April 2008 …

April 2008                                                                       Jan F. Prins


                                 CURRICULUM VITAE

                                    Dr. Jan F. Prins
                                        April 2008

Department of Computer Science                                       Tel: +1-919-962-1913
University of North Carolina                                         Fax: +1-919-962-1799
CB #3175 Sitterson Hall                                          Email: prins@cs.unc.edu
Chapel Hill, NC 27599-3175                               http://www.cs.unc.edu/~prins/


Education
  Ph.D. 1987        Computer Science                 Cornell University
          1986-87   Programming Languages Group      Univ. of Wisconsin at Madison
          1983-84   Programming Research Group       Oxford University, UK
  M.Sc. 1983        Computer Science                 Cornell University
  B.Sc. 1978        Mathematics (Honors)             Syracuse University

   My thesis research was supervised by David Gries at Cornell University and described a
   framework for reusability and rapid prototyping in program development; my minor
   concentration was in neurobiology. I was a member of the Programming Research Group at
   Oxford University during the 1983-84 academic year and spent an undergraduate year in
   1977 at the Technische Hogeschool Eindhoven (The Netherlands) with the research group
   directed by Edsger Dijkstra.

Academic Experience
   7/04­     Department Chair, Department of Computer Science, University of North
             Carolina at Chapel Hill.
   4/01­     Faculty member, Program in Bioinformatics and Computational Biology, UNC-
             CH.
   5/98­     Faculty member, Program in Molecular and Cellular Biophysics, UNC-CH.
   7/96­7/97 Visiting Professor, Institute for Theoretical Computer Science, Swiss Federal
             Institute of Technology (ETH), Zürich, Switzerland.
   8/87­     Assistant Professor (8/87 ­ 12/93), Associate Professor (1/94 ­ 12/01), Full
             Professor (1/02 ­ ), Department of Computer Science, University of North
             Carolina, Chapel Hill, NC.
   6/87­6/94 Instructor, IBM University-Level Course Curriculum. Condensed one-week
             courses taught in various locations around the country. Courses taught include
             Algorithms, Programming Languages & Environments, and Software
             Engineering Principles.
   9/86­8/87 Research Associate to Tom Reps, Department. of Computer Sciences,
             University of Wisconsin - Madison, Madison, WI. Investigation of issues in
             programming languages and systems.




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April 2008                                                                         Jan F. Prins


   6/84­7/84    Instructor, Johns Hopkins Center for Academically Talented Youth. An
                intensive introduction to the mathematical foundations of computer science for
                nationally selected students aged 12-15.
   1/80­5/81    Teaching Fellow, Cornell University, Ithaca, NY.           Instructor for two
                introductory programming courses based on APL and PASCAL respectively.

Commercial Experience
  5/00 ­ 8/00 3rdTech, Inc. Consultant and software developer for DeltaSphere 3D Laser
              Scanner system.
  4/95 ­ 7/96 Gerald Pechanek, IBM MWAVE group, RTP, NC (spun-out to create BOPS,
              Inc.). Consultant on parallel computing issues in DSP chip and system design.
  6/81 ­ 8/83 Ken Wilson, Department of Physics, Cornell University, Ithaca, NY.
              Development of a machine code optimizer for the FPS array processors using
              stochastic methods.
  4/78 ­ 8/81 STSC, Inc., Rockville, MD. Systems Programmer. Member of the four man
              development team responsible for the design and implementation of the
              APL*PLUS interpreters, primarily the production time-sharing system
              programmed in IBM 370 assembler code.
  9/75 ­ 1/81 Digital Effects, Inc., New York. Founding member. Development of an
              animation production system and rendering software, used to produce computer
              generated film sequences for the television and motion picture industry.
              Sample productions include portions of the film "TRON".

Research Areas
   High-performance computing: algorithms, programming languages, compilers and
   architectures. Scientific computing with focus on computational biology and bioinformatics.
   High-level programming languages and problem solving environments. Formal techniques
   in program development.

Post-doctoral Supervision
   Susan Paulsen, Ph.D. 1994 Quantitative Genetics, Duke University (2003 - 2007),
   Martin Simons, Ph.D. 1996 Computer Science, Technische Universität Berlin (1998-1999).
   Lars Nyland, Ph.D. 1991 Computer Science, Duke University (1991-1997)

Student Supervision
   Ph.D. committee memberships: 44 Ph.D. committees, 6 as supervisor, 9 as committee chair,
   2 as external examiner. Ph.D. students supervised:
       Edoardo S. Biagioni, Ph.D. May 1992 (Co-advisor with G. Magó), Scan-Directed Load
           Balancing, Systems Scientist, Carnegie Mellon University (FOX group on
           foundations of programming languages); Associate Professor, Univ. of Hawaii.
       Daniel W. Palmer, Ph.D. Nov. 1996, Compiling High-Level Data-Parallel Programs for
           Parallel Execution, Professor, John Carroll University.
       Rickard E. Faith, Ph.D. Dec. 1997, Debugging Programs After Structure-Changing
           Transformation, Member of the Technical Staff, NetApp, Inc.



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April 2008                                                                         Jan F. Prins


       James W. Riely, Ph.D. Aug. 1999, Abstract Values and Cost Models for Concurrent
          Programs, Research Associate, Concurrency and Functional Languages project,
          University of Sussex, Brighton, England; Associate Professor, DePaul University.
       Wolf Pfannenstiel, Ph.D. Dec. 2000 (TU Berlin), Piecewise Execution of Nested Data
          Parallel Programs, (Co-advisor with S. Jaehnichen, TU Berlin), Member of the
          Technical Staff, VW Gedas, Berlin.
       Jun (Luke) Huan, Ph.D. Oct. 2006, Discovering Patterns in Families of Protein
          Structures, (Co-advisor with W. Wang), Assistant Professor, Department of EECS,
          Kansas University.
       Stephen L. Olivier, (current Ph.D. candidate) Scalable Load Balancing Techniques.

   MS committee memberships: 8 MS (thesis-option) committees, 1 as advisor and committee
   chair. MS student supervised:
      J. Christopher Ramming, M.Sc. Sep. 1989, LLPT: A Little-Language Prototyping Tool,
      DARPA Strategic Technology Office Program Manager.

Professional Activities
   Journal Editorial Boards
       Journal of Scientific Programming (2004 - )
       Co-editor, special issue of Scientific Programming on Applications of Cell B.E.
       Processor. (2008)
   IBM Academic Supercomputing Advisory board (1994 ­ 1997)
   Program committee member, 5th IEEE International Workshop on High Performance
   Computational Biology (HiCOMB 2006).

University Activities
   ORST Program Review Committee (Internal Member, Feb 2008)
   Provost's Committee on Research Computing (2008 - )
   Provost's Advisory Group on Classroom Technology Planning (2008)
   RENCI Advisory Board for Research Computing (2008 - )
   IAH Fellow in Academic Leadership Program (2006 - 07)
   Search Committee for the Dean of Arts and Sciences (2006 - 07)
   Advisory Board member, School of Information and Library Science (2006 - )
   AGEP Program liaison for Computer Science (2006 - )
   Award Recommendation Panel, UNC General Administration, Office of the President.
   Executive Advisory Committee, Bioinformatics and Computational Biology training
      program
   University Faculty Council (1992 ­ 1995).

Departmental Activities
   Chairman (2004-)
   Current Committees
      10-year Review, Graduate Studies, F. P. Brooks Computer Science Building.



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Honors
  Fellow of the Institute of Arts and Humanities, Fall 2006.
  Outstanding Teaching Award, CSSA May 2001
  Research Development Award, UNC-CH 1995
  Junior Faculty Development Award, UNC-CH 1989




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April 2008                                                                      Jan F. Prins



Research Support

                                                                    Total
Role   Agency                         Title                         Award        Dates
PI     IBM      Novel Applications for Cell B.E. (Faculty            $15,000    2006-07
                Research Award)
Co-    NIH      Protein Structure/Function Specific Packing        $1,089,388    9/1/06-
PI              Motifs (1R01GM068665-01A3)                                       8/31/10/
PI     IBM      Shared University Research (Equipment Grant)          $83,000    2006-07
SI     NIEHS    Superfund Basic Research Program -                 $5,000,000   10/1/2006
                Mathematical and Statistical Analysis and                           ­
                Modeling Core (P42ES05948)                                      9/30/2010
Co-    NSF      Identifying Spatial Motifs for Classification of    $300,000    7/15/05 ­
PI              Protein Structure and Function (CCF-EMT                          7/14/08
                0523875)
Co-    EPA      Carolina Environmental Bioinformatics              $4,000,000    8/1/05 ­
PI              Research Center (EPA R832720)                                    7/31/10
SI     ARO      Computer Generated Force Scalability using         $2,400,000   1/15/05 ­
                GPUs                                                             1/14/08
Co-    NIH      (P20) Carolina Center for Experimental Genetic     $1,795,000   10/1/04 ­
PI              Analysis (P20-RR2075)                                            9/30/07
Co-    NSA      Parallel Unbalanced Tree Search                     $500,000     5/1/04 ­
PI                                                                              12/31/06
SI     UNC GA UNC Training Program in Bioinformatics                $450,000    4/19/02 ­
                                                                                 8/31/05
Co-    Lucite   Parallel Programming Paradigms for Distributed      $345,000     4/1/02 ­
PI     Foundn   Memory and DSM multiprocessors                                   6/30/03
Co-    DOE      Environmental Modeling System                       $969,000     2/1/02 ­
PI                                                                               1/31/05
Co-    NSF      A Distributed, High-Performance Computing          $1,024,000   9/01/01 ­
PI              Environment for the Applied Sciences                             8/31/04
Co-    Lucite   Parallel Programming Paradigms for Distributed      $325,000    11/01/00­
PI     Foundn   Memory and DSM multiprocessors                                   3/31/02
Co-    NSF      ITR-ACS: Self-Scheduling N-body simulation          $450,649    10/1/00 ­
PI              algorithms                                                       9/30/03
Co-    EPA      An Object-oriented Integrated Framework for         $863,049    8/20/00 ­
PI              Multi-discipline Ecosystem Modeling                              9/30/02
SI     NIH      Parallel Computing in Structural Biology           $2,500,000   10/1/98 ­
                                                                                 9/30/03
PI     NSF      Cooperative Research (with TU Berlin): Nested        $10,060     3/1/98 ­
                Parallelism in Fortran 90 Programs                               8/31/01


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April 2008                                                                      Jan F. Prins


                                                                     Total
Role   Agency                         Title                          Award       Dates
SI     NSF      SGI Reality Monster (equipment grant)              $1,900,000   9/1/98 ­
                                                                                8/31/01
Co-    Cray     Nested Parallelism in Fortran 90                      $8,000    1/1/98 ­
PI     NCSC                                                                     12/31/98
Co-    Intel    Computing Power for Collaborative Science         $2,858,747    8/1/97 ­
PI     Corp.    (equipment grant)                                               7/31/00
PI     CSCS,    Generating efficient parallel implementations      CHF 7,500    9/1/96 ­
       CH       for irregular problems on the NEC SX-4                          8/31/98
       ETH      Salary support for visiting sabbatical position   CHF 80,000    7/15/96 ­
       Zürich                                                                    7/15/97
PI     ARPA     Software Infrastructure for the Rapid               $193,447    8/28/95 ­
                Development of Interactive and Collaborative                     8/27/97
                Educational Simulations
PI     UNC      University Faculty Research Grant                     $1,500    4/26/96 ­
       (URC)                                                                     4/25/98
PI     Cray     High Performance Irregular Algorithms via             $8,000    1/1/96 ­
       NCSC     High-Level Notations and Novel Compilation                      12/31/97
                Techniques
PI     UNC      Research Development Award                             $700     2/1/95 ­
                                                                                12/31/95
PI     NSWC     Advanced Geoserver Prototyping Experiment            $12,499    8/1/94 ­
                                                                                9/30/94
PI     Rome     A Refinement-Based Methodology for the              $990,000    5/1/94 ­
       Labs     Architecture-Independent Design and                             8/15/96
                Development of Parallel Software
SI     NIH      Parallel Computing Resource for Structural        $3,349,000    7/1/93 ­
                Biology                                                         6/30/98
PI     EPA      Application of Highly Parallel Computers to Air      $78,370    10/1/92 ­
                Quality Simulation                                               6/30/94
PI     DARPA    A Prototyping System for Parallel and             $2,150,000    9/1/92 ­
                Distributed Applications                                        2/29/96
SI     NCI      HPCC Technology for Realtime Medical                $460,432    9/1/92 ­
                Decision Support                                                8/31/95
PI     STSC,    Use of APL*PLUS in a Programming                     $36,000    8/17/92 ­
       inc.     Paradigms course (software)                                     12/31/94




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April 2008                                                                     Jan F. Prins


                                                                    Total
Role   Agency                         Title                         Award       Dates
Co-    ARO       An Investigation of Fluid Flow and Contaminant   $2,356,310   7/1/92 ­
PI               Transport Processes in Heterogeneous                          6/30/97
                 Multiphase Systems
PI     DARPA     Design and Demonstration of a Common              $720,000    5/1/91 ­
                 Prototyping System                                            6/30/92
PI     MasPar    Research Agreement                                 $18,225    2/1/91 ­
       Corp.                                                                   1/31/92
PI     DARPA     Proposal for a Common Prototyping Language        $500,000    5/1/90 ­
                 Based on Unity, Refine and SETL                               4/30/91
PI     ONR       Compiling Data-Parallel Programming                $87,000    3/15/89 ­
                 Languages for SIMD Execution                                   6/30/90
PI     UNC-CH Investigation of Issues in Parallel Programming        $3,000    1/1/89 ­
       Found'n                                                                 12/31/89




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April 2008                                                                     Jan F. Prins



Courses Taught


   Parallel Computing
      High Performance Computing (UNC COMP 633 graduate core course)
      Parallel Computing: Theory and Practice (ETH D-INFK undergraduate course)
      Parallel and Distributed Computing (with P. Widmayer, ETH D-INFK, graduate course)
      Parallel Algorithms (UNC COMP 290 graduate course)
      Parallel Programming Languages (UNC COMP 390 graduate course)

   Algorithms
      High Performance Algorithms (UNC COMP 290 graduate course)
      Advanced Algorithms (IBM internal university-level course)

   Compiler Construction
     Advanced Compiler Design (UNC COMP 240 graduate course)
     Compilers (UNC COMP 140 undergraduate course)

   Programming Languages
      Advanced Topics in Programming Languages (UNC COMP 244 graduate course)
      Programming Paradigms (UNC COMP 290 graduate course)
      Comparative Programming Languages (UNC COMP 217)
      Programming Languages and Programming Environments (IBM internal course)

   Algorithms and Theory of Computation
      Models of Languages and Computation (UNC COMP 181 undergraduate course)
      Algorithm Design and Analysis (IBM internal course)

   Software Engineering
      Formal Methods in Software Engineering (CMU SEI/UNC graduate course)
      Software Engineering (IBM internal course)

   Introduction to Programming
       Introduction to Programming (UNC COMP 14 undergraduate core course)
       Introduction to Functional Programming (UNC COMP 15 undergraduate core course)




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April 2008                                                                               Jan F. Prins



Publications


I. Book Chapters, Edited Volumes, and Journal Articles

1. L. Nyland, M. Harris, J. Prins, "Fast N-Body Simulation with CUDA" in GPU Gems 3, H.
    Nguyen, ed., Addison Wesley, 2007 (pp 677 ­ 696).
2. J. Huan, J. Prins, W. Wang, "Local Structure Comparison of Proteins", Computational
    Biology and Bioinformatics (Advances in Computers 68), Chau-Wen Tseng (ed.), Elsevier,
    2006 (pp 178 ­ 253).
3. D. Bandyopadhyay, J. Huan, J. Liu, J. Prins, J. Snoeyink, W. Wang, A. Tropsha, "Structure-
    based function inference using protein family-specific fingerprints", Protein Science 15 (6),
    2006 (pp 1537 ­ 1543).
4. J. Huan, W. Wang, D. Bandyopadhyay, J. Snoeyink, J. Prins, and A. Tropsha, "Comparing
    graph representations of protein structure for mining family-specific residue-based packing
    motifs", Journal of Computational Biology (JCB) 12 (6), 2005 (pp 657 ­ 671).
5. C. Pan, J. Prins, C. Miller, "A High-performance Lattice Boltzmann Implementation to
    Model Flow in Porous Media", Computer Physics Communications 158, 2004 (pp 89 ­ 105).
6. G. Mann, R. Yun, L. Nyland, J. Prins, J. Board, J. Hermans, "The Sigma MD program and a
    generic interface applicable to multi-functional programs with complex, hierarchical
    command structure", in Computational Methods for Macromolecules, T. Schlick, H.-H. Gan,
    eds., LNCSE 24, Springer ­ Verlag, 2002 (pp 129 ­ 145).
7. S. Midkiff, J. Moreira, S. Chatterjee, J. Ferrante, M. Gupta, J. Prins, C-W Tseng, eds.,
    Thirteenth International Workshop on Languages and Compilers for Parallel Computing
    (LCPC 2000), LNCS 2017, Springer-Verlag, 2001 (383 pp).
8. L. Nyland, J. Prins, A. Goldberg, P. Mills, "A Design Methodology for Data-Parallel
    Applications", Transactions on Software Engineering 26 (4), IEEE, 2000 (pp 293 - 315).
9. L. Carter, J. Ferrante, S. Chatterjee, Z. Li, J. Prins, D. Sehr, P. Yew, eds., Proceedings of the
    Twelfth International Workshop on Languages and Compilers for Parallel Computing
    (LCPC 99), Springer-Verlag 2000.
10. A. Goldberg, J. Prins, J. Reif, R. Faith, Z. Li, P. Mills, L. Nyland, D. Palmer, J. Riely,
    S. Westfold, "The Proteus System for the Development of Parallel Applications", in
    Prototyping and Software Development, M. Harrison, ed., Springer-Verlag (44 pp)
11. J. Prins, S. Chatterjee, M. Simons, "Irregular Computations in Fortran ­ Expression and
    Implementation Strategies", Scientific Programming 7, 1999 (pp 313-326).
12. J. Prins, J. Hermans, G. Mann, L. Nyland, M. Simons, "A Virtual Environment for Steered
    Molecular Dynamics", Future Generation Computer Systems 15, 1999 (pp 485-495)
13. S. Chatterjee, J. Prins, L. Carter, J. Ferrante, Z. Li, D. Sehr, P. Yew, eds., Proceedings of the
    Eleventh International Workshop on Languages and Compilers for Parallel Computing
    (LCPC 98), LNCS 1656, Springer-Verlag, 1999 (384 pp).




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April 2008                                                                            Jan F. Prins


14. L. Nyland, J. Prins, R.H. Yun, J. Hermans, H.-C. Kum, L. Wang, "Achieving Scalable
    Parallel Molecular Dynamics Using Dynamic Domain Decomposition Techniques", Journal
    of Parallel and Distributed Computing, 1998. (pp 125-138)
15. J. Prins, M. Ballabio, M. Boverat, M. Hodous, D. Maric, "Fast Primitives for Irregular
    Computations on the NEC SX-4", Crosscuts 6 (4), CSCS, 1997. (pp 6-10)
16. S. Kumar, S. Goddard, J. Prins, "Connected Components Algorithms for Mesh-Connected
    Parallel Computers", in Parallel Algorithms, S. Bhatt, ed., AMS, 1997. (pp 43-58)
17. J. Leech, J. Prins, J. Hermans, "SMD: Visual Steering of Molecular Dynamics for Protein
    Design", Computational Science & Engineering 3 (4), IEEE, 1996. (pp 38-45)
18. S. Horwitz, J. Prins, T. Reps, "Integrating Non-Interfering Versions of Programs", in
    Software Merging and Slicing, V. Berzins (Ed.), IEEE Computer Society Press, Los
    Alomitos, CA, 1995. (pp 137-190)
19. Goldberg, P. Mills, L. Nyland, J. Prins, J. Reif, J. Riely, "Specification and Development of
    Parallel Algorithms with the Proteus System", in Specification of Parallel Algorithms, G.
    Blelloch, M. Chandy, S. Jagannathan, eds., AMS, 1995. (pp 383-399)
20. P. Mills, L.Nyland, J. Prins, J. Reif, "Software Issues in High-Performance Computing and a
    Framework for the Development of HPC Applications", in Computer Science Agendas for
    High Performance Computing, U. Vishkin, ed., 1994. (pp 110-117)
21. J. Butterworth, J. Prins, "A Comparison of Lattice-Gas Automata Implementations on the
    MasPar MP-1", in Parallel Computational Fluid Dynamics, J. Häuser, ed., Elsevier
    Scientific, 1993. (pp 42-56)
22. E. Biagioni, J. Prins, "Scan-Directed Load Balancing for Mesh-Connected Highly-Parallel
    Computers", in Unstructured Scientific Computation on Scalable Multiprocessors, P.
    Mehrotra, J. Saltz, R. Voigt (eds.), MIT Press, 1992. (pp 371-395)
23. S. Horwitz, J. Prins, T. Reps, "Integrating Non-Interfering Versions of Programs",
    Transactions on Programming Languages and Systems 11 (3), ACM, 1989. (pp 345-387)
24. T. Reps, S. Horwitz, J. Prins, "Support for Integrating Program Variants in an Environment
    for Programming in the Large", in Software Version and Configuration Control, J. Winkler
    (ed), Teubner, 1988. (pp 197-216)
25. D. Gries, J. Prins, "McLaren's Masterpiece", Science of Computer Programming 8, 1987.
    (pp 139-145)
26. J. Prins, Partial Implementations in Program Derivation, Ph. D. thesis, Cornell University,
    1987. (153 pp)


II. Refereed Conference Papers
27. S. Olivier, J. Prins, "Scalable Load Balancing Using UPC", to appear in Proc. Intnl Conf on
    Parallel Programming (ICPP), 2008.
28. S. Olivier, J. Prins, J. Derby, K. Vu, "Porting the GROMACS Molecular Dynamics Code to
    the Cell Processor", Proc. of 8th IEEE Intl. Workshop on Parallel and Distributed Scientific
    and Engineering Computing (PDSEC-07), 2007.



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April 2008                                                                          Jan F. Prins


29. J. Dinan, S. Olivier, J. Prins, G. Sabin, P. Sadayappan, C.-W. Tseng, "Dynamic Load
    Balancing of Unbalanced Computations Using Message Passing", Proc. of 6th Intl.
    Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and
    Distributed Systems (PMEO-PDS 2007), 2007.
30. J. Liu, Q. Zhang, W. Wang, L. McMillan, J. Prins, "Poclustering: lossless clustering of
    dissimilarity data", Proc 7th SIAM Conference on Data Mining (SDM), 2007.
31. S. Olivier, J. Huan, J. Liu, J. Prins, J. Dinan, P. Sadayappan, C.-W. Tseng, "UTS: An
    Unbalanced Tree Search Benchmark", 19th International Workshop on Languages and
    Compilers for Parallel Computing (LCPC), 2006.
32. J. Liu, Q. Zhang, W. Wang, L. McMillan, J. Prins, "Clustering pair-wise dissimilarity data
    into partially ordered sets", Proc. 12th ACM International Conference on Knowledge
    Discovery and Data Mining (SIGKDD), 2006.
33. J. Huan, D. Bandyopadhyay, J. Prins, J. Snoeyink, A. Tropsha, W. Wang, "Distance-based
    Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining",
    Computational Systems Bioinformatics Conference (CSB), 2006.
34. J. Liu, S. Paulsen, X. Sun, W. Wang, A. Nobel, J. Prins, Mining Approximate Frequent
    Itemsets In the Presence of Noise: Algorithm and Analysis, SIAM Conference on Data
    Mining (SDM), 2006.
35. J. Huan, D. Bandyopadhyay, J. Liu, J. Prins, J. Snoeyink, A. Tropsha, W. Wang, "Rapid
    determination of local structural features common to a set of proteins" (demo), Proceedings
    of the 13th International Conference on Intelligent Systems for Molecular Biology (ISMB),
    2005.
36. J. Liu, S. Paulsen, W. Wang, A. Nobel, J. Prins, "Mining Approximate Frequent Itemsets
    from Noisy Data", Proceedings of the 5th IEEE International Conference on Data Mining
    (ICDM), 2005
37. D. Bandyopadhyay, J. Huan, J. Liu, J. Prins, J. Snoeyink, A. Tropsha, and W. Wang,
    "Function inference using family-specific subgraph fingerprints mined from protein
    families", Proceedings of the 13th International Conference on Intelligent Systems for
    Molecular Biology (ISMB), 2005.
38. J. Huan, W, Wang, J. Prins, J. Yang, "SPIN: Mining Maximal Frequent Subgraphs from
    Graph Databases", in Proceedings of the 10th ACM SIGKDD International Conference on
    Knowledge Discovery and Data Mining (KDD), 2004.
39. M. Farthing, C. Miller, D. Sassen, J. Prins, "A problem solving environment for subsurface
    flow and transport phenomena", in International Conference on Computational Methods in
    Water Resources XV (CMWR), Elsevier, 2004.
40. J. Huan, W. Wang, D. Bandyopadhyay, J. Snoeyink, J. Prins, A. Tropsha, "Mining Protein
    Family Specific Residue Packing Patterns From Protein Structure Graphs", in Proceedings of
    the Intl Conf on Research in Computational Molecular Biology (RECOMB), 2004.
41. C. Miller, C. Abhishek, A. Sallerson, J. Prins, M. Farthing, "A comparison of computational
    and algorithmic advances for solving Richards' equation" in International Conference on
    Computational Methods in Water Resources XV (CMWR), Elsevier, 2004.




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April 2008                                                                             Jan F. Prins


42. J. Huan, W. Wang, A. Washington, J. Prins, R. Shah, A. Tropsha, "Accurate classification of
    protein structural families using coherent subgraph analysis", in Proceedings of the Pacific
    Symposium on Biocomputing (PSB), 2004.
43. K. Berlin, J. Huan, J. Prins, W. Pugh, P. Sadayappan, J. Spacco, C.-W. Tseng, "Evaluating
    the Impact of Programming Language Features on the Performance of Parallel Applications
    on Cluster Architectures", Proceedings of the 14th International Workshop on Languages
    and Compilers for High Performance Computing (LCPC), 2003.
44. J. Huan, W. Wang, J. Prins, "Efficient mining of frequent subgraphs in the presence of
    isomorphism", Proceedings of the 3rd IEEE International Conference on Data Mining
    (ICDM), 2003.
45. J. Huan, J. Prins, W. Wang, T. Vision, "Reconstructing of ancestral gene order after
    segmental duplication and gene loss", Proceedings of the IEEE Computer Society
    Bioinformatics Conference (CSB), 2003.
46. C. Pan, J. Prins, and C. Miller, "A High-Performance Lattice Boltzmann Implementation of
    Multiphase Flow in Porous Media", Workshop on Simulation and Optimization, Statistical
    and Applied Mathematical Sciences Institute, Research Triangle Park, North Carolina, 28-30
    April 2003.
47. D. Stotts, J. Prins, L. Nyland, "CobWeb: Visual Design of Collaboration Protocols for
    Dynamic Group Web Browsing", Workshop on Visual Computing (part of Distributed
    multimedia Systems 2002), IEEE, 2002.
48. J. Riely, J. Prins, "Flattening is an Improvement", in Proceedings of the Seventh Static
    Analysis Symposium (SAS), LNCS 1284, Springer-Verlag, 2000.
49. L. Nyland, J. Prins, R.H. Yun, J. Hermans, H.-C. Kum, L. Wang, "Modeling Dynamic Load
    Balancing in Molecular Dynamics to Achieve Scalable Parallel Execution", in Fifth
    International Symposium on Solving Irregularly Structured Problems in Parallel (Irregular
    98), Ferreira, A. and Rolim, J. and Simon, H. and Teng, S.-H, eds., LNCS 1457, Springer-
    Verlag, 1998. (pp 356-365)
50. J. Prins, S. Chatterjee, M. Simons, "Expressing Irregular Computations in Modern Fortran
    Dialects", in Languages, Compilers and Runtime Systems (LCR98), D. O'Hallaron, ed.,
    LNCS 1511, Springer-Verlag, 1998 (pp 1-16).
51. R. Faith, L. Nyland, J. Prins, "Khepera: A System for the Rapid Implementation of Domain
    Specific Languages, Proc. ACM/USENIX conference on Domain Specific Languages, ACM,
    1997. (pp 243-255)
52. L. Nyland, S. Chatterjee, J. Prins, "Parallel Solutions to Irregular Problems Using HPF", First
    HPF UG meeting, Santa Fe, NM, Feb. 1997.
53. L. Nyland, J. Prins, A. Goldberg, P. Mills, J. Reif, R. Wagner, "A Refinement Methodology
    for Data-Parallel Applications", in Proc. EuroPar 96 Parallel Processing Conference, Lyon,
    France, LNCS 1123, Springer-Verlag, 1996 (pp 145-151).
54. D. Palmer, J. Prins, S. Chatterjee, R. Faith, "Piecewise Execution of Nested Data-Parallel
    Programs", in Languages and Compilers for Parallel Computing (LCPC 95), Huang et al.,
    eds., LNCS 1033, Springer-Verlag 1996. (pp 346-362)




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April 2008                                                                             Jan F. Prins


55. J. Riely, J. Prins, S. Iyer, "Provably Correct Vectorization of Nested Parallel Programs",
    Massively Parallel Programming Models: Suitability, Realization and Performance, Berlin,
    IEEE 1995. (pp 213-223)
56. D. Palmer, J. Prins, "Work-efficient Nested Data-Parallelism", Proc. of the 5th Symposium
    on the Frontiers of Massively Parallel Processing, IEEE, 1995. (pp 186-193)
57. L. Nyland, J. Prins, J. Reif, "A Data-Parallel Implementation of the Adaptive Fast Multipole
    Algorithm", 1993 DAGS/PC Workshop on Practical Parallel Algorithms, Dartmouth
    University, 1993. (17 pp)
58. J. Prins, D. Palmer, "Transforming High-level Data-Parallel Programs into Vector
    Operations", Proc. 5th ACM Symposium on Principles and Practice of Parallel
    Programming, ACM, 1993. (pp 119-128)
59. P. Mills, J. Prins, J. Reif, "Rate-Control as a Language Construct for Parallel and Distributed
    Programming", Proc. IEEE Workshop on Parallel and Distributed Real-Time Systems, IEEE,
    1993. (pp 164-171)
60. M. Parris, C. Mueller, J. Prins, A. Duggan, Q. Zhou, E. Erikson, "A Distributed
    Implementation of an N-body Virtual World Simulation", IEEE Workshop on Parallel and
    Distributed Real-Time Systems, IEEE, 1993. (pp 66-- 71)
61. W. Hightower, J. Prins, J. Reif, "Implementations of Randomized Sorting on Large Parallel
    Machines", Proc. 3rd Symposium on Parallel Architectures and Algorithms, ACM, 1992.
    (pp 158-167)
62. P. Mills, L. Nyland, J. Prins, J. Reif, "Prototyping High-performance Parallel Computing
    Applications in Proteus", Proc. 1992 DARPA Software Technology Conference, Meridian,
    1992. (pp 443-442)
63. P. Mills, L. Nyland, J. Prins, J. Reif, "Prototyping N-body simulation in Proteus", Proc. 6th
    International Parallel Processing Symposium, IEEE, 1992. (pp 476-482)
64. L. Nyland, J. Prins, "Prototyping Parallel Algorithms", 1992 DAGS /PC Workshop on Issues
    and Obstacles in the Implementation of Parallel Algorithms and the Use of Parallel
    Machines, Dartmouth University, 1992. (pp 31-39)
A. Varshney, J. Prins, "An Environment-Projection Approach to Radiosity for Mesh-Connected
    Computers", in Third Eurographics Workshop on Rendering, A. Chalmers, D. Paddon, F.
    Sillion (eds), lpha Press (U.K.), 1992. (pp 271-281)
65. J. Prins, D. Palmer, "Transforming High-level Data-Parallel Programs into Vector
    Operations", International Workshop on Array Structures, University of Montreal, 1992 (13
    pp).
66. P. Mills, L. Nyland, J. Prins, J. Reif, R. Wagner, "Prototyping Parallel and Distributed
    Programs in Proteus", Proc. 3rd Symposium on Parallel and Distributed Processing , IEEE,
    1991. (pp 26-34)
67. J. Prins, "A Framework for Efficient Execution of Array-based Languages on SIMD
    Computers", Proc. of the 3rd Symposium on the Frontiers of Massively Parallel Processing,
    IEEE, 1990. (pp 462-470)
68. J. Prins, J. Smith, "Parallel Sorting of Large Arrays on the MasPar MP-1", Proc. of the 3rd
    Symposium on the Frontiers of Massively Parallel Processing, IEEE, 1990. (pp 59-64)


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April 2008                                                                       Jan F. Prins


69. S. Horwitz, J. Prins, T. Reps, "Integrating Non-Interfering Versions of Programs",
    Conference Record of the 15th ACM Symposium on Principles of Programming Languages,
    ACM, 1988. (pp 133-145)
70. S. Horwitz, J. Prins, T. Reps, "On the Adequacy of Program Dependence Graphs for
    Representing Programs", Conference Record of the 15th ACM Symposium on Principles of
    Programming Languages, ACM, 1988. (pp 146-157)
71. D. Gries, J. Prins, "A New Notion of Encapsulation", Proceedings ACM SIGPLAN
    Symposium on Programming Languages and Environments, ACM, 1985. (pp 131-139)
72. D. Jacobs, J. Prins, P. Siegel, K. Wilson, "Monte Carlo Methods in Code Optimization",
    Proc. 15th Conference on Microprogramming, IEEE/ACM, 1982. (pp 143-148)
73. D. Jacobs, J. Prins, K. Wilson, "Report on the Construction of a Monte Carlo Optimizer",
    Proceedings ARRAY 82, 1982, FPS. (pp 44-53)
74. J. Prins, "Automated Testing in APL: An Application of Exception Handling", Proceedings
    APL82 Conference, 1982, ACM. (pp 260-264)




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