Wake Forest University

Summary of Professional Activity and Publications

DEPARTMENT OF COMPUTER SCIENCE

July 1, 2003 - June 30, 2004

 

 

I.    Publications, Performances, Exhibits

II.   Papers and Presentations

III.  Editorships, Offices, and Consultancies

IV.  External Grants Received

 

 

I.  Publications, Performances, Exhibits

 

Burg, Jennifer J.

(with Wong, Y., and McCoy, L.)  “Developing a Strategy for Creating and Assessing Digital Media Curriculum Material,” The IMEJ of Computer-Enhanced Learning, Volume 6, Number 1, May 2004.

 

4-7 December 2003:  “Fibonacci and Phi,” a blend of dance, poetry, music, and digital media, performed at Scales Fine Arts Auditorium.  I wrote the central poem and did parallel computation for real-time fractal display, and created digital images for a backdrop for the performance.

 

Cañas, Daniel A.

None

 

Fetrow, Jacquelyn

(with Cammer, S. A., Hoffman, B. T., Speir, J. A., Canady, M., Nelson, M. R., Knutson, S. T., Gallina, M., and Baxter,  S. M.)  Structure-based active site profiles for genome analysis and sub-family classification.  J. Mol. Biol. 2003 Nov 28;334(3):387-401.

 

(with Baxter, S. M., Rosenblum, J. S., Knutson, S. T., Nelson, M. R., Montimurro, J. S., Di Gennaro, J. A., Speir, J. A., and  Burbaum, J. J.)  Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast.  Mol Cell Proteomics. 2003 2004 Mar;3(3):209-25.

 

(with Herrgard, S., Cammer, S. A., Speir, J. A., Hoffman, B. T., Knutson, S., Gallina, M., and Baxter, S. M.)  Prediction of deleterious nsSNPs using a library of structure-based function descriptors.  Proteins Struct Funct Gen. 2003 Dec 1;53(4):806-16.

 

(with Zhou, H., Gallina, M., Mao, H., Betz, S. F., and Domaille, P. J.)  1H, 13C, and 15N resonance assignments and secondary structure for the human protein tyrosine phosphatase, PRL-2.  J. Biomol. NMR. 2003 27(4):397-398.

 

(with Baxter, S., and  Knutson, S.)   The importance of structure-based function annotation to drug discovery.  Protein Structure Determination, Analysis and Modeling for Drug Discovery. D. I. Chasman, Ed., Dekker Publishing. 2003.  p. 369-387.  (book chapter)

 

Patent allowed:  Methods and Systems for Predicting Protein Function.  US99/11913.  Inventors:  Skolnick, J. and Fetrow, J. S.  US Patent #6,631,332, issued 10/7/03.

 

Fulp, Errin W.

(with Reeves, Douglas S.)  “Bandwidth Provisioning and Pricing for Networks with Multiple Classes of Service,” Computer Networks Journal, Elsevier B.V.

 

Hemler, Paul F.

None

 

John, David J.

None

 

Miller, Timothy E.

S. S. Adler et al.  Bose-Einstein correlations of charged pion pairs in Au+Au collisions at GeV.  LANL pre-print version nucl-ex/0401003.
 
S. S. Adler et al.  Measurement of non-random event-by-event fluctuations of average transverse momentum in GeV Au+Au and p+p collisions.  Pre-print nucl-ex/0310005.
 
K. Adcox et al.  PHENIX Central Arm Tracking Detectors.  Nucl. Instrum. Meth. A 499, 489 (2003).
 
K. Adcox et al.  PHENIX Detector Overview.  Nucl Instr Meth A 499, 469 (2003).
 
S. S. Adler et al. High-p(T) charged hadron suppression in Au+Au collisions at GeV.  Phys Rev C 69, 034910 (2004).
 
S. S. Adler et al.  Identified charged particle spectra and yields in Au+Au collisions at GeV.  Phys Rev C 69, 034909 (2004).
 
K. Adcox et al.  Single identified hadron spectra from GeV Au+Au collisions.  Phys Rev C 69, 024904 (2004).
 
S. S. Adler et al.  J/psi production from proton-proton collisions at GeV. Phys Rev Lett 92, 051802 (2004).
 
S. S. Adler et al.  Absence of suppression in particle production at large transverse momentum GeV d+Au collisions.  Phys Rev Lett 91, 072303 (2003).
 
S. S. Adler et al.  Scaling properties of proton and anti-proton production in GeV Au+Au collisions.  Phys Rev Lett 91, 172301 (2003).
 
S. S. Adler et al.  J/psi production in Au+Au collisions at GeV at the Relativistic Heavy Ion Collider.  Phys Rev C 69,  014901 (2004).
 
S. S. Adler et al.  Elliptic flow of identified hadrons in Au+Au collisions at GeV.  Phys Rev Lett 91, 182301 (2003).
 
S. S. Adler et al.  Suppressed p0 production at large transverse momentum in central Au+Au collisions at GeV.  Phys Rev Lett  91, 072301 (2003).
S. S. Adler et al.  Mid-rapidity neutral pion production in proton-proton collisions at GeV.  Phys Rev Lett 91, 241803 (2003).
 

4-7 December 2003:  “Fibonacci and Phi,” a collaboration between Alban Elved dance company, Wake Forest University and independent artists “to bring together artists, scientists and humanists from all walks of life.”  My role was providing the interface between the supercomputing resources, the artists and the networking infrastructure in the Information Systems department.  Performed in the Scales Fine Arts Auditorium.

 

Pauca, V. Paúl

(with Prasad, S., Torgersen, T. C., Plemmons, R. J., and  van der Gratch, J.)  "Restoring Images with Space Variant Blur via Pupil Phase Engineering," Optics in Info. Systems, Special Issue on Comp. Imaging, SPIE Int. Tech. Group Newsletter, Vol. 14, No. 2, pp. 4-5, Aug. 2003.  (invited paper)

 

Plemmons, Robert J.

(with Chu, M., and Funderlic, R.)  “Structured Low Rank Approximation,” Linear Algebra and Its Applications,” Vol. 366, (2003), pp. 157-172.

 

(with Prasad, S., Torgersen, T., Pauca, V., and van der Gracht, J.)  “Restoring Images with Space Variant Blur via Pupil Phase Engineering,'' in Optics in Info. Systems, Special Issue on Comp. Imaging, SPIE Int. Tech. Group Newsletter, Vol. 14, No. 2, pp. 4-5, Aug. 2003.  (invited paper)

 

 (with Yuan, J., Golub, G., and Cecilio, W.)  “Semi-Conjugate Direction Methods for Real Positive Definite Systems,” BIT Numerical Mathematics, Vol. 44 (1), 189-207, 2004.

 

Thomas, Stan J.

None

 

Torgersen, Todd C.

(with Prasad, S., Plemmons, R., Pauca, V., and van der Gracht, J.)  “Restoring Images with Space Variant Blur via Pupil Phase Engineering,'' in Optics in Info. Systems, Special Issue on Comp. Imaging, SPIE Int. Tech. Group Newsletter, Vol. 14, No. 2, pp. 4-5, Aug. 2003.  (invited paper)

 

Wong, Yue-Ling

4-7 December 2003:  “Fibonacci and Phi” dance production performed at Scales Fine Arts Auditorium.

 

29 May – 5 July, 2003:  One piece of charcoal drawing submitted to the Associated Artists of Winston-Salem (AAWS) exhibition, Back to Basics—an exhibit of drawings and sketches by all Members, at AAWS Gallery, Winston-Salem.


II.  Papers and Presentations

 

Burg, Jennifer J.

Paper and presentation:  (with Lausier, Angelique, and Strokanova, Victoria)  "Motivating Learning and Creativity With Fibonacci, Fractals, and Phi," Proceedings of ED-MEDIA 2004, Lugano, Switzerland, June 2004.

 

Paper and presentation:  (with Wong, Yue-Ling, and Strokanova, Victoria)  "Digital Media in the Computer Science Curricula," Proceedings of 35th SIGCSE:  Technical Symposium on Computer Science Education, Norfolk, Virginia, March 3-7, 2004, pp. 427-430.

 

Technical Reports (published in-house)

 (with Wong, Yue-Ling)  "Dancing With Fractals and Antique Snowflakes," Technical Report 2004-1, Wake Forest University Department of Computer Science, January 2004 (submitted to IEEE Computer).

 

(with Miller, Tim)  "Cluster Computation in Step with Real-Time Dance:  An Experiment in Art/Science Collaboration," Technical Report 2004-2, Wake Forest University Department of Computer Science, April 2004 (submitted to the 17th International Conference on Parallel and Distributed Computing Systems). 

 

(with Wong, Yue-Ling, and Strokanova, Victoria)  "Digital Media in Undergraduate Computer Science Curricula:  Updated and Detailed Report," Technical Report 2003-2, Wake Forest University Department of Computer Science, August 2003 (a longer version of the paper accepted for publication at SIGCSE 2004).

 

Cañas, Daniel A.

None

 

Fetrow, Jacquelyn

Presentation:  IPAM Workshop on Structural Proteomics, May 10-14, 2004, UCLA Institute for Pure and Applied Mathematics; invited talk entitled “Combining computational and chemical approaches to proteome analysis—serine hydrolases in yeast.”

Presentation:  Gordon Research Conference on Enzymes, Co-enzymes, and Metabolic Pathways, July, 2003. Kimball Union Academy, NH; invited talk entitled “Combining computational and chemical approaches to proteome analysis.”

 

Fulp, Errin W.

Presentation:  "Pricing Methods for E-Content Servers." Presented at the Internet Economics Seminar, International Conference and Research Center for Computer Science, Dagstuhl, Germany 2003. (by invitation only from the German Government)

 

Hemler, Paul F.

None

 

John, David J.

Paper and presentation:  (with Francel, Margaret)  “An algorithm for constructing an even grammar from a language sample,” Proceedings of the 42nd Southeastern Regional Meeting of the ACM, pages 240-245, ACM Press, Huntsville, Alabama,  April, 2004.

 

 

Miller, Timothy E.

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

 

Technical Report (published in-house)

(with Burg, J.)  “Cluster Computation in Step with Real-Time Dance:  An Experiment in Art/Science Collaboration,” Technical Report 2004-2, Wake Forest University Department of Computer Science, April 2004 (submitted to the 17th International Conference on Parallel and Distributed Computing Systems). 

 

Pauca, V. Paúl

Paper and presentation:  (with Shahnaz, F., Berry, M. W., and Plemmons, R. J.)  "Text Mining using Non-Negative Matrix Factorizations," in Proceedings of the Fourth SIAM International Conference on Data Mining, Lake Buena Vista, FL, April 22, 2004, pp. 452-456.

 

Paper and presentation:  (with Prasad, S., Plemmons, R. J., Torgersen, T. C., and van der Gratch, J.)  "An Integrated Optical-Digital Approach for Improved Image Restoration," in Proceedings of the 2003 AMOS Technical Conference, Maui, HI, September 8-12, 2003.

 

Paper and presentation:  (with Prasad, S., Plemmons, R. J., Torgersen, T. C., and van der Gratch, J.)  "Integrated Optical-Digital Approaches for Enhancing Image Restoration and Focus Invariance," in Proceedings of the SPIE Conference on Advanced Signal Processing:  Algorithms, Architectures, and Implementations XIII,  edited by F. Luk, San Diego, CA, August 6-8, 2003, pp. 348-357.

 

Paper and presentation:  (with Prasad, S., Torgersen, T., Plemmons, R., and van der Gracht, J.)  “Engineering the Pupil Phase to Improve Image Quality,” in Proceedings of the SPIE Vol. 5108 Visual Information Processing XII, edited by Z. Rahman, R. Schowengerdt, and S. Reichenbach, Orlando, FL, pp. 1-12, 2003. (invited paper)

 

Oral Presentations

(with van der Gracht, J., Setty, H., Narayanswamy, R., Plemmons, R. J., Prasad, S., and  Torgersen, T. C.)   SPIE Conference on Defense and Homeland Security, Orlando, April 2004.

 

Poster Presentations

(with Piper, J., Plemmons, R. J.,  Giffin, M., and Hamada, K.)  “Non-Imaging Identification and Classification of Space Objects from Spectral Sensor Data,” 4th Annual Meeting of the Fitzpatrick Center for Photonics and Communication Systems, Duke University, Durham, NC, May 12, 2004.

 

(with Plemmons, R. J., Giffin, M., and Hamada, K.)  “Unmixing Spectral Data for Space Objects using Low-Rank Non-Negative Matrix Factorization,” Partnership in Research Excellence and Transition (PRET) Review, Maui Scientific Research Center, Maui, HI, January 20, 2003.

 

Plemmons, Robert J.

Paper and presentation:  (with Prasad, S., Torgersen, T., Pauca, V., and van der Gracht, J.)  “Engineering the Pupil Phase to Improve Image Quality,” in Proceedings of the SPIE Vol. 5108 Visual Information Processing XII, edited by Z. Rahman, R. Schowengerdt, and S. Reichenbach, Orlando, FL, pp. 1-12, 2003.  (invited paper)

 

Paper and presentation:  (with Prasad, S., Pauca, V., Torgersen, T. C., and van der Gratch, J.)  "Integrated Optical-Digital Approaches for Enhancing Image Restoration and Focus Invariance," in Proceedings of the SPIE Conference on Advanced Signal Processing:  Algorithms, Architectures, and Implementations XIII,  edited by F. Luk, San Diego, CA, August 6-8, 2003, pp. 348-357.

 

Paper and presentation:  (with Prasad, S., Pauca, V., Torgersen, T. C., and van der Gratch, J.)  "An Integrated Optical-Digital Approach for Improved Image Restoration," in Proceedings of the 2003 AMOS Technical Conference, Maui, HI, September 8-12, 2003.

 

Paper and presentation:  (with Shahnaz, F., Berry, M. W., and Pauca, P.)  "Text Mining using Non-Negative Matrix Factorizations," in Proceedings of the Fourth SIAM International Conference on Data Mining, Lake Buena Vista, FL, April 22, 2004, pp. 452-456.

 

Presentations

“Overview of Image Quality Control by Pupil Phase Engineering,” International Congress on Industrial and Applied Mathematics, Sydney, Australia, July 2003.

 

"Tutorial on Integrated Optical-Digital Approach for Enhancing Images," Institute for Pure and Applied Mathematics Workshop on Inverse Problems, UCLA, Los Angeles, CA, October 2003.

 

“Tutorial on Mining Scientific Data,” Workshop on Scientific Computation, Singapore, December 2003.

 

“Some Inverse Problems in Imaging,” International Conference on Image Processing, Singapore, December 2003.

 

(with van der Gracht, J., Prasad, S., Pauca, P., and Torgersen, T.)  “Iris Recognition with Enhanced Depth-of-field Image Acquisition,” DOD Conference on Defense and Security, Orlando, April 2004.

 

(with Piper, J., Pauca, P., Giffin, M., and Hamada, K.)  “Non-imaging Identification and Classification of Space Objects from Spectral Sensor Data,”  Fitzpatrick  Center Annual Conference, Durham, NC, May 2004.

 

Thomas, Stan J.

None

 

Torgersen, Todd C.

Paper and presentation:  (with Prasad, S., Plemmons, R., Pauca, V., and van der Gracht, J.)  “Engineering the Pupil Phase to Improve Image Quality,” in Proceedings of the SPIE Vol. 5108 Visual Information Processing XII, edited by Z. Rahman, R. Schowengerdt, and S. Reichenbach, Orlando, FL, pp. 1-12, 2003.  (invited paper)

 

Paper and presentation:  (with Prasad, S., Plemmons, R. J., Pauca V., and van der Gratch, J.)  "Integrated Optical-Digital Approaches for Enhancing Image Restoration and Focus Invariance," in Proceedings of the SPIE Conference on Advanced Signal Processing:  Algorithms, Architectures, and Implementations XIII,  edited by F. Luk, San Diego, CA, August 6-8, 2003, pp. 348-357.

 

Paper and presentation:  (with Prasad, S., Pauca, V., Plemmons, R., and van der Gratch, J.)  "An Integrated Optical-Digital Approach for Improved Image Restoration," in Proceedings of the 2003 AMOS Technical Conference, Maui, HI, September 8-12, 2003.

 

Presentation:  “Engineering the Pupil Phase to Improve Image Quality,” given at the 5th International Congress for Industrial and Applied Mathematics (ICIAM), July 7-11, 2003, Sydney, Australia.

 

Presentation:  “A Fisher-Information Based Approach to Phase-Diversity Speckle Imaging,” given at the 2003 AMOS Technical Conference, September 8-12, 2003, Wailea, HI.

 

Presentation:  “Current Projects for Improved Phase-Diversity Speckle Imaging,” given at the 2004 PRET Workshop, Jan. 19-22, 2004, Kihei, HI.

 

Wong, Yue-Ling

Paper:  (with Burg, Jennifer, and Strokanova, Victoria)   "Digital Media in Computer Science Curricula," ACM SIGCSE Conference, March 3-7, 2004.

 

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

 

Cañas, Daniel A.

Club de Investigacion Tecnologica, Costa Rica, Summer 2003

 

Fetrow, Jacquelyn

Editorial Board Service for journal:  Proteins:  Structure Function and Genetics

 

Board of Directors, Quantum Bio, State College, PA (teleconference, a two-hour board meeting/month)

 

Fulp, Errin W.

None

 

Hemler, Paul F.

None

 

John, David J.

None

 

Miller, Timothy E.

None

 

Pauca, V. Paúl

None

 

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

 

Vice Chair, Activity Group on Imaging Science, Society for Industrial and Applied Mathematics

 

Workshop Organizer, NSF Institute for Pure and Applied Mathematics at UCLA

 

Consultant, Boeing Phantom Works, Seattle, WA, 2 weeks per year

 

Consultant, Air Force Space Command, 1 month in summer

Thomas, Stan J.

None

 

Torgersen, Todd C.

None

 

Wong, Yue-Ling

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

 

Conducted a one-day workshop on Photography Science in SciMax, “The Science of Art” (funded by NSF), for middle-school teachers, July 11, 2003

 

IV.  External Grants Received

 

Burg, Jennifer J.

1st year: $92,461          Integrated Digital Media Curriculum Development (co-PI), National Science

                                    Foundation’s CCLI Program (Course, Curriculum, and Laboratory Improvement)

 

Cañas, Daniel A.

None

 

Fetrow, Jacquelyn     

None

 

Fulp, Errin W.

1st year:  $48,532         Network Firewalls, Department of Energy

 

Hemler, Paul F.

None

 

John, David J.

None

 

Miller, Timothy E.

None

 

Pauca, V. Paúl           

None

 

Plemmons, Robert J.

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

 

$65,000                       Space Situational Awareness, AFOSR – Subcontract from UNM

 

$786,022                     Wavefront Coding for Iris Recognition, CDM Optics, Inc., Central Intelligence Agency,

                                    Supplement to Core ARO Grant

 

$250,000                     Novel Integrated Optical Systems for Iris Recognition, CIA, Supplement to Core ARO

                                    Grant

 

$492,000                     Novel Integrated Optical Systems for Iris Recognition, CIA, Supplement to Core ARO

                                    Grant, CDM Optics, Inc.

 

Thomas, Stan J.

None

 

Torgersen, Todd C.

None

Wong, Yue-Ling        

1st year: $92,461          Integrated Digital Media Curriculum Development (PI), National Science

                                    Foundation’s CCLI Program (Course, Curriculum, and Laboratory Improvement)