regional Conference, Winston-Salem, NC.  March 2007.

 

(with Knaggs, M. H., Salsbury, F. R., and Edgell, M. H.) “Insights into CheY relaxation and relaxation derived from molecular dynamics simulations.”  Biophys. J.  2006 Dec. 15 [Epub ahead of print].

 

(with John, D. J.) “Bioinformatics and computing curriculum.  A new model for interdisciplinary courses.”

Inroads—SIGCSE Bulletin.  2006. 38:185-190. 

 

Fulp, Errin W.

 

(with LaMarche, B. L., Hopkins, D. F, Hughes, C. O., and McKenna, T.) “A Network Layer for Teleoperations in High Speed Environments.” Proceedings of the IEEE INFOCOM, High Speed Networking Workshop, 2007.

 

(with Wheeler, Patrick) “A Taxonomy of Parallel Techniques for Intrusion Detection.” Proceedings of the ACM Southeast Conference Special Session on Computer Security, 2007.

 

“An Independent Function-Parallel Firewall Architecture for High-Speed Networks” (short paper).  Proceedings of the International Conference on Information and Communications Security, 2006.

 

(with Horvath, Michael R., and Kopek, Christopher C.)  “Managing Security Policies for High-Speed Function Parallel Firewalls.”  Proceedings of the SPIE International Symposium on High Capacity Optical Networks and Enabling Technology, 2006.

 

John, David J.

 

(with Olex, A., Hiltbold, E., and Fetrow, J.) “Additional limitations of the clustering validation method Figure of Merit.” Proceedings of the 45th Southeast ACM Conference, ACM Press, 2007, pp. 238-243.

 

(with Allen, E., Diao, L., Fetrow, J., Loeser, R., and Poole, L.) “The Shuffle Index and Evaluation of Models of Signal Transduction Pathways.” Proceedings of the 45th Southeast ACM Conference, ACM Press, 2007, pp. 250-255.

 

Pauca, V. Paúl

 

(with Piper, J., and Plemmons, R.) “Nonnegative Matrix Factorization for Spectral Data Analysis.” Lin. Alg. and its Applic., Vol. 416, No. 1, pp. 29-47, July 2006.

 

(with Barnard, R., Plemmons, R. J., Torgersen, T. C., Prasad, S., van der Gracht, J., Nagy, J., Chung, J., Behrmann, G., Mathews, S., and Mirotznik, M.) “High-Resolution Iris Image Reconstruction from Low-Resolution Imagery.”  Proceedings SPIE, Advanced Signal Processing Algorithms, Architectures, and Implementations XVI, Vol. 6313, pp. D1-D13, San Diego, CA, Aug. 2006.

 

(with Torgersen, T., Prasad, S., Mathews, S., Mirotznik, M., Barnard, R., Gray, B., Plemmons, R., van der Gracht, J., and Behrmann, G.) “PERIODIC: Integrated Computational Array Imaging Technology.”  OSA Technical Digest, Conference on Computational Optical Sensing and Imaging (COSI), Vancouver, June 2007.

 

Plemmons, Robert J.

 

(with Pauca, P., and Piper, J.) “Nonnegative Matrix Factorization for Spectral Data Analysis.” Lin. Alg. and its Applic., Vol. 416, No. 1, pp. 29-47, July 2006.

 

“Inverse Problems in Atmospheric Imaging.” Computer Mathematics and Applications: Advances and Development., Edited by E. Lipitakis, LEA Press, Athens, Greece, pp. 195-204, 2006.

 

(with Ng, M.) “Blind Deconvolution and Structured Matrix Computations with Applications to Array Imaging.” 46-page chapter in Blind Image Deconvolution: Theory and Applications. Edited by P. Campisi and K. Egiazarian, CRC Press, 2007.

 

(with Barnard, R., Pauca, V. P., Torgersen, T. C., Prasad, S., van der Gracht, J., Nagy, J., Chung, J., Behrmann, G., Mathews, S., and Mirotznik, M.) “High-Resolution Iris Image Reconstruction from Low-Resolution Imagery.”  Proceedings SPIE, Advanced Signal Processing Algorithms, Architectures, and Implementations XVI, Vol. 6313, pp. D1-D13, San Diego, CA, Aug. 2006.

 

(with Torgersen, T., Prasad, S., Mathews, S., Mirotznik, M., Barnard, R., Gray, B., Pauca, V., van der Gracht, J., and Behrmann, G.) “PERIODIC: Integrated Computational Array Imaging Technology.”  OSA Technical Digest, Conference on Computational Optical Sensing and Imaging (COSI), Vancouver, June 2007.

 

Thomas, Stan J.

 

None

 

Torgersen, Todd C.

 

(with Barnard, R., Pauca, V. P., Plemmons, R. J., Prasad, S., van der Gracht, J., Nagy, J., Chung, J., Behrmann, G., Mathews, S., and Mirotznik, M.) “High-Resolution Iris Image Reconstruction from Low-Resolution Imagery.”  Proceedings SPIE, Advanced Signal Processing Algorithms, Architectures, and Implementations XVI, Vol. 6313, pp. D1-D13, San Diego, CA, Aug. 2006.

 

(with Plemmons, R., Prasad, S., Mathews, S., Mirotznik, M., Barnard, R., Gray, B., Pauca, V., van der Gracht, J., and Behrmann, G.) “PERIODIC: Integrated Computational Array Imaging Technology.”  OSA Technical Digest, Conference on Computational Optical Sensing and Imaging (COSI), Vancouver, June 2007.

 

Turkett, William H.

 

“Dynamic DDN Construction for Lightweight Planning Architectures.”  Proceedings of the 20th International FLAIRS Conference (FLAIRS 2007), pp. 158-163.

 

Wong, Yue-Ling

 

None

 

II.  Papers and Presentations Presented at Professional Meetings

 

Burg, Jennifer J.

 

Presentations:

“Interdisciplinary Digital Media Course and Curriculum Development,” the International Digital Media and Arts Conference, San Diego, CA, October 2006.

 

“The Love Song of J. Alfred Prufrock:  A Video Interpretation,” Center for Design Innovation, April 2007.

 

Poster presentation:  “Revitalizing Computer Science Education by Teaching Digital Media as Science,” SIGCSE 2007, Covington, KY, March 2007.

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

Invited Conference Presentations:

Thiol-based Redox Regulation Gordon Research Conference, speaker and session chair, June 18-23, 2006, Biddeford, ME.          

 

ACMSE 2007, April 23-24, 2007, two students presented papers describing research done in collaboration with me.

 

Invited Seminars:

 

Cell and Molecular Biology Lunch Discussion Group (Biology Dept.):  speaker, April 2007.

 

Wake Forest Institute for Regenerative Medicine seminar series: speaker, February 7, 2007.

 

Wake Forest Medical School Cancer Center weekly forum: speaker, February 23, 2007.

 

University of Richmond seminar series: speaker, Sept. 18, 2006.

 

Fulp, Errin W.

 

Invited presentation:  “Techniques for Improving the Performance of Signature-Based Network IDS,” 2006.  DOE Pacific Northwest National Laboratory, Cyber Security Group Seminar.

 

Presentation: ICICS ’06, “SPIE High Speed Networks,” 2006. ACM Southeastern Conference Special Session on Computer Security, IEEE INFOCOM Workshop on High-Speed Networks 2007.

 


John, David J.

 

Presentations:

(with Allen, E.) “Proteomic Network Consensus Modeling Over Multiple Discretizations (I & II).”  DIMACS DREAM Conference, Wave Hill Conference Center, NY, NY, September 7-8, 2006.

 

(with Norris, J.) “Modeling signaling pathways in chondrocytes (Introduction to Continuous Bayesian Modeling).” SCB Discussion Group, Winston-Salem, NC, October 23, 2006.

 

(with Allen, E., Poole, L., Loeser, R., and Fetrow, J.) “The Role of Discretization in Modeling Signal Transduction Networks.” ISCB Rocky ’06, Snowmass, CO, December 1-3, 2006.

 

(with Norris, J.) “Metropolis-Hastings Algorithm and Multiple Regression for Finding Next-State Models for Proteomic Modification.”  Atlantic Coast Conference on Mathematics in the Life and Biological Sciences, Virginia Tech, May 3-5, 2007.

 

Pauca, V. Paúl

 

Poster Presentations:

(with Zhang, Q., and Plemmons, R.) “Spectral Unmixing Using Nonnegative Tensor Factorization.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

(with Abraham, Y., Torgersen, T., Schmitt, J., and Harris, R.) “Automating the Development of Quantum Computational Software.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

(with Barnard, R., Gray, B., Torgersen, T., Mirotznik, M., van der Gracht, J., Plemmons, R., Behrmann, G., Mathews, S., and Prasad, S.)  “PERIODIC: State-of-the-Art Array Imaging Technology.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

Plemmons, Robert J.

 

Invited Presentations:

“Nonnegative Matrix Factorization and Applications.” International Conference on Nonnegative Matrices, Maynooth, Ireland, July 2006.

 

“Tensor Methods in Spectral Imaging.”  International Conference on Applied Linear Algebra, Amsterdam,

The Netherlands, July 2006.

 

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

 

“Spectral Unmixing for Object Identification.”  SIAM Southeast Asia Conference, Sapporo, Japan, July 2006.

 

“Nonnegative Tensor Factorization.”  National Institute for Statistical Sciences, Cary, NC, February 2007.

 

“PERIODIC: State of the art in Array Imaging.”  OSA meeting on Computational Optical Sensing and Imaging, Vancouver, BC, Canada, June 2007.

 

Presentations:

“Tensor Factorization Methods for EEG Analysis.”  Riken Brain Science Institute, Tokyo, Japan, July 2006.

 

“PERIODIC: State-of-the-Art Array Imaging.”  PERIODIC Phase I Demonstration for the Department of Defense and the Intelligence Agencies, McLean, VA, December 2006.

 

“Spectral Diversity for the PERIODIC Camera.”  Disruptive Technology Office Workshop, Washington, DC,

March 2007.

 

(with Zhang, Q., and Pauca, V.) “Spectral Unmixing Using Nonnegative Tensor Factorization.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

“Burn Assessment Clinical Trials.”  PERIODIC-Montagne PI Review, Falls Church, VA, May 2007.

 

 (with Barnard, R., Gray, B., Pauca, V., Mirotznik, M., van der Gracht, J., Torgersen, T., Behrmann G., Mathews, S., and Prasad, S.)  “PERIODIC: State-of-the-Art Array Imaging Technology.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

Thomas, Stan J.

 

None

 

Torgersen, Todd C.

 

Poster Presentations:

(with Pauca, V., Abraham, Y., Schmitt, J., and Harris, R.) “Automating the Development of Quantum Computational Software.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

(with Barnard, R., Gray, B., Pauca, V., Mirotznik, M., van der Gracht, J., Plemmons, R., Behrmann G., Mathews, S., and Prasad, S.)  “PERIODIC: State-of-the-Art Array Imaging Technology.”  Proceedings 2007 ACM Southeast Conference, Mar. 2007.

 

Presentation: (with Tyler, David) “Object and regularization dependence on Zernike estimation in phase diverse speckle imaging.”  Presented at the 2007 PRET Final Review meeting, Jan. 29-31, 2007, Kihei, HI.

 

Turkett, William H.

 

Presentation: “Dynamic DDN Construction for Lightweight Planning Architectures.”  20th International FLAIRS Conference (FLAIRS 2007), May 8, 2007, Key West, Florida.

 

Poster presentation:  “Evaluating Bayesian network structure learning approaches to biological modeling.”  Ohio State University Mathematical Biosciences Institute Workshop for Young Researchers in Mathematical Biology, March 14, 2007, Columbus, Ohio. 

 

Wong, Yue-Ling

 

None

 

 
III.  Editorships, Offices, and Consultancies

 

Burg, Jennifer J.

 

Board Member, International Digital Media and Arts Association

 

Cañas, Daniel A.

 

Editorial & Advisory Board, International Journal of Information and Computer Security

 

Program Committee, ACMSE 2007 Regional Conference

 

Referee for ACMSE 2007

 

Fetrow, Jacquelyn S.

 

Editorial Board for journal:  Proteins:  Structure, Function and Bioinformatics, regular reviewer and editorial manager for papers submitted to this journal

 

Program committee (reviewed submitted papers for presentation at conference), Intelligent Systems for Molecular Biology/European Conf. Comput. Biology International Conference

 

Nominated to candidacy for the International Protein Society Executive Council (April 2007)

 

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

 

Board of Directors, Quantum Bio, State College, PA

 

Fulp, Errin W.

 

Research and Development Advisor for GreatWall Systems, consulted one day each week from September to current.

 

Computer Network Researcher, Department of Energy Pacific Northwest National Laboratories, Richland, Washington, July 2006 to present.

 

John, David J.

 

None

 

Pauca, V. Paúl

 

Editor, Proceedings of the 45th Annual ACM Southeast Meeting, March 2007

 

Co-Chair, Advanced Signal Processing Algorithms, Architectures, and Implementations XVI Conference, International Symposium on Optical Science and Technology, the SPIE 51st Annual Meeting, San Diego, CA, August 2006

 

Conference Program Co-Chair, ACMSE 2007, 45th ACM Southeast Conference, Winston-Salem, NC, March 2007

 

Consultant, Disruptive Technologies Office, for research work for the PERIODIC Advanced Imaging Project, during May through August 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, ended December 2006

 

Plemmons, Robert J.

 

Editorial Board, Electronic Transactions on Numerical Analysis

 

Chair of Section Committee, SIAM

 

Thomas, Stan J.

 

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

 

Torgersen, Todd C.

 

UT Battelle, LLC.  One month distributed over summer and fall 2007.

 

Turkett, William H.

 

None

 

Wong, Yue-Ling

 

None

 

IV.  External Grants Received

 

Burg, Jennifer J.

 

None

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

$1,073,245 for 4 years Algebraic and Statistical Models of Redox Signaling (PI), NIH-NIGMS 1R01

($262,342 for year 2) GM075304

 

$242,342 for 2 years                Profiling of Redox-Sensitive Signaling Proteins (co-Investigator), NIH-NCI ($100,000 for year 2) 1R21 CA112145

 

$507,157 for 3 years                Integrated process for functional site feature analysis (PI), NSF MCB-0517343

($170,967 for year 2)                 

 

$41,360                                   Integrin function in cartilage (consultant), NIH-NIAMS  (funded; award letter in

                                                process)

 

Fulp, Errin W.

 

None

 

John, David J.

 

$1,073,245 for 4 years Algebraic and Statistical Models of Redox Signaling (co-Investigator),

($262,342 for year 2) NIH-NIGMS 1R01 GM075304

 

Pauca, V. Paúl           

 

$80,000                                   Systematic Development of Quantum Computational Software, North Carolina

                                                Biotechnology Center

 

$80,000                                   Enhanced Iris Recognition Systems for Personal Identification, Army Research

                                                Office

 

$16,000                                   Computational Methods for Quantum Molecular Dynamics, Targacept, Inc.

 

Plemmons, Robert J.

 

$62,026                                   Array Imaging, DTO supplement to ARO grant

 

$15,000                                   Space Situational Awareness, AFOSR supplement to subcontract from UNM

 

$112,849                                 PERIODIC Camera Development, DTO/Rosettex/UNM

 

Thomas, Stan J.

 

$1,073,245 for 4 years Algebraic and Statistical Models of Redox Signaling (co-Investigator),

($262,342 for year 2) NIH-NIGMS 1R01 GM075304

 

Torgersen, Todd C.

 

$84,926 for Jan. 2007 to Innovative Methods for High Resolution Imaging and Feature Extraction, ARO

Jan. 4, 2008

 

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.

 

None

 

Fulp, Errin W.

 

Awarded the 2007 Wake Forest Reid-Doyle Prize for excellence in teaching.

 

John, David J.

 

None

 

Pauca, V. Paúl

 

None

 

Plemmons, Robert J.

 

None

 

Thomas, Stan J.

 

None

 

Torgersen, Todd C.

 

None

 

Turkett, William H.

 

None

 

Wong, Yue-Ling

 

None