Wake Forest University

Summary of Professional Activity and Publications

DEPARTMENT OF COMPUTER SCIENCE

July 1, 2004 - June 30, 2005

 

 

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.

 

Collaboration with the Alban Elved Dance Company,  "Une Journée Abstraite" – a blend of dance, poetry, music, and digital media introducing concepts of computer science and machine computation.  December 1-4, 2004, Scales Fine Arts Auditorium.  See my web page for details  (www.cs.wfu.edu/~burg).  Poetry and projections are linked from the web pages.

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

(with Allen, E. E., John, D. J., Thomas, S. J.) “Heuristics for Dependency Conjectures in Proteomic Signaling Pathways.” Proceedings of the 43rd Annual Association for Computing Machinery Southeast Conference (Victor A. Clincy, ed.), Kennesaw, Georgia, March 2005. (peer-reviewed)

 

Fulp, Errin W.

 

(with Tarsa, Stephen J.) “Network Firewall Policy Representation using Ordered Sets and Tries.” Proceedings of the IEEE International Symposium on Computer Communications, 2005.

 

(with Antrosio, Joseph V.) “Malware Defense Using Network Security Authentication." Proceedings of the Third IEEE International Information Assurance Workshop, 2005.

“Middleware-based connection management for QoS-enabled networks.” SPIE Information and Technology Communication Symposium (special session on multimedia communications), Oct 2004.


John, David J.

 

(with Allen, E. E., Fetrow, Jacquelyn S., Thomas, S. J.) “Heuristics for Dependency Conjectures in Proteomic Signaling Pathways.” Proceedings of the 43rd Annual Association for Computing Machinery Southeast Conference (Victor A. Clincy, ed.), Kennesaw, Georgia, March 2005. (peer-reviewed)

 

(with Francel, Margaret) “Constructing an even grammar from a 2-element sample.” Proceedings of the 43rd Southeast ACM Conference, ACM Press, 2005, pages 69-74.

 

Miller, Timothy E.

 

NOTE:  These are the publications of the PHENIX collaboration, of which I am a participating member.  I have worked on this experiment helping to collect the data and support the operations of the detector.  As is the standard practice of my field (high energy physics), I am listed as an author on these papers (one of about 450 authors) as I have contributed time and effort to the data analyzed in them.  However, I feel compelled to clearly delineate that I am not primary author of the papers presented below.

 

(with Adler, S. S., et al.)  “Centrality dependence of direct photon production in GeV Au + Au collisions.”  Submitted to Phys Rev Lett.  http://www.arxiv.org/ e-Print Archive:  nucl-ex/0503003.

 

(with Adler, S. S., et al.)  “Measurement of single electron event anisotropy in Au + Au collisions at GeV.”  Submitted to Phys Rev C.  e-Print Archive:  nucl-ex/0502009.

 

(with Adler, S. S., et al.)  “Mid-rapidity direct-photon production in p+p collisions at GeV.” 

Phys Rev D71, 071102 (2005).

 

(with Adler, S. S., et al.)  “Nuclear modification factors for hadrons at forward and backward rapidities in deuteron-gold collisions at GeV.”  Phys Rev Lett 94, 082302 (2005).

 

(with Adler, S. S., et al.) “Saturation of azimuthal anisotropy in Au + Au collisions at GeV to 200 GeV.”  Submitted to Phys Rev Lett.  e-Print Archive: nucl-ex/0411040.

 

(with Adler, S. S., et al.)  “Production of Phi mesons at mid-rapidity in GeV Au + Au collisions at RHIC.”  Submitted to Phys Rev C.  e-Print Archive: nucl-ex/0410012.

 

(with Adler, S. S., et al.) “Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC:  Experimental evaluation by the PHENIX collaboration.”  Accepted for publication in Nucl Phys A.  e-Print Archive:  nucl-ex/0410003.

 

(with Adler, S. S., et al.)  “Centrality dependence of charm production from single electrons measurement in Au + Au collisions at GeV.”  Phys Rev Lett 94, 082301 (2005).

 

(with Adler, S. S., et al.)  “Systematic studies of the centrality and dependence of the  and  in heavy ion collisions at mid-rapidity.”  Phys Rev C71, 034908 (2005).  e-Print Archive:

nucl-ex/0409015.

 

(with Adler, S. S., et al.)  “Jet structure of baryon excess in Au + Au collisions at GeV.”  Submitted to Phys Rev Lett.  e-Print Archive: nucl-ex/0408007.

 

(with Adler, S. S., et al.)  “Deuteron and antideuteron production in Au + Au collisions at GeV.”  Phys Rev Lett 94, 122302 (2005).

 

(with Adler, S. S., et al.)  “Double helicity asymmetry in inclusive mid-rapidity 0 production for polarized p+p collisions at GeV.”  Phys Rev Lett 93, 202002 (2004)

 

(with Adler, S. S., et al.) “Bose-Einstein correlations of charged pion pairs in Au+Au collisions at GeV.”  Phys Rev Lett 93, 152302 (2004)

 

(with Adler, S. S., et al.)  “Measurement of non-random event-by-event fluctuations of average transverse momentum in GeV Au+Au and p+p collisions.”  Phys Rev Lett 93, 092301 (2004)

 

Pauca, V. Paúl

 

(invited) (with Prasad, S., Torgersen, T. C., Plemmons, R. J.,  van der Gracht, J.)  “High-Resolution Imaging Using Integrated Optical Systems.” Int. Journal on Imaging Systems and Technology, Vol. 14, No. 2, pp. 67-74, (2004).

 

(with Piper, J., Plemmons, R., and Giffin M.) “Object Characterization from Spectral Data Using Nonnegative Matrix Factorization and Information Theory.” AMOS Technical Conference, Maui, HI, September, 2004.

 

(with van der Gracht, J., Setty, H., Narayanswamy, R., Plemmons, R. J., Prasad, S., and Torgersen, T.) “Iris Recognition with Enhanced Depth-of-Field Image Acquisition.” Proceedings of the SPIE Defense and Homeland Security Symposium, Vol. 5358, Orlando, FL, (2004).

 

(with Plemmons, R. J., Giffin, M., and Hamada, K.) “Mining Scientific Data for Non-Imaging Identification and Classification of Space Objects.” AMOS Technical Conference, Maui, HI, September, 2004.

 

(with Prasad, S., Plemmons, R. J., Torgersen, T. C., and van der Gracht, J.) “Pupil-Phase Optimization for Extended-Focus Aberration-Corrected Imaging Systems.” Proceedings of SPIE, Advanced Signal Processing Algorithms, Architectures, and Implementations XIV, Vol. 5559, pp. 335-345, (2004).

 

(with Plemmons, R. J., Horvath, M. E., Leonhardt, E. N., Prasad, S., Robinson, S., Setty, H., Torgersen, T. C., van der Gracht, J., Dowski, E., Narayanswamy, R., and  Silveira, P. E. X.) “Computational Imaging Systems for Iris Recognition.” Proceedings of SPIE, Advanced Signal Processing Algorithms, Architectures, and Implementations XIV, Vol. 5559, pp. 346-357, (2004).

 

Plemmons, Robert J.

 

(with Prasad, S., Torgersen, T., Pauca, P., and van der Gracht, J.) “High-Resolution Imaging Using Integrated Optical Systems.” invited paper for the International Journal of Imaging Systems and Technology, Vol. 14,

no. 2, pp. 67-75, August 2004.

 

(with Catral, M., Han, Lixing, and Neumann, Michael) “On Reduced Rank Nonnegative Matrix Factorization for Symmetric Matrices.” Linear Algebra and Applications, Vol. 393, pp. 107-126, December 2004.

 

(with Horvath, M., Leonhardt, E., Pauca, P., Prasad, S., Robinson, S., Setty, H., Torgersen, T., van der Gracht, J., Dowski, E., Narayanswamy, R., and Silveira, P.) “Computational Imaging Systems for Iris Recognition.” Proceedings of SPIE 49th Annual Meeting, Vol. 5559, pp. 346-357, August 2004.

 

(with Pauca, P., Giffin, M., and Hamada, K.) “Unmixing Spectral Data using Independent Component Analysis and Non-Negative Matrix Factorization.” Proceedings of AMOS Technical Conference, Maui, HI, September 2004, on CD.

 

(with Prasad, S., Pauca, V. P., Torgersen, T. C., and van der Gracht, J.) “Pupil-phase Optimization for Extended Focus, Aberration-Corrected Imaging System.” Proceedings of SPIE 49th Annual Meeting, Vol. 5559, pp. 335-345, August 2004.

 

(with Piper, J., Pauca, P., and Giffin, M.) “Object Characterization from Spectral Data using Independent Component Analysis and Information Theory.” Proceedings of AMOS Technical Conference, Maui, HI,

September 2004, on CD.

 

(with Chu, M.) “Nonnegative Matrix Factorization and Applications.” invited paper for the Bulletin of the

Internationalinear Algebra Society, to be published May 2005.

 

Thomas, Stan J.

 

(with Allen, E. E., Fetrow, Jacquelyn S., John, D. J.) “Heuristics for Dependency Conjectures in Proteomic Signaling Pathways.” Proceedings of the 43rd Annual Association for Computing Machinery Southeast Conference (Victor A. Clincy, ed.), Kennesaw, Georgia, March 2005. (peer-reviewed)

 

Torgersen, Todd C.

 

(with Prasad, S., Pauca, V. P., Plemmons, R., van der Gracht, J.) “High-Resolution Imaging Using Integrated Optical Systems.” International Journal on Imaging Systems and Technology,  2004.

 

(with Plemmons, Robert, Horvath, Michael, Leonhardt, Emily, Pauca, Paul, Prasad, Sudhakar, Robinson, Stephen, Setty, Harsha, van der Gracht, Joseph, Dowski, Edward, Narayanswamy, Ramkumar, and  Silveira, Paulo E. X.)  “Computational Imaging Systems for Iris Recognition.”  Proceedings of  SPIE Annual Meeting, Denver, July 2004.

 

(with Prasad, S., Pauca, V. P., Plemmons, R. J., and van der Gracht, J.) “Pupil-phase Optimization for Extended-Focus, Aberration-Corrected Imaging Systems.” Proceedings of  SPIE Annual Meeting, Denver, July 2004.

 

Turkett, William H.

 

(with Rose, John R., Oroian, Iulia C., Laegreid, William W, and Keele, John)  2005. “Correlation of amino acid preference and mammalian viral genome type.”  Bioinformatics 21: 1349 - 1357.


Wong, Yue-Ling

 

The Bridge dance production, MainStage at Wake Forest University. Dec. 2-5, 2004.

 

The Sixth Sock dance production, Moving Poets, Charlotte, NC. Dec. 8-19, 2004.


II.  Papers and Presentations Presented at Professional Meetings

 

Burg, Jennifer J.

 

Paper and presentation: (with Miller, Tim) "Cluster Computation in Step with Real-Time Dance:  An Experiment in Art/Science Collaboration." Proceedings of the 17th International Conference on Parallel and Distributed Computing Systems, Sept. 15-17 2004.

 

Presentations:

"Computer Science and Art in Digital Media." iDMAa 2005 (the second annual conference of the International Association of Digital Media and Arts),  March 16, 2005.

 

"A New Publication Model for Open-Access Journals." Given by invitation at the spring 2005 meeting of ANCHASL (Association of North Carolina Health and Sciences Libraries),  April 1, 2005, Wesley Long Community Hospital, Greensboro, North Carolina.

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

Invited Conference Presentations:

Symposium on Computational Methods as Aids in Drug Design, April 3-6, 2005, Virginia Tech European Study Center, Riva san Vitale, Switzerland.

 

National Capital Region Biomedical Engineering and Science Research (Virginia Tech), March 3-4, 2005, Bethesda, MD.

 

Triangle Biophysics Symposium, Nov 3-4, 2004, Chapel Hill, NC.

 

Invited Seminars:

UC San Francisco Women Leaders in Science Seminar Series, Jan 11, 2005.

 

St. Jude’s Children’s Hospital Bioinformatics Seminar Series, Jan 19, 2005.

 

University of Nebraska, Center for Redox Biology Seminar Series, Mar 1, 2005.

 

Fulp, Errin W.

 

Paper: "Optimization of Network Firewalls Policies using Directed Acyclical Graphs." (extended abstract)   Proceedings of the IEEE Internet Management Conference, 2005.

 

Presentations:

“Firewall Architectures for High-Speed Networks.” UltraNet 2004, DOE PI Meeting 2004, DOE FermiLab.

 

 “Firewall Optimization Techniques and Architectures for High-Speed Networks.”  Invited presentation at the DOE Pacific Northwest National Laboratories (Cyber Security Group), Richland Washington.

 

Papers and Presentations:

“Middleware-based connection management for QoS-enabled network.”  SPIE Information and Technology Communication Symposium (special session on multimedia communications), Oct 2004.

 

"Intelligent Malware Defense for Insider Threats in Mobile Networks." (extended abstract)  Proceedings of the U.S. Department of Homeland Security Working Together: Research & Development Partnerships in Homeland Security, 2005. By invitation only - “most innovative and promising research.”

 

John, David J.

 

“Heuristics for Dependency Conjectures in Proteomic Signaling Pathways.” March 18, 2005, ACMSE, Kennesaw, Georgia.

 

(with Allen, Ed) “Dependency modeling of biological signaling networks using computational algebraic algorithms.” October 18, 2004, Structural and Computational BioPhysics Journal Club, Wake Forest University. 

 

Miller, Timothy E.

 

17th International Conference on Parallel and Distributed Computing Systems PDCS-2004 conference.  Paper accepted on the “Fibonacci and Phi” performance titled “Cluster Computation in Step with Real-Time Dance:  An Experiment in Art/Science Collaboration”. 

 

“Grid Computing 101” talk given on 25 May 2004 at the monthly meeting of the Winston-Salem Section of the IEEE.

 

Pauca, V. Paúl

 

Presentations:

“Novel Methods for the Removal of Non-Uniform Blur.” SIAM Southeast Section Meeting, Charleston,

March 2005.

 

“Optical-Digital Approach for Enhanced Biometric Imaging.” SIAM Conference in Computational Science & Engineering, Orlando, February 2005.

 

Paper: “Object Characterization from Spectral Data Using Nonnegative Matrix Factorization and Information Theory.” 2004 AMOS Technical Conference, Maui, September 2004.

 

Plemmons, Robert J.

 

Presentations:

“Low-Rank Nonnegative Matrix Factorization for Spectral Imaging.” International Conference on Imaging Science, Cortona, Italy, September 2004.

 

“Pupil Phase Engineering for Extending the Depth of Focus.” Southeastern Optical Society of America Conference, Charlotte, NC, October 2004.

 

“Nonnegative Matrix Factorizations and Applications.” Haifa Matrix Theory Conference, Haifa, Israel, January 2005.

 

“Computational Imaging Systems for Iris Recognition.” CIA Workshop on Iris Recognition Systems, McLean, VA, February 2005.

 

“High-Resolution Compound Imaging Systems.” ARDA Workshop on Advanced Imaging, Oak Ridge National Laboratory, TN, March 2005.

 

Thomas, Stan J.

 

Paper: (with John, David, Fetrow, Jacquelyn, Allen, Ed) “Heuristics for Dependency Conjectures in Proteomic Signaling Pathways.” Proceedings of ACM-SE/05, March 18-20, 2005, Kennesaw, Georgia.

 

Torgersen, Todd C.

 

Presentation:  “Pupil-Phase Optimization for Improved Imaging System Performance.” Optics in the Southeast 2004, November 4-5, 2004, Charlotte, NC.

 

Turkett, William H.

 

Paper and poster presentation:  (with Rose, John R.) “Exploiting Belief Locality in Run-Time Decision Theoretic Planners.” Proceedings of FLAIRS 2005 (Florida Artificial Intelligence Research Symposium),

May 15-17, 2005.  Accepted as peer-reviewed short paper and poster presentation.

 

Wong, Yue-Ling

 

None

 


III.  Editorships, Offices, and Consultancies

 

Burg, Jennifer J.

 

Editor, The IMEJ of Computer-Enhanced Learning, an interactive multimedia electronic journal published twice a year at Wake Forest University

 

Member of the board of the International Digital Media and Arts Association

 

Cañas, Daniel A.

 

Editorial Board IJICS (International Journal of Information and Computer Security)

 

Fetrow, Jacquelyn S.

 

Editorial Board Service for Professional Journal:  Proteins:  Structure Function and Genetics

Responsibilities:  Serve as editorial manager for manuscripts submitted to journal; serve as reviewer when requested

 

Board of Directors, Quantum Bio, State College, PA

            Responsibilities:  Participate in monthly Board meetings with senior management and other Board

            members

 

Fulp, Errin W.

 

Proposal reviewer for the Department of Energy SBIR program, 2005

 

Proposal reviewer for the Department of Energy Early CAREER program, 2005

 

Computer Security Researcher (responsible for research group consisting of one graduate and two undergraduate students), Cyber-Security Group, Department of Energy Pacific Northwest National Laboratories, Richland Washington, May 31 – August 10, 2005

 

John, David J.

 

None

 

Miller, Timothy E.

 

None

 

Pauca, V. Paúl

 

Co-Chair of the Advanced Signal Processing Algorithms, Architectures, and Implementations XIV Conference, International Symposium on Optical Science and Technology, the SPIE 49th Annual Meeting, Denver, Colorado, August, 2004

 

Served as research consultant with Targacept Inc. during the Summer and Fall of 2004 for a total of 10 days

 

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

 

Boeing Phantom Works, Seattle, WA, two weeks per year

 

Air Force Space Command, one month in summer

 

Thomas, Stan J.

 

None

 

Torgersen, Todd C.

 

None

 

Turkett, William H.

 

None

 

Wong, Yue-Ling

 

Creative Director, IMEJ (Interactive Multimedia Electronic Journal), Wake Forest University

 

 


IV.  External Grants Received

 

Burg, Jennifer J.

 

None

 

Cañas, Daniel A.

 

None

 

Fetrow, Jacquelyn S.

 

$1,073,242 for            Algebraic and Statistical Models of Redox Signaling (PI), NIH-NIGMS 1R01

4 years                        GM075304

 

$242,320 for               Profiling of Redox-Sensitive Signaling Proteins (co-investigator), NIH-NCI 1RO1

2 years                        GM075304

 

Fulp, Errin W.

 

None

 

John, David J.

 

$1,073,242 for            Algebraic and Statistical Models of Redox Signaling (PI), NIH-NIGMS 1R01

4 years                        GM075304

 

Miller, Timothy E.

 

None

 

Pauca, V. Paúl          

 

$66,337.65                  Computational Methods for Quantum Molecular Dynamics (PI), National Institute of

                                    Standard and Technology

 

$238,180                     Innovative Methods for High Resolution Imaging and Feature Extraction, Army

                                    Research Office

 

$162,000                     Innovative Methods for High Resolution Imaging ande Feature Extraction (co-PI),

Army Research Office

 

Plemmons, Robert J.

 

$50,000                       Pupil Phase Engineering, ARO Grant Supplement from the CIA, September 2004

 

$55,000                       Space Situational Awareness, AFOSR – Subcontract from UNM, January 2005

 

$162,000                     PERIODIC System for Ultra-thin Cameras, ARDA, May 2005

 

$80,000                       Novel Integrated Optical Systems for Iris Recognition, CIA, Supplement through

                                    DynCorp, Inc., May 2005

 

Thomas, Stan J.

 

$1,073,242 for            Algebraic and Statistical Models of Redox Signaling (PI), NIH-NIGMS 1R01

4 years                        GM075304

 

Torgersen, Todd C.

 

$238,180                     Innovative Methods for High Resolution Imaging and Feature Extraction (PI), ARO

 

Turkett, William H.

 

None

 

Wong, Yue-Ling

           

None

 

 


V.  Awards for Distinguished Teaching, Research, or Professional Activities

 

Burg, Jennifer J.

 

The article

 

Jennifer Burg, Yue-Ling Wong, and Leah McCoy, "Developing a Strategy for Creating and Assessing Digital Media Curriculum Material," The IMEJ of Computer-Enhanced Learning, Volume 6, Number 1, May 2004

 

was a finalist for award of "Best Education Research Article in an Open Access Journal, 2004" given by the Communication of Research Special Interest Group of the American Educational Research Association.

 

Cañas, Daniel A.

 

The 2004 Teaching and Research Award, given by the Board of Computer Eng. of Costa Rica, for outstanding lifetime contribution in computer science education and research.

 

Fetrow, Jacquelyn S.

 

None

 

Fulp, Errin W.

 

None

 

John, David J.

 

None

 

Miller, Timothy E.

 

None

 

Pauca, V. Paúl

 

None

 

Plemmons, Robert J.

 

Recognized by the Wake Forest Office of Research and Sponsored Programs, April 2005, for:

 

      1.  Most external funding received

      2.  Largest single funding award

 

Thomas, Stan J.

 

None


 

Torgersen, Todd C.

 

None

 

Turkett, William H.

 

None

 

Wong, Yue-Ling

 

None