1. John H. Reif (Editor), VLSI Algorithms and Architectures,
3rd Aegean Workshop on Computing, AWOC 88, Corfu, Greece, June 28 - July 1 1988, 476
pages, Springer-Verlag Lecture Notes in
Computer Science, Vol. 319 (1988).
2. John H. Reif (Editor), Synthesis of
Parallel Algorithms, 22 chapters, 1011 pages. Kluwer Academic Publishers, San Mateo, California, 1993.
3. Robert Paige, John H. Reif, and Ralph Wachter (Editors), Parallel
Algorithm Derivation and Program Transformation, 228 pages.
Published by Kluwer Academic Publishers, 1993.
4. Sanguthevar Rajasekaran, pp. M. Pardalos, John H. Reif
and J. Rolim (Editors), Handbook of Randomized Computing (Edited
by), Kluwer Volume I and II, Academic Press, London, 2001.
5. Proceedings of the 34th ACM
Symposium on Theory of Computing (STOC2002), (Edited by John H. Reif), Montréal,
Québec, Canada, May 19-21, 2002. Also, John
H. Reif, Guest Editor, Special Issue of Selected
Papers from Proceedings of the Thirty-Fourth Annual ACM Symposium on Theory of
Computing (STOC2002) Journal of Computer and System Sciences(JCSS), Volume 67,
Issue 2, Page 211, (September 2003). Guest
Editor’s Foreword, Page 211. [PDF]
6. Junghuei Chen and John
H. Reif (Editors), Proceedings of the Ninth
International Meeting on DNA Based Computers (DNA9), Madison, Wisconsin,
June 1-3, 2003, 225 pages, Lecture Notes in
Computer Science Vol. 2943, Springer-Verlag, New York, (2004).
7. John H. Reif (Editor), Proceedings of the First
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices(FNANO04), Snowbird, Utah, (April 21-23, 2004), Published by
Sciencetechnica (2004). Editor’s Foreword [PDF]
8. John H. Reif (Editor), Proceedings of the Second
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices(FNANO05), Snowbird, Utah, (April 24-28, 2005), Published by
Sciencetechnica (2005). Editor’s Foreword [PDF]
9. John H. Reif (Editor), Proceedings of the Third
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices(FNANO06), Snowbird, Utah, (April 23-27, 2006), Published by
Sciencetechnica (2006).
10. John H. Reif (Editor), Proceedings of the Fourth
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices(FNANO07), Snowbird, Utah, (April 18-22, 2007), Published by
Sciencetechnica (2007).
11. Sanguthevar
Rajasekaran and John H. Reif (Editors), Handbook of
Parallel Computing: Models, Algorithms and Applications, Published
by Taylor & Francis, Boca Raton, FL. ISBN 978-1584886235
(December, 2007). [PDF]
12. John H. Reif (Editor), Proceedings of the Fifth
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices(FNANO08), Snowbird, Utah, (April 21-25, 2008), Published by
Sciencetechnica (2008).
13. John H. Reif and Marya Lieberman, editors, Proceedings
of the Sixth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices(FNANO09), Snowbird, Utah, Published by Sciencetechnica
(April 20-24, 2009).
14. Sudheer Sahu and John H. Reif, DNA-based
Self-assembly and Nanorobotics, Published by VDM Verlag, Dr. Mueller
e.K., Saarbrücken, Germany, 128 pages, (November 10, 2008) ISBN-10: 363909770X,
ISBN-13: 978-3639097702.
15. John H. Reif and Marya Lieberman, editors, Proceedings
of the Seventh Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices(FNANO10), Snowbird, Utah, Published by
Sciencetechnica (April 27-30, 2010).
16. John H. Reif and Marya Lieberman, editors, Proceedings
of the Eighth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices(FNANO11), Snowbird, Utah, Published by
Sciencetechnica, (April 11-15, 2011).
John H. Reif and Marya Lieberman, editors, Proceedings of
the Ninth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices(FNANO12), Snowbird, Utah, Published by
Sciencetechnica, (April 16-19, 2012).
Papers (most are
downloadable)
1. John H. Reif, Combinatorial
Aspects of Symbolic Program Analysis. Ph.D. Thesis, Harvard University, July
1977. [PDF] (Preface
& Introductory Chapter 1:[PDF], Chapter
2(pub. #3):[PDF], Chapter
3:[PDF], Chapter
4(pub. #5):[PDF],Chapter
5(pub. #4):[PDF])
2. Richard Barakat and John H.
Reif, Numerical Solution of the Fokker-Plank Equation via Chebyschev
Approximations with Reference to First Passage Time Probability Functions. Journal of Computational Physics, Vol.
23, No. 4, April 1977, pp. 425-445. [PDF]
3. John H. Reif and Harry R.
Lewis, Symbolic Evaluation and the Global Value Graph. 4th ACM Symposium on Principals of Programming Languages, Los Angeles, CA, January 1977, pp.
104-118. [PDF] Published
as Efficient Symbolic Analysis of Programs, in Journal of Computer and System Sciences, Vol. 32, No. 3, June 1986, pp. 280-314. [PDF]
4. John H. Reif, Code Motion.
Presented at Conference on Theoretical
Computer Science, University of
Waterloo, Canada, 1977. Published in SIAM
Journal on Computing, Vol. 9, No. 2, May 1980, pp. 375-395. [PDF]
5. John H. Reif, Symbolic
Program Analysis in Almost Linear Time. 5th
Annual ACM Symposium on Principals of Programming Languages, Tucson, AZ,
January 1978, pp. 76-83. [PDF] Published
as John H. Reif and R.E. Tarjan, SIAM
Journal on Computing, Vol. 11, No. 1, February 1982, pp. 81-93. [PDF]
6. John H. Reif, Data Flow
Analysis of Communicating Processes. 6th
Annual ACM Symposium on Principals of Programming Languages, San Antonio, TX, January 1979, pp.
257-268. [PDF] Published
as John H. Reif and Scott A. Smolka, International
Journal of Parallel Programming, Vol. 19, No. 1, February 1990. [PDF]
7. John H. Reif, The Complexity
of Extending a Graph Imbedding. Computer Science Department, University of
Rochester, TR-42, October 1978. [PDF]
8. Ion S. Filotti, Gary Miller, and John H. Reif, On
Determining the Genus of a Graph in 0(v^0(g)) Steps, 11th Annual ACM Symposium on Theory of Computing(STOC79), Atlanta,
GA, April 1979, pp. 27-37. [PDF]
9. John H. Reif, Universal
Games of Incomplete Information. 11th
Annual ACM Symposium on Theory of Computing, Atlanta, GA, April 1979, pp.
288-308. Harvard University TR-35-81. [PDF] Published
as The Complexity of Two-Player Games of Incomplete Information. Journal of Computer and System Sciences,
Vol. 29, No. 2, October 1984, pp. 274-301. [PDF]
10. Gary L. Peterson and John H. Reif,
Multiple-Person Alternation. 20th Annual
IEEE Symposium on Foundations of Computer Science, San Juan, Puerto Rico,
October 1979, pp. 348-363. Published as Gary L. Peterson, John H. Reif, and
Selman Azhar, Lower Bounds for Multiplayer Noncooperative Games of Incomplete
Information, Computers and Mathematics with Applications, Volume 41, April 2001,
pp. 957-992. [PDF]
11. John H. Reif, Complexity of
the Mover's Problem and Generalizations. 20th
Annual IEEE Symposium on Foundations of Computer Science, San Juan, Puerto
Rico, October 1979, pp. 421-427. [PDF] Published
as Complexity of the Generalized Mover's Problem, Chapter 11 in Planning, Geometry and Complexity of Robot
Motion, Jacob Schwartz, ed., Ablex Pub., Norwood, NJ, 1987, pp. 267-281. [PDF]
12. Gary L. Peterson and John
H. Reif, A Dynamic Logic of Multiprocessing with Incomplete Information. 7th Annual ACM Symposium on Principles of
Programming Languages, Las Vegas,
NV, January 1980, pp. 193-202. [PDF]
13. John H. Reif, Logics for
Probabilistic Programming. 12th Annual
ACM Symposium on Theory of Computing,
Los Angeles, CA, April 1980, pp. 8-13. [PDF]
14. John H. Reif and Paul G.
Spirakis, Random Matroids. 12th Annual
ACM Symposium on Theory of Computing,
Los Angeles, CA, April 1980, pp. 385-397. Revised as Probabilistic Analysis
of Random Extension-Rotation Algorithms, Harvard University TR-28-81, 1980. [PDF]
15. John H. Reif and Paul G.
Spirakis, Distributed Algorithms for Synchronizing Interprocess Communication
Within Real Time. 13th Annual ACM
Symposium on Theory of Computing, Milwaukee,
WI, 1981, pp. 133-145. Published as Real-Time Synchronization of Interprocess
Communications: ACM Journal of
Transactions on Programming Languages and Systems, Vol. 6, No. 2, April
1984, pp. 215-238. [PDF]
16. John H. Reif, Minimum s-t
Cut of Planar Undirected Network in 0(n log^2n) Time, 8th Colloquium on
Automata, Languages and Programming, (Shimon Even and Oded Kariv, editors)
volume 115 of Lecture Notes in Computer Science, pp. 56-67, Acre (Akko), Israel,
13-17 July 1981. Springer-Verlag. Published in SIAM Journal on Computing, Vol. 12, No. 1, February 1983, pp.
71-81. [PDF]
17. John H. Reif, Symmetric
Complementation. 14th Annual ACM
Symposium on Theory of Computing, San
Francisco, CA, May 1982, pp. 201-214. Presented at the NSF/AMS on Probabilistic Computational Complexity, Durham, NH, June 1982. Published in Journal of the ACM(JACM), Vol. 31, No. 2, April 1984, pp.
401-421. [PDF]
18. Joseph Y. Halpern and John
H. Reif, The Propositional Dynamic Logic of Deterministic, Well-Structured
Programs, 22nd Annual IEEE Symposium on
Foundations of Computer Science, Nashville,
TN, October 1981, pp. 322-334. Published in Journal
of Theoretical Computer Science, Vol.
27, 1983, pp. 127-165. [PDF]
19. John H. Reif and Paul G.
Spirakis, Unbounded Speed Variability in Distributed Communication Systems. 9th Annual ACM Symposium on Principals of
Programming Languages(POPL80), Albuquerque,
NM, January 1982, pp. 46-56. [PDF] Published
in SIAM Journal on Computing, Vol. 14, No. 1, February 1985, pp.
75-92. [PDF]
20. Gary L. Peterson and John
H. Reif, Decision Algorithms for Multiplayer Games of Incomplete Information.
Harvard University, TR-34-81. Published as Gary L. Peterson, John H. Reif, and
Selman Azhar, Decision Algorithms for Multiplayer Non-Cooperative Games of
Incomplete Information. Computers and Mathematics with Applications, Vol. 43,
Jan. 2002, pp. 179-206. [PDF]
21. John H. Reif and Paul G.
Spirakis, K-connectivity in Random Undirected Graphs, Discrete Mathematics, Vol.
54, No. 2, April 1985, pp. 181-191. [PDF] (Also,
John H. Reif and Paul G. Spirakis, Strong k-connectivity in Digraphs and Random
Digraphs, Harvard University TR-25-81. [PDF])
22. John H. Reif and Paul G.
Spirakis, Strong k-connectivity in Digraphs and Random Digraphs, Harvard
University TR-25-81. [PDF]
23. John H. Reif, On the Power
of Probabilistic Choice in Synchronous Parallel Machines. Harvard University
TR-30-81. 9th International Colloquium on
Automata, Languages and Programming, Aarhus,
Denmark, 1982, pp. 442-450. Published as On Synchronous Parallel Computations
with Independent Probabilistic Choice in SIAM
Journal on Computing, Vol. 13, No. 1, February 1984, pp. 46-56. [PDF]
24. John H. Reif and Paul G.
Spirakis, Real Time Resource Allocation in Distributed Systems, ACM Symposium on Principals of Distributed
Computing, Ottawa, Canada, August
1982, pp. 84-94. [PDF]
25. John H. Reif, Parallel Time
0(log n) Time Acceptance of Deterministic CFLs. 23rd Annual IEEE Symposium on Foundations of Computer Science, Chicago, IL, November 1982, pp.
290-296. Published as Phlip Klein and John H. Reif, Parallel Time 0(log n) Time Acceptance of Deterministic CFLs on an Exclusive-Write
P-RAM, SIAM Journal on Computing, Vol. 17, No. 3, June 1988, pp. 463-485.
[PDF]
26. John H. Reif and Paul G.
Spirakis, Expected Parallel Time and Sequential Space Complexity of Graph and
Digraph Problems, Algorithmica,
Special Issue on Graph Algorithms, Vol. 7, Numbers 5 & 7, pp. 597-630,
1992. [PDF]
27. Leslie G. Valiant and John
H. Reif, A Logarithmic Time Sort for Linear Size Networks. 15th Annual ACM Symposium on Theory of Computing, Boston, MA, April 1983, pp. 10-16. [PDF] Published
in Journal of the ACM(JACM), Vol. 34, No. 1, January 1987, pp.
60-76. [PDF]
28. John H. Reif and W.L.
Scherlis, Deriving Efficient Graph Algorithms. Logics
of Programs Workshop, Carnegie-Mellon University, Pittsburgh, PA, June 1983,
Lecture Notes in Computer Science, Vol. 164, 1984, pp. 421-441. Published in:
Verification: Theory and Practice: Essays Dedicated to Zohar Manna on the
Occasion of His 64th Birthday (edited by Nachum Dershowitz), LNCS series Vol.
2772, pp. 645-681, 2004. [PDF] or [PDF]
29. John H. Reif and A.P.
Sistla, A Multiprocess Network Logic with Temporal and Spatial Modalities, 10th International Colloquium on Automata,
Languages and Programming, Barcelona, Spain, July 1983; Lecture Notes in Computer Science, Vol.
154, 1983, pp. 629-639. Published in Journal
of Computer and System Sciences, Vol.
30, No. 1, February 1985, pp. 41-53. [PDF]
30. John H. Reif, Logarithmic
Depth Circuits for Algebraic Functions. 24th
Annual IEEE Symposium on Foundations of Computer Science, Tucson, AZ,
November 1983, pp. 138-145. Published in SIAM
Journal on Computing, Vol. 15,
No. 1, February 1986, pp. 231-242. [PDF]
31. John H. Reif, An n1+epsilon
Processor, 0(log n) Time Probabilistic Sorting Algorithm. SIAM 2nd Conference on the Applications of Discrete Mathematics, Cambridge, MA, June 1983, pp. 27-29. [PDF]
32. John H. Reif, Probabilistic
Parallel Prefix Computation, 13th Annual
International Conference on Parallel Processing, Michigan, 1984. Published in Computers
and Mathematics with Applications, Vol. 26, Number 1, July 1993, pp.
101-110. [PDF]
33. John H. Reif and Paul G.
Spirakis, Probabilistic Bidding Gives Optimal Distributed Resource Allocation. 11th International Colloquium on Automata, Languages
and Programming, Antwerp,
Belgium, July 1984. Published in Lecture
Notes in Computer Science, Vol. 172, pp. 391-402. [PDF]
34. John H. Reif, Depth-First
Search is Inherently Sequential. Information
Processing Letters, Vol. 20, No.
5, June 12, 1985, pp. 229-234. [PDF]
35. John H. Reif, A Topological
Approach to Dynamic Graph Connectivity. Information
Processing Letters, Vol. 25, No.
1, April 20, 1987, pp. 65-70. [PDF]
36. Gautam Kar, Christos N.
holaou, and John H. Reif, Assigning Processes to Processors: A Fault-Tolerant
Approach, 14th International Conference
on Fault-Tolerant Computing, Kissimmee,
FL, June 1984, pp. 306-309. [PDF]
37. Micheal Ben-Or, Dextor
Kozen, and John H. Reif, The Complexity of Elementary Algebra and Geometry. 16th Annual Symposium on Theory of
Computing, Washington, DC, April-May 1984, pp. 457-464. [PDF] Published
in Journal of Computer and Systems
Sciences, Vol. 32, No. 2, April
1986, pp. 251-264. [PDF]
38. Ravi Nair, Anni Bruss, and
John H. Reif, Linear Time Algorithms for Optimal CMOS Layout, International Workshop on Parallel Computing
and VLSI, Amalfi, Italy, May 1984; VLSI:
Algorithms and Architectures, North-Holland,
pp. 327-338. [PDF]
39. John H. Reif and Doug
Tygar, Efficient Parallel Pseudo-random Number Generation. CRYPTO-85, Proceedings, Vol. 218, H. Williams and E. Brickell, ed.,
Springer-Verlag, New York, NY, 1986, pp. 433-446 Presented at the Mathematical
Theory of Security, Boston, MA, 1985. Published in SIAM Journal on Computing, Vol. 17, No. 2, April 1988, pp. 404-411.
[PDF]
40. Peter Gacs and John H.
Reif, A Simple Three-dimensional Real-time Reliable Cellular Array. 17th Annual ACM Symposium on Theory of
Computing, Providence, RI, May 1985, pp. 388-395. [PDF] Published
in Journal of Computer and System
Sciences, Vol. 36, No. 2, April
1990, pp. 125-147. [PDF]
41. Victor Y. Pan and John H.
Reif, Efficient Parallel Solution of Linear Systems. 17th Annual ACM Symposium on Theory of Computing(STOC85),
Providence, RI, (ACM Press, New York) May 1985, pp. 143-152. Presented at the meeting on Efficient Algorithms,
Mathematisches Forschungsinstitut, Oberwolfach, W. Germany, November 1984.
Presented at 2nd SIAM Conference on
Applied Linear Algebra, Raleigh, NC, April 1985. Published as Fast and
Efficient Parallel Solution of Sparse Linear Systems. SIAM Journal on Computing, Vol 22, No. 6, pp. 1227-1250, December
1993. [PDF] or [PDF]
42. Gary Miller and John H.
Reif, Parallel Tree Contraction and its Application. Harvard University
TR-18-85. 26th Annual IEEE Symposium on
Foundations of Computer Science, Portland, OR, October 1985, pp. 478-489.
42a Portions Published as Parallel Tree Contraction Part I:
Fundamentals, Parallel Tree Contraction Part 1:
Fundamentals. In Randomness and Computation, (Advances in Computing Research, Vol. 5., Silvio
Micali, editor), pp. 47–72, JAI Press,
Greenwich, Connecticut, 1989. [PDF]
42b Portions Published as Parallel Tree Contraction Part II:
Further Applications, SIAM Journal on
Computing, Vol. 20, No. 6, pp. 1128-1147, December 1991. [PDF]
43. Sanguthevar Rajasekaran and
John H. Reif, An Optimal Parallel Algorithm for Integer Sorting. 26th Annual IEEE Symposium on Foundations of
Computer Science, Portland, OR, October 1985, pp. 496-503. Published as Optimal and Sublogarithmic Time
Randomized Parallel Sorting Algorithms, SIAM
Journal on Computing, Vol. 18, No. 3, June 1989, pp. 594-607. [PDF] or [PostScript] [PDF]
44. John H. Reif and M. Sharir,
Motion Planning in the Presence of Moving Obstacles, 26th Annual IEEE Symposium on Foundations of Computer Science,
Portland, OR, October 1985, pp.
144-154. Published in Journal of the ACM (JACM),
41:4, July 1994, pp. 764-790. [PDF] or [PostScript] [PDF]
45. John H. Reif, Probabilistic
Algorithms in Group Theory. Foundations of Computation Theory (FCT85), Cottbus,
Democratic Republic of Germany, September 1985; Lecture Notes in Computer Science, Vol. 199, 1985, pp. 341-350.
Also TR85-01, Dept. of Computer Science, Harvard University, (1985). Published
as Selman Azhar and John H. Reif, Efficient Algorithmic Learning of the
Structure of Permutation Groups by Examples, Computers & Mathematics with Applications, Volume 37, Issue 10,
May 1999, pp. 105-132. [PDF]
46. Victor Y. Pan and John H.
Reif, Fast and Efficient Algorithms for Linear Programming and for the Linear
Least Squares Problem, 12th International
Symposium on Mathematical Programming,
MIT, Cambridge, MA, pp. 283-295, August 1985. Abstract published as
Efficient Parallel Linear Programming, Operations
Research Letters, Vol. 5, No. 3,
August 1986, pp. 127-135. [PDF] Also presented as Fast and Efficient Parallel
Linear Programming and Least Squares Computations at Aegean Workshop on
Computing, Loutraki, Greece, July 1986; Lecture
Notes in Computer Science, Springer-Verlag, Vol. 227, 1986, pp. 283-295.
Full Paper published as Fast and Efficient Linear Programming and Linear
Least-Squares Computations, Computers and
Mathematics with Applications, Vol.
12A, No. 12, 1986, pp. 1217-1227. [PDF]
47. John H. Reif, Parallel
Interpolation Search. 23rd Annual
Allerton Conference on Communication, Control and Computing, Monticello, IL, October 1985. Published
as D.E. Willard and John H. Reif, Parallel Processing can be Harmful: the
Unusual Behavior of Interpolation Search, Journal
of Information and Computation, Vol. 81, No. 3, June 1989, pp. 364-379. [PDF]
48. John H. Reif and Scott A.
Smolka, The Complexity of Reachability in Distributed Communicating Processes, Journal of Acta Informatica, Vol. 25(3), April 1988, pp.333-354. [PDF]
49. Steve Homer and John H.
Reif, Arithmetic Theories for Computational Complexity Problems, Journal of Information and Control, Vol.
69, nos. 1-3, April/May/June 1986, pp. 1-11. [PDF]
50. James A. Storer and John H.
Reif, A Parallel Architecture for High Speed Data Compression, 3rd Symposium on the Frontiers of Massively
Parallel Computation, College Park, MD, October 1990, pp. 238-243.
Published in Journal of Parallel and Distributed Computation, No. 13, 1991, pp.
222-227. [PDF]
51. Victor Y. Pan and John H.
Reif, Fast and Efficient Parallel Solution of Dense Linear Systems. Computers and Mathematics with Applications,
Vol. 17, No. 11, 1989, pp. 1481-1491. [PDF]
52. John H. Reif and James A.
Storer, Shortest Paths in the plane with polygonal obstacles, Journal of the ACM(JACM) 41:5,
September, 1994, pp. 982-1012. [PDF]
53. John H. Reif and James A.
Storer, Minimizing Turns for Discrete Movement in the Interior of a Polygon, IEEE Journal of Robotics and Automation, Vol. 3, No. 3, June 1987, pp. 182-193.
[PDF]
54. John H. Reif, Efficient
VLSI Fault Simulation. Computers and
Mathematics with Applications, Vol 25, No. 2, Jan. 1993, pp. 15-32. [PDF]
55. Richard E. Ladner and John
H. Reif, The Logic of Distributed Protocols. Conference on Theoretical Aspects of Reasoning about Knowledge, Los
Altos, CA, March 1986, pp. 207-223. [PDF]
56. Victor Y. Pan and John H.
Reif, Extension of the Parallel Nested Dissection Algorithm to Path Algebra
Problems. Presented at 6th Conference on
Foundation of Software Technology and Theoretical Computer Science, New Delhi, India; Lecture Notes in Computer Science, Springer Verlag, Vol. 241, pp.
470–487, 1986. An abstract of this paper appears as Parallel Nested Dissection
for Path Algebra Computations, Operations
Research Letters, Vol. 5, No. 4,
October 1986, pp. 177-184. [PDF] Published
as Fast and Efficient Solution of Path Algebra Problems, Journal of Computer and Systems Sciences, Vol. 38, No. 3, June
1989, pp. 494-510. [PDF]
57. John
Canny and John H. Reif, New Lower Bound Techniques for Robot Motion Planning
Problems. 28th Annual IEEE Symposium on
Foundations of Computer Science,
Los Angeles, CA, October 1987, pp. 49-60. [PDF]
58. Richard Barakat and John H.
Reif, Lower Bounds on the Computational Efficiency of Optical Computing
Systems. Journal of Applied Optics, Vol. 26, No. 6, March 15, 1987, pp.
1015-1018. [PDF]
59. Richard Barakat and John H.
Reif, Polynomial Convolution Algorithm for Matrix Multiplication with
Application for Optical Computing. Published in Journal of Applied Optics, Vol.
26, No. 14, July 15, 1987, pp. 2707-2711. [PDF]
60. John H. Reif, A Survey on
Advances in the Theory of Computational Robotics. Proceedings of the Fourth
Workshop of Adaptive Systems Control Theory, Princeton, NJ, 1986. Also as
Chapter in Book: Adaptive and Learning Systems: Theory and Applications, Princeton,
NJ (edited by K.S. Narendra), Plenum
Press, New York, NY, pp. 421--427 1986. [PDF]
61. Phlip Klein and John H.
Reif, An Efficient Parallel Algorithm for Planarity. 27th Annual IEEE Symposium on Foundations of Computer Science,
Toronto, Canada, October 1986, pp. 465-477. Published in Journal of Computer and System Sciences, Vol. 37, No. 2, October 1988, pp.
190-246. [PDF]
62. Charles E. Leiserson, J.P.
Mesirov, L. Nekludova, S.M. Omohundro, John H. Reif, and W. Taylor, Solving
Sparse Systems of Linear Equations on the Connection Machine. Annual SIAM Conference, Boston, MA, July
1986. [PDF]
63. T. Opsahl
and John H. Reif, Solving Very Large, Sparse Linear Systems on Mesh-Connected
Parallel Computers. First Symposium on
Frontiers of Scientific Computing, NASA,
Goddard Space Flight Center, Greenbelt, MD, September 1986, pp. 2241-2248. [PDF]
64. John H.
Reif, Simon Kasif, and Deepak Sherlekar, Formula Dissection: A Parallel Algorithm for
Constraint Satisfaction. IEEE Workshop on
Computer Architecture for Pattern Analysis and Machine Intelligence,
Seattle, WA, October 1987, pp. 51-58. Published in Computers and Mathematics
with Applications, Vol. 5, (2008), pp. 1170-1177. [PDF]
[PDF]
65. John
H. Reif and Sandeep Sen, Optimal Randomized Parallel Algorithms for
Computational Geometry. 16th
International Conference on Parallel Processing, St. Charles, IL, August
1987, pp. 270-276. Published in Algorithmica,
Vol. 7, No. 1, January 1992, pp. 91-117. [PDF]
66. John Canny, B. Donald, John
H. Reif and Patrick G. Xavier. On the Complexity of Kinodynamic Planning. 29th Annual IEEE Symposium on Foundations of
Computer Science, White Plains,
NY, October 1988, pp. 306-316. Published as Kinodynamic Motion Planning, Journal of the ACM, Vol 40(5), November
1993, pp. 1048-1066. [PDF]
67. Sanguthevar Rajasekaran and
John H. Reif, Randomized Parallel Computation. Presented at Foundations of Computation Theory Conference, Kasan, USSR, June 1987; Lecture Notes in
Computer Science, Vol. 278, 1987,
pp. 364-376. Published in Chapter 11 of Concurrent
Computations: Algorithms, Architecture and Technology, S.K. Tewksbury, B.W.
Dickinson and S.C. Schwartz, ed., 1988, pp. 181-202. [PDF]
68. John H. Reif and Steve R.
Tate, On Threshold Circuits and Polynomial Computation. 2nd Structure in Complexity Theory Conference, Ithaca, NY, June 1987. Published in SIAM Journal on Computing, Vol.21, No. 5, October 1992, 896-908. [PDF] or [PostScript] [PDF]
69. Vijaya Ramachandran and
John H. Reif, An Optimal Parallel Algorithm for Graph Planarity. 30th Annual IEEE Symposium on Foundations of
Computer Science, Research Triangle Park, NC, October 1989, pp. 282-287.
Published as Planarity Testing in Parallel,
Journal of Computer and System Sciences, 49:3, December, 1994, pp. 517-561. [PostScript] [PDF]
70. Sanguthevar Rajasekaran and
John H. Reif, Nested Annealing: A Provable Improvement to Simulated Annealing.
Presented at Workshop on Applications of
Combinatorics and Graph Theory to Computer Science, Institute for
Mathematics and its Applications, University of Minnesota, December 1987.
Presented at the 15th International
Colloquium on Automata, Languages and Programming, Tampere, Finland, July 1988; Lecture
Notes in Computer Science, Vol. 317, 1988, pp. 455-472. Published in Journal of Theoretical Computer Science,
99(1):157-176, 1 June 1992. [PDF]
71. Victor Y. Pan and John H.
Reif, Some Polynomial and Toeplitz Matrix Computations. 28th Annual IEEE Symposium on Foundations of Computer Science, Los
Angeles, CA, October 1987, (IEEE Computer Society Press) pp. 173-184. [PDF]
72. James A. Storer and John H.
Reif, Real-time Compression of Video on a Grid-connected Parallel Computer. 3rd International Conference on
Supercomputing, Boston, MA, May
1988. [PDF]
73. Edward W. Davis and John H.
Reif, Architecture and Operation of the BLITZEN Processing Element. 3rd International Conference on
Computing on Supercomputing, Boston,
MA, May 1988. Also revised as Donald W. Blevins, Edward W. Davis, and John H.
Reif, Processing Element and Custom Chip Architecture for the BLITZEN Massively
Parallel Processor, MCNC Technical Report TR87-22, October 1987, revised June
1988. [PDF]
74. John H. Reif and Sandeep
Sen, An Efficient Output-Sensitive Hidden-Surface Removal Algorithm and its
Parallelization. 4th Annual ACM Symposium
on Computational Geometry, Urbana,
IL, June 1988, pp. 193-200.
Published as An Efficient Output-Sensitive Hidden-Surface Removal Algorithm for
Polyhedral Terrains, Journal of
Mathematical and Computer Modeling, Vol. 21, No. 5, pp. 89-104, 1995. [PDF] or [PDF]
75. Lars S. Nyland and John H.
Reif, An Algebraic Technique for Generating Optimal CMOS Circuitry in Linear
Time, Computers and Mathematics with
Applications Vol 31, No. 1, Jan. 1996, pp.85-108. [PDF]
76. Donald W. Blevins, Edward
W. Davis, Richard A. Heaton and John H. Reif, BLITZEN: A Highly Integrated
Massively Parallel Machine. 2nd Symposium
on Frontiers of Massively Parallel Computation, Fairfax, VA, October 1988. Published in Journal of Parallel and Distributed Computing, Vol. 8, February
1990, pp. 150-160. [PDF]
77. John H. Reif and Steve R.
Tate, Optimal Size Integer Division Circuits. 21st Annual ACM Symposium on Theory of Computing, Seattle, WA, May
1989, pp. 264-273. Presented at
meeting on Efficient Algorithms, Mathematisches Forschungsinstitut, W. Germany,
September 1989. Published in SIAM Journal
on Computing, Vol. 19, No. 5, October 1990, pp. 912-924. [PDF] or [PostScript] [PDF] or [PostScript]
78. John H. Reif and Sandeep
Sen, Polling: A New Randomized Sampling Technique for Computational Geometry, 21st Annual ACM Symposium on Theory of
Computing, Seattle, WA, May 1989, pp. 394-404. [PDF] Revised as
Optimal Parallel Randomized Algorithms for Three-Dimensional Convex Hulls and
Related Problems, Published in SIAM
Journal on Computing, Vol. 21, No. 3, June 1992, pp. 466-485. [PDF] or [PDF] (see also
Erratum: Optimal parallel randomized algorithms for three-dimensional convex
hulls and related problems. SIAM Journal on Computing, 23(2):447-448, April
1994. [PDF])
79. John
H. Reif and A. Tyagi, Energy Complexity of Optical Computations, 2nd IEEE Symposium on Parallel and
Distributed Processing, Dallas, TX, December 1990, pp. 14-21. Revised for Journal
Publication in International Journal of Unconventional Computing, 2016,
Vol. 12 Issue 5/6, pp. 393-412. [PDF]
80. John H. Reif, Optical
expanders give constant time holographic routing using O(N log N) switches,
1988 [PDF]. Full
paper appeared as E.S. Maniloff, K. Johnson, and John H. Reif, Holographic
Routing Network for Parallel Processing Machines Holographic Optics II: Principals and Applications, G. Michael
Morris; Ed. SPIE Proceedings Series,
Vol. 1136, EPS/EUROPTICA/SPIE International Congress on Optical Science and
Engineering, Paris, France, April 1989, pp. 283-289. [PDF]
81. John H.
Reif, Doug Tygar, and Akitoshi Yoshida, The Computability and Complexity of
Optical Beam Tracing. 31st Annual IEEE
Symposium on Foundations of Computer Science, St. Louis, MO, October 1990,
pp. 106-114. Published as The Computability and Complexity of Ray Tracing in Discrete & Computational Geometry,
11: pp. 265-287 (December 1994). [PDF]
82. Selman
Azhar, Andrew McLennan and John H. Reif, Computation of Equilibria in
Noncooperative Games, Duke University Technical Report CS-1991-36. Proc. Workshop for Computable Economics,
Dec. 1992. Published in Computers & Mathematics
with Applications, Volume 50, Issues 5-6, September 2005, pp. 823-854. [PDF]
83. R. Paturi, Sanguthevar
Rajasekaran, and John H. Reif, Efficient and Robust Learning Using Statistical
Bootstrap, Proceedings of the 2nd Annual
Workshop on Computational Learning Theory, Santa Cruz, CA, August 1989. [PostScript] [PDF] Published
as The Light Bulb Problem, Information
and Computation, 117(2):187-192, March 1995. [PDF]
84. John H. Reif and Sandeep
Sen, Randomized Parallel Algorithms. IBM
Workshop on Capabilities and Limitations of Parallel Computing, San Jose,
CA, December 1988. Information Processing
89, G. Ritter, ed., Elsevier Science
Publishers, North Holland, 1989, pp. 455-458. [PDF] A Case for
Randomized Parallel Algorithms in Opportunities
and Constraints of Parallel Computing, J.L.C. Sanz (ed.), Springer-Verlag New York, 1989, pp. 101-105. Also
presented as Randomization in Parallel Algorithms and its Impact on
Computational Geometry, in Optimal
Algorithms;Lecture Notes in Computer
Science, Vol. 401, 1989, pp. 1-8. [PDF] Also
presented as C. Pandurangan, Sanguthevar Rajasekaran, John H. Reif, Sandeep
Sen, Studies on Sequential and Parallel Randomized Algorithms, Indo-US Workshop
on Cooperative Research in Computer Science, Bangalore, India, August 4-6,
1992. [PDF]
85. Victor Y. Pan and John H.
Reif, On the Bit-Complexity of Discrete Approximations to PDEs. International Colloquium on Automata,
Languages, and Programming(ICALP 90), Warwich, England, Springer Lecture
Notes in Computer Science 443, pp. 612-625, July 1990. [PDF] Published
as The Bit-Complexity of Discrete Solutions of Partial Differential Equations:
Compact Multigrid, Computers and
Mathematics with Applications, Vol. 20, No. 2, 1990, pp. 9-16. [PDF].
86. John H. Reif and A. Tyagi,
Efficient Algorithms for Optical Computing with the DFT Primitive, Presented at
10th Conference on Foundations of
Software Technology and Theoretical Computer Science, Bangalore, India, Lecture Notes in Computer Science, pp.
149-160 (December 1990). Published as Efficient Algorithms for Optical
Computing with the discrete Fourier transform (DFT) primitive, Journal of Applied Optics, Vol. 36,
1997, pp. 7327-7340. [PDF] or [PostScript] [PDF]
87. John Canny, A. Rege, and
John H. Reif, An Exact Algorithm for Kinodynamic Planning in the Plane. 6th Annual ACM Symposium on
Computational Geometry, Berkeley, CA, June 1990, pp. 271-280. [PDF] Published
in Discrete and Computational Geometry,
Vol. 6, 1991, pp. 461-484. [PDF]
88. John H. Reif and Sandeep Sen, Randomized Algorithms for
Binary Search and Load Balancing on Fixed Connection Networks with Geometric
Applications. 2nd Annual ACM Symposium on
Parallel Algorithms and Architectures, Crete, Greece, July 1990, pp.
327-337. Published in SIAM Journal of
Computing 23:3, June, 1994, pp.633-651. [PDF]
89. John H. Reif, Efficient
Parallel Algorithms: Theory and Practice. SIAM
35th Anniversary Meeting, Denver, CO, October 1987. XI World Computer Congress, IFIP 89, San Francisco, CA, 1989.
90. Hristo Djidjev and John H.
Reif, An Efficient Algorithm for the Genus Problem with Explicit Construction
of Forbidden Subgraphs. 23rd Annual ACM
Symposium on Theory of Computing, New Orleans, LA, May 1991, pp. 337-347. [PDF]
91. Hillel Gazit and John H.
Reif, A Randomized Parallel Algorithm for Planar Graph Isomorphism. 2nd Annual ACM Symposium on Parallel
Algorithms and Architectures, Crete, Greece, July 1990, pp. 210-219.
Published in Journal of Algorithms, Vol.
28, No. 2, pp. 290-314, August 1998. [PostScript] [PDF]
92. Victor Y. Pan and John H.
Reif, The Parallel Computation of Minimum Cost Paths in Graphs by Stream
Contraction, Information Processing
Letters, Vol. 40, October 25,1991, pp. 79-83. [PDF]
93. John H. Reif and Steve R.
Tate, Approximate Kinodynamic Planning Using L2-norm Dynamic Bounds. Duke University Technical Report
CS-1990-13, 1989. Published in Computers
and Mathematics with Applications, Vol. 27, No.5, pp.29-44, March 1994. [PostScript] [PDF]
94. Royals, M., Tassos Markas,
N. Kanopoulos, John H. Reif and James A. Storer, On the Design and
Implementation of a Lossless Data Compression and Decompression Chip, IEEE Journal of Solid State Circuits (JSSC), Vol. 28, No.
9, pp. 948-953, Sep. 1993. [PDF]
95. Micheal Karr, S. Krishnan,
John H. Reif, Derivation of the Ellipsoid Algorithm, Duke University Technical
Report CS-1991-17, (1990). [PDF]
96. John H. Reif and A. Tyagi,
An Optical Delay Line Memory Model with Efficient Algorithms. Advanced Research in VLSI Conference,
MIT Press, Santa Cruz, CA, March 1991. Published in Optical Engineering, 36(09), pp. 2521-2535, Sept. (1997). [PostScript] [PDF]
97. Selman Azhar and John H.
Reif, Crypto-Complexity Based Models of Efficiency in Capital Markets, 1994. [PDF]
98. John H. Reif and Steve R.
Tate, Continuous Alternation: The Complexity of Pursuit in Continuous Domains,
Special Issue on Computational Robotics: the Geometric Theory of Manipulation,
Planning and Control, Algorithmica,
Vol. 10, pp. 151-181, 1993. [PostScript] [PDF]
99. John H. Reif and Akitoshi
Yoshida, Optical Expanders with Applications in Optical Computing, Journal of Applied Optics, 32, 1993, pp.
159-165. [PDF] or [PostScript] [PDF]
100. James A. Storer and John
H. Reif, Low-Cost Prevention of Error Propagation for Data Compression with
Dynamic Dictionaries, Proceedings: IEEE
Data Compression Conference (DCC'97) Snowbird, UT, IEEE Computer Society
Press, James A. Storer, Martin Cohn (Eds.), March 1997, pp. 171-180. Published
as Error Resilient Optimal Data Compression, SIAM Journal of Computing
(SICOMP), Vol 26, Num 4, July 1997, pp. 934-939. [PostScript] [PDF]
101. Peter H. Mills, Lars S.
Nyland, J.F. Prins, John H. Reif and Robert A. Wagner, Prototyping Parallel and
Distributed Programs in Proteus. 3rd IEEE Symposium on Parallel and
Distributed Processing, Dallas, TX, pp. 10-19, IEEE, 1991. [PostScript] [PDF]
102. James A. Storer, Tassos
Markas and John H. Reif, A Massively Parallel VLSI Compression System using a
Compact Dictionary. IEEE Workshops on
VLSI & Signal Processing, 1990, San Diego, CA. Published as A Massively
Parallel VLSI Design for Data Compression Using a Compact Dictionary, VLSI Signal Processing, No. 4, 1990
(edited by H.S. Moscovitz and K. Yao and R. Jain), Chapter 32, IEEE Press,
1990, New York, NY, pp. 329-338. [PDF]
103. S. Krishnan and John H.
Reif, Towards Randomized Strongly Polynomial Algorithms for Linear Programming,
Duke University Technical Report CS-1991-18. [PDF]
104. Victor Y. Pan and John H.
Reif, Decreasing the Precision of Linear Algebra Computations by Using Compact
Multigrid and Backward Interval Analysis. 4th
SIAM Conference in Applied Linear Algebra, Minneapolis, MN, September 1991. Published as Compact Multigrid, SIAM Journal of Scientific and Statistical
Computing, Vol. 13, No. 1, pp. 119-127, (1992). [PDF]
105. Tassos Markas and John H.
Reif, Fast Computations of Vector Quantization Algorithms. NASA Technical
Report TR-91-58, 1991.
106. Tassos Markas and John H.
Reif, Image Compression Methods with Distortion Controlled Capabilities. IEEE Data Compression Conference (DCC 91),
Snowbird, UT, IEEE Computer Society Press, April 1991, pp. 93-102. Published as
Quad Tree Structures for Image Compression Applications, special issue of Journal of Information Processing and
Management, 1992, pp. 707-721. [PDF]
107. Joseph Cheriyan and John
H. Reif, Algebraic Methods for Testing the k-Vertex
Connectivity of Directed Graphs, 3rd
Annual ACM-SIAM Symposium on Discrete Algorithms, Orlando, Florida, 1992, pp. 203-210. [PDF] Published
as Directed s-t Numberings, Rubber
Bands, and Testing Digraph k-Vertex
Connectivity, in Combinatorica 14(4)
pp. 435-451, 1994. [PDF]
108. John H. Reif and Akitoshi
Yoshida, Optical Techniques for Image Compression. 2nd Annual IEEE Data Compression Conference (DCC 92), Snowbird, UT,
IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), March 1992,
pp. 32-41. Also in Image and Text
Compression, edited by James A. Storer, Kluwer Academic Publishers, 1992.
Published as "Optical Computing Techniques for Image/Video
Compression," in Proceedings of the
IEEE, 82:6, June 1994, pp. 948-954. [PDF]
109. John H. Reif and Hongyan
Wang, On Line Navigation Through Regions of Variable Densities. ARO
Computational Geometry Workshop, Raleigh, North Carolina, October, 1993.
Rewritten as On-Line Navigation Through Weighted Regions. [PostScript] [PDF]
110. Ming Kao, John H. Reif,
and Steve R. Tate, Searching in an Unknown Environment: An Optimal Randomized
Algorithm for the Cow-Path Problem, Proceedings
of the 4th Annual ACM-SIAM Symposium
on Discrete Algorithms (SODA'93), Austin, TX, Jan 1993, pp.441-447.
Published in Information and Computation,
Vol 131, No. 1 (1996), p 63-80. [PostScript] [PDF]
111. John H. Reif, O(log2 n)
Time Efficient Parallel Factorization of Dense, Sparse Separable, and Banded
Matrices. 5th Annual ACM Symposium on
Parallel Algorithms and Architectures (SPAA'94), Cape May, NJ, June 1994,
pp. 114-121. [PostScript] [PDF]
112. John H. Reif, An O(n
log^3 n) Algorithm for the Real Root
Problem. 34th Annual IEEE Conference on
Foundations of Computer Science (FOCS '93) Proceedings, November 1993, Palo
Alto, CA, pp. 626-635. Revised as An Efficient Algorithm for the Real Root and
Symmetric Tridiagonal Eigenvalue Problems, 1994. [PostScript] [PDF] and [PostscriptFigures]
113. Tassos Markas and John H.
Reif, Memory-Shared Parallel Architectures for Vector Quantization Algorithms,
1992. Picture Coding Symposium, Lusanne Switzerland, March, 1993.
114. Peter H. Mills, Lars S.
Nyland, Jan Prins, and John H. Reif, Prototyping N-body Simulation in Proteus, Sixth International Parallel Processing Symposium, IEEE, Beverly
Hills, CA, pp. 476-482, 1992. [PostScript] [PDF]
115. Deganit Armon and John H.
Reif, Space and time
efficient implementations of parallel nested dissection,
4th Annual ACM Symposium
on Parallel Algorithms and Architectures, San Diego, CA, July 1992.
Submitted
for journal publication as Space and Time Efficient Implementations of a
Parallel Direct Solver using Nested Dissection. [PDF]
116. Peter H. Mills, Lars S.
Nyland, Jan Prins, and John H. Reif, Prototyping High-Performance Parallel
Computing Applications in Proteus. DARPA Software Technology Conference,
May, 1992. [PostScript] [PDF]
117. Victor Y. Pan, John H.
Reif, Steve R. Tate. The Power of Combining the Techniques of Algebraic and
Numerical Computing: Improved Approximate
Multipoint Polynomial Evaluation and Improved Multipole Algorithms, 32th Annual
IEEE Symposium on Foundations of Computer Science (FOCS'92), Pittsburgh, PA,
Oct. 1992, pp. 703-713. Rewritten as John H. Reif and Steve R. Tate,
"N-body simulation I: Fast algorithms for potential field evaluation and
Trummer's problem". Tech. Report. #N-96-002, Univ. of North Texas, Dept.
of Computer Science (1996). [PostScript] [PDF] Submitted
for journal publication as as John H. Reif and Steve R. Tate, Efficient
N-body Simulation: Fast Algorithms for Potential Field Evaluation and Trummer’s
Problem [PDF].
118. William L. Hightower, Jan
Prins, and John H. Reif, Implementations of Randomized Sorting on Large
Parallel Machines. 4th Annual ACM
Symposium on Parallel Algorithms and Architectures (SPAA'92), San Diego,
CA, pp. 158-167, July 1992. [PDF]
119. Yijie Han, Victor Y. Pan,
and John H. Reif, Efficient Parallel Algorithms for Computing All Pair Shortest
Paths in Directed Graphs. University of Kentucky Technical Report 204-92. 4th Annual ACM Symposium on Parallel
Algorithms and Architectures, San Diego, CA, July 1992, pp. 353-362.
Published in Algorithmica, Vol 17, pp. 399-415, 1997. [PDF]
120. John H. Reif and Hongyan
Wang, Social Potential Fields: A Distributed Behavioral Control for Autonomous
Robots, Workshop on Algorithmic
Foundations of Robotics (WAFR'94), San Francisco, California, February,
1994; The Algorithmic Foundations of Robotics, A.K.Peters, Boston, MA. 1995,
pp. 431-459. Published in Robotics and Autonomous Systems, Vol. 27, no.3,
pp.171-194, (May 1999). [PostScript] [PDF]
121. John H. Reif and Steve R.
Tate, Dynamic Algebraic Algorithms, Proceedings
of the 5th Annual ACM-SIAM Symposium
on Discrete Algorithms (SODA'94), TX, Jan. 1994. pp.290-301. Published as
On Dynamic Algorithms for Algebraic Problems, Journal of Algorithms, Volume 22,
Number 2, pp. 347-371, February 1997. [PostScript] [PDF]
122. John H. Reif and Steve R.
Tate, Dynamic Parallel Tree Contraction, 5th
Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'94),
Cape May, NJ, June 1994. pp.114-121. Revised version submitted for journal
publication. [PDF]
123. Deganit Armon and John H.
Reif, A Dynamic Separator Algorithm with Applications to Computational Geometry
and Nested Dissection, 3rd Annual
Workshop on Algorithms and Data Structures (WADS '93), Montreal, Quebec,
Canada, August, 1993, pp. 107-118. [PDF]
124. Selman Azhar, Greg J.
Badros, Arman Glodjo, Ming Kao, and John H. Reif, Data Compression Techniques
for Stock Market Prediction, Proceedings:
IEEE Data Compression Conference (DCC'94), Snowbird, UT, IEEE Computer
Society Press, James A. Storer, Martin Cohn (Eds.), March 1994, pp. 72-82. [PDF]
125. Joseph Cheriyan and John
H. Reif, Parallel and Output Sensitive Algorithms for Combinatorial and Linear
Algebra Problems, 1992. 4th Annual ACM
Symposium on Parallel Algorithms and Architectures (SPAA'93), Velon,
Germany, July 1993, p.50-56. Published as John H. Reif, Parallel Output
Sensitive Algorithms for Combinatorial and Linear Algebra Problems, Journal of Computer and System Sciences,
Vol. 62, May 2001, pp. 398-412. [PostScript] [PDF]
126. Sotiris E. Nikoletseas,
John H. Reif, Paul G. Spirakis, Moti Yung, Stochastic Graphs Have Short Memory:
Fully Dynamic Connectivity in Poly-Log Expected Time. Proceedings of the 22nd Annual Colloquium on Automata, Languages and
Programming (ICALP'95), Szeged, Hungary, July 1995, pp. 159-170. [PDF]
127. Steve R. Tate and John H.
Reif, The Complexity of N-body Simulation, Proceedings
of the 20th Annual Colloquium on Automata, Languages and Programming (ICALP'93),
Lund, Sweden, July, 1993, pp. 162-176. [PostScript] [PDF]
128. Tassos Markas and John H.
Reif, Multispectral Image Compression Algorithms, Proceedings: IEEE Data Compression Conference (DCC'93), Snowbird, UT, IEEE Computer Society Press, James A.
Storer, Martin Cohn (Eds.), pp. 391-400, March 1993. [PDF]
129. Peter H. Mills, Jan Prins,
and John H. Reif, Rate Control as a Language Construct for Parallel and
Distributed Programming, Proc. IEEE Workshop on Parallel and Distributed
Real-Time Systems (IPPS'93), pp. 164-170, 1993. [PostScript] [PDF]
130. Richard Barakat and John
H. Reif, Diffraction Realization of an Optical Expander, (1993). [PDF]
131. Lars S. Nyland, Jan F.
Prins, and John H. Reif, A Data Parallel Implementation of the Adaptive Fast
Multipole Algorithm. Dartmouth Institute
for Advanced Graduate Studies (DAGS '93), Hanover, NH, June, 1993, pp.
111-123. [PostScript] [PDF]
132. Sefeng Chen and John H.
Reif, Using difficulty of prediction to decrease computation: fast sort,
priority queue and convex hull on entropy bounded inputs, 34th Annual IEEE Conference on Foundations of Computer Science (FOCS
'93) Proceedings, November 1993, Palo Alto, CA, pp. 104-112. [PDF]
133. Andrew Neff and John H.
Reif, An O(n^{1+epsilon} log b)
Algorithm for the Complex Roots Problem. 35th
Annual IEEE Conference on Foundations of Computer Science (FOCS '94)
Proceedings, Santa Fe, NM, November 1994. pp. 540-547. Improved Paper
Published as An Efficient Algorithm for the Complex Roots Problem, Journal of
Complexity, 12(2) pp. 81-115, (June 1996). [PostScript] [PDF]
134. Andrew
Goldberg, Jan Prins, Rickard Faith, Zhiyong Li, Peter H. Mills, Lars S. Nyland,
Daniel Palmer, John H. Reif, James Riely, and Stephen Westfold, The Proteus
System for the Development of Parallel Applications. Prototyping and Software
Development (Malcolm C. Harrison, ed.), Chapter 6, pp. 151-190, Digital Book,
1996. [PostScript]
[PDF]
135. Peter H. Mills, Lars S.
Nyland, J.F. Prins, and John H. Reif, Software Issues in High-Performance
Computing and a Framework for the Development of HPC Applications. In Developing a Computer Science Agenda for
High Performance Computing (U. Vishkin, ed.) pp. 110-117, ACM, 1994. [PostScript] [PDF]
136. Andrew Goldberg, Peter H.
Mills, Lars S. Nyland, Jan F. Prins, John H. Reif, and J. Riely, Specification
and Development of Parallel Algorithms with the Proteus System, Specification
of Parallel Algorithms, DIMACS Series in
Discrete Mathematics and Theoretical Computer Science, AMS Press, Vol. 18,
1994, pp. 383-399. [PostScript] [PDF]
137. Victor Y. Pan and John H.
Reif, Generalized Compact Multi-grid, Computers
Math Applications, Volume 25, Number 9, pp. 3-5, May 1993. [PDF]
139. Sefeng Chen and John H.
Reif, Fast Pattern Matching for Entropy Bounded Text. Proceedings: IEEE Data Compression Conference (DCC'95) Snowbird,
UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), March
1995, pp. 282-301. [PDF]
140. John H. Reif, Efficient
Parallel Solution of Sparse Eigenvalue and Eigenvector Problems, Proceedings of the 36th Annual IEEE
Symposium on Foundations of Computer Science (FOCS'95) Milwaukee, WI,
October 23-25, 1995, pp. 123-132. Published as Efficient Parallel Computation
of the Characteristic Polynomial of a Sparse, Separable Matrix, Algorithmica,
29: 487-510 (2001). [PDF]
141. Akitoshi
Yoshida, Jannick P. Rolland and John H. Reif, Design and Applications of a
High Resolution Insert Head-Mounted Display. IEEE Virtual Reality Annual International Symposium (VRAIS'95),
Research Triangle Park, NC, March 11-15, 1995, pp. 84-93. [PostScript]
[PDF]
Also, Jannick P. Rolland and Akitoshi Yoshida, and John H. Reif,
Optical design and analysis of a head-mounted display with a high-resolution
insert, (Novel Optical Systems Design and Optimization, Jose M. Sasian; Ed.,),
Proc. SPIE Vol. 2537, pp. 71-82, Aug. 1995. Published as Jannick
P. Rolland, Akitoshi Yoshida, Larry D.
Davis, and John H. Reif, High resolution inset head-mounted display, Applied
Optics: Optical Technology and Biomedical Optics, 37(19), 4183-4193 (1998). [PDF]
142. Sandeep K. S. Gupta,
Zhiyong Li, and John H. Reif, Generating Efficient Programs for Two-Level
Memories from Tensor-Products. Proceedings
of the 7th IASTED/ISMM International Conference on Parallel and Distributed
Computing and Systems Washington DC, October 1995, pp. 510-513. [PostScript] [PDF]
143. John H. Reif, Parallel
Biomolecular Computation: Models and Simulations. Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and
Architectures (SPAA'95) Santa Barbara, CA, July 1995, pp. 213-223.
Published in Algorithmica, special issue on Computational Biology, Vol. 25, No.
2, 142-176, 1999. [PDF] [PostScript] and [PostScriptFigures]
144. John H. Reif, Work
Efficient Parallel Solution of Toeplitz Systems and Polynomial GCD. Proc. of the 27th ACM Symposium on Theory of
Computing (STOC 95), Las Vegas, NV, May 29-June 1, 1995, pp. 751-761.
Revised as Efficient Parallel Factorization and Solution of Structured and
Unstructured Linear Systems, Journal of
Computer and System Sciences, Vol.
71, Issue 1 (July 2005), pp. 86 - 143. [PDF] [PDF]
145. Sandeep K. S. Gupta, Zhiyong
Li, and John H. Reif, Synthesizing Efficient Out-of-Core Programs for Block
Recursive Algorithms using Block-Cyclic Data Distributions. Proceedings of the 1996 International
Conference on Parallel Processing, Bloomingdale, IL, Vol. II, pp. 142-149,
(August 1996). Published in IEEE
Transactions on Parallel and Distributed Systems, Vol. 10, No. 3, March
1999, pp. 297-315. [PDF] or [PDF]
146. Lars S. Nyland, Jan Prins,
Andrew Goldberg, Peter H. Mills, John H. Reif, and Robert Wagner. A Refinement
Methodology for Developing Data-Parallel Applications, Second International
Euro-Par Conference (Euro-Par'96 Parallel Processing), Lyon, France, Springer
Lecture Notes in Computer Science, pp.145-150, 1996. [PDF]
147. Sefeng Chen and John H.
Reif, Compression of Trees and Digraphs, Abstract, Proceedings: IEEE Data Compression Conference (DCC'96), Snowbird,
UT, James A. Storer, Martin Cohn (Eds.), IEEE Computer Society Press, March
1996. [PDF]
148. John H. Reif and Hongyan
Wang, Nonuniform Discretization for
Kinodynamic motion planning and its applications, Workshop on Foundations of Robotics, Toulouse, France, July 1996,
pp. 97-112. Published in SIAM Journal of Computing (SICOMP), Volume 30, No. 1,
pp. 161-190, (2000). [PostScript] [PDF]
149. Zhiyong Li, Peter H.
Mills, and John H. Reif, Models and Resource Metrics for Parallel and
Distributed Computation, Proc. 28th
Annual Hawaii International Conference on System Sciences (HICSS-28
Parallel Algorithms Software Technology Track), Wailea, Maui, Hawaii, pp.
133-143, January 3-6, 1995. Published in Parallel
Algorithms and Applications, Vol. 8, pp. 35-59, 1996. [PostScript] [PDF]
150. Erol Gelenbe, Nestor
Schmajuk, John Staddon, and John H. Reif, Autonomous Search and the Search for
Robots and Mines: A Survey, Robotics and Autonomous Systems, Vol. 22, pp.
23-33. (November 1997). [PostScript] [PDF]
151. John H. Reif, Approximate
Complex Polynomial Evaluation in Near Constant Work Per Point. Proc. 29th ACM
Symposium on Theory of Computing (STOC97), El Paso, Texas, pp. 30-39 (May 4-6,
1997). Published in SIAM Journal of
Computing (SICOMP), Vol. 28, Number 6, pp.
2059-2089, 1999. [PostScript] [PDF]
152. John H. Reif, Efficient
Approximate Solution of Sparse Linear Systems, Published in Computers and Mathematics with Applications,
Vol. 36, No. 9, Nov. 1998, pp. 37-58. [PostScript] [PDF] (Also, see
errata, Computers and Mathematics with Applications, Vol. 38, No. 9, 1999, pp.
141-141. [PDF])
153. John H. Reif and Steve R.
Tate, Fast spatial decomposition and closest pair computation for limited
precision input, Journal of Algorithmica, Volume 28, Number 3, pp. 271-287
(2000). [PDF] or [PostScript] [PDF]
154. Sefeng Chen and John H.
Reif, Fast and Compact Fast and Compact Volume Rendering in the Compressed
Transform, Proceedings: IEEE Data
Compression Conference (DCC'97) Snowbird, UT, James A. Storer, Martin Cohn
(Eds.), IEEE Computer Society Press, March 1997, pp. 271-280. [PDF]
155. John H. Reif and Doreen
Yen, Derivation of Parallel Graph Connectivity Algorithms via Stream
Contraction, Duke University Technical Report, 1989. [PDF]
156. John H. Reif, Local
Parallel Biomolecular Computation, Proc. DNA-Based Computers, III: University
of Pennsylvania, June 23-26, 1997. DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, H. Rubin and D. H. Wood, editors. American Mathematical
Society, Providence, RI, vol. 48, 1999, pp. 217-254. [PDF] Revised as
invited paper of special issue "Biomolecular Computing - From Theory to
Practical Applications" of International Journal of
Unconventional Computing, Vol. 8, pp. 459-507 (2014). [PDF] or [PDF]
157. John H. Reif, On the
Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth, Information and Computation, Jan 2000,
pp. 1-20. [PDF]
158. John H. Reif, (Yin, Guo et
al. 2004)s: Robust, Adaptive and Dynamic Motion, 19th NSF Design and
Manufacturing Grantees Conference, Monterrey, Mexico, Jan 1998. [PostScript] [PDF]
159. John H. Reif and Sandeep
Sen, Parallel Computational Geometry: An approach using randomization.
Published as Chapter 8 in Handbook of
Computational Geometry, Edited by Jorge Urrutia and Jörg-Rudiger Sack,
Elsevier Science Publishing, Amsterdam, the Netherlands, pp. 765-828. 1999. [PDF] or [PDF]
160. John H. Reif, Paradigms
for Biomolecular Computation, First
International Conference on Unconventional Models of Computation, Auckland,
New Zealand, January 5-9, 1998. Published in
Unconventional Models of Computation, (edited by C.S. Calude, J. Casti, and
M.J. Dinneen), DMTCS Series, Springer-Verlag, Singapore, January 1998, pp.
72-93. [PostScript] [PDF]
161. John H. Reif and James A.
Storer, Optimal Lossless Compression of a Class of Dynamic Sources, Data
Compression Conference (DCC'98), Snowbird, UT, James A. Storer, Martin Cohn
(Eds.), IEEE Computer Society Press, pp. 501-510, March, 1998. Published as
Optimal Encoding of Non-stationary Sources, Special Issue of Information
Sciences, Volume 135, pp. 87-105 (2001). [PDF]
162. John H. Reif and Hongyan
Wang, The Complexity of the Two Dimensional Curvature-Constrained Shortest-Path
Problem, Third International Workshop on
Algorithmic Foundations of Robotics (WAFR98),
Pub. by A. K. Peters Ltd, Houston, Texas, pp. 49-57, June, 1998. [PostScript] [PDF]
163. John H. Reif and Zheng
Sun, The Computational Power of Frictional Mechanical Systems, Third International Workshop on Algorithmic
Foundations of Robotics, (WAFR98),
Pub. by A. K. Peters Ltd, Houston, Texas, pp. 223-236, Mar. 5-7 1998. Published
as On Frictional Mechanical Systems and Their
Computational Power, SIAM Journal of Computing (SICOMP), Vol. 32, No. 6,
pp. 1449-1474, (2003). [PDF] or [PDF]. Talk: [HTML]
164. A. Gehani and John H.
Reif, Micro Flow Bio-Molecular Computation, 4th DIMACS Workshop on DNA Based
Computers, University of Pennsylvania, June 15-19, 1998. DNA Based Computers, IV, DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, (ed. H. Rubin), American Mathematical
Society, 1999. Also in a special issue of Biosystems, Journal of Biological and
Informational Processing Sciences, Vol. 52, Nos. 1-3, (Edited By L. Kari, H.
Rubin, and D. H. Wood), pp. 197-216, (October 1999). [PostScript] [PDF] or [PDF] Talk: [PDF]
165. John H. Reif, Alternative
Computational Models: A Comparison of Biomolecular and Quantum Computation,
Invited paper, 18th International
Conference on Foundations of Software Technology and Theoretical Computer
Science (FSTTCS1998), Chennai, India (December, 17-19, 1998). [PDF]
166. John H. Reif and Zheng
Sun, Nano-Robotics Motion Planning and Its Applications in Nanotechnology and
Biomolecular Computing, NSF Design and
Manufacturing Grantees Conference, Jan 5-8, 1999. [HTML]
167. Thomas H. LaBean, Hao Yan,
Jens Kopatsch, Furong Liu, Erik Winfree, John H. Reif and Nadrian C. Seeman,
The construction, analysis, ligation and self-assembly of DNA triple crossover
complexes, Journal of American Chemistry
Society(JACS) 122, pp. 1848-1860 (2000). [PDF]
168. John H. Reif and Sukhendu
Chakraborty, Efficient and Exact Quantum Compression, Journal of Information
and Computation, Vol. 205, pp. 967-981 (2007). [PDF] [PDF]
169. John H. Reif, Quantum
Computing. In book “Bio-inspired and Nanoscale Integrated Computing”, Chapter
3, pp. 67-110 (edited by Mary Mehrnoosh Eshaghian-Wilner), Publisher: Wiley,
Hoboken, NJ, USA, (February 2009). [PDF]
170. John Fischer and John H.
Reif, Nonparametric Multiscale Multimodal Model for Detection/Recognition,
Multi-Modality Image Fusion Conference, Rochester, NY, Oct 6-7, 1999. [PDF]
171. A. Gehani, Thomas H.
LaBean, and John H. Reif, DNA-based Cryptography, Proc. DNA Based Computers V:
Cambridge, MA, June 14-16, 1999. Published in DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, Volume 54, edited by Erik Winfree
and D.K. Gifford, American Mathematical Society, Providence, RI, pp. 233-249,
(2000). [PDF] Talk: [PDF]. Published
as an invited chapter in "Aspects of Molecular
Computing - Essays dedicated to Tom Head on the occasion of his 70th
Birthday", Springer Verlag series in Natural Computing (edited by N. Jonoska, G.
Paun and G. Rozenberg) LNCS 2950 Festschrift, Springer, pp. 167-188, (2004). [PDF]
172. Thomas H. LaBean, Erik
Winfree, and John H. Reif, Experimental Progress in Computation by
Self-Assembly of DNA Tilings, Proceeding of DNA Based Computers V: Cambridge,
MA, June 14-16, 1999. Published in DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, Volume 54, edited by Erik Winfree and D.K.
Gifford, American Mathematical Society, Providence, RI, pp. 123-140, (2000). [PostScript] [PDF] Talk: [HTML Lecture]
173. John H. Reif and Zheng
Sun. An efficient approximation algorithm for weighted region shortest path
problem. In Proceedings of the 4th Workshop on Algorithmic Foundations of
Robotics (WAFR2000), A. K.
Peters Ltd Publishers, Hanover, New Hampshire, pp. 191-203, Mar. 16-18 2000. [PDF] [PostScript]. Published as Zheng Sun and John H. Reif, On Finding Approximate Optimal Paths in Weighted Regions,
Journal of Algorithms, Volume 58, Number 1, pp. 1-32, January 2006. [PDF]
174. John H. Reif and Zheng
Sun. Movement planning in the presence of flows. In Proceedings of the 7th
International Workshop on Algorithms and Data Structures (WADS2001),
volume 2125 of Lecture Notes in Computer Science, pp. 450-461, Brown
University, Providence, RI, August 8-10, (2001). Published in Algorithmica,
Volume 39, Number 2, pp. 127-153, February 2004. [PDF] or [PDF]. Talk: [PDF]
175. John H. Reif and Thomas H.
LaBean, Computationally Inspired Biotechnologies: Improved DNA Synthesis and
Associative Search Using Error-Correcting Codes and Vector-Quantization, Sixth
International Meeting on DNA Based Computers (DNA6), Leiden, The Netherlands (June 2000). DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, Edited by A. Condon and G.
Rozenberg. Lecture Notes in Computer Science, Springer-Verlag, Berlin
Heidelberg, vol. 2054, pp. 145-172 (2001) [PostScript] [PDF] Talk: [PDF]
176. John H. Reif, Thomas H.
LaBean, and Nadrian C. Seeman, Challenges and Applications for Self-Assembled
DNA Nanostructures, Proc. Sixth International Workshop on DNA-Based Computers,
Leiden, The Netherlands, June 13-17, 2000. Published in DIMACS Series in
Discrete Mathematics and Theoretical Computer Science, Edited by A. Condon and
G. Rozenberg. Lecture Notes in Computer Science, Springer-Verlag, Berlin
Heidelberg, vol. 2054, 2001, pp. 173-198. [PostScript] [PDF] Talk: [PDF] [PPT]
177. Chengde Mao, Thomas H. LaBean, John H. Reif, Nadrian C. Seeman,
Logical Computation Using Algorithmic Self-Assembly of DNA Triple-Crossover
Molecules, Nature, vol. 407, pp. 493-495 (Sept. 28 2000); C. Erratum: Nature
408, 750-750 (2000). [PDF] or [PDF]
178. John H. Reif and Thomas H.
LaBean, and Nadrian C. Seeman. Programmable Assembly at the Molecular Scale:
Self-Assembly of DNA Lattices, Invited paper, 2001 IEEE International
Conference on Robotics and Automation (ICRA2001), Seoul, Korea, ed. Lee Beom, pp. 966-971 (May, 2001). [PDF]
179. Zheng Sun and John H.
Reif. BUSHWHACK: An approximation algorithm for minimal paths through
pseudo-Euclidean spaces. In Proceedings of the 12th Annual International
Symposium on Algorithms and Computation(ISAAC01),
Christchurch, New Zealand, Dec 19-21, 2001, Volume 2223 of Lecture Notes in
Computer Science, pp. 160-171, Dec, 2001. Published in IEEE Transactions
on Systems, Man, and Cybernetics (SMC), Part B: Cybernetics, Vol. 37, No. 4,
pp. 925-936 (2007). [PDF] [PDF]
180. John H. Reif, Thomas H.
LaBean, M. Pirrung, V. Rana, B. Guo, K. Kingsford, and G. Wickham, Experimental
Construction of Very Large Scale DNA Databases with Associative Search
Capability, Seventh International Meeting on DNA Based Computers (DNA7), Tampa, FL, June 11-13, 2001. Lecture Notes in Computer Science, Springer-Verlag, New
York, Volume 2340, pp. 231-247, (2002). [PostScript] [PDF] Talk: [PDF] [PPT]. Also
published as John H. Reif, Michael Hauser, Michael Pirrung, and Thomas LaBean, Application of Biomolecular Computing to Medical Science: A
Biomedical Database System for Storage and Retrieval of Genetic Information and
Material, Chapter 3 of Complex Systems Science in Biomedicine (Edited by
Thomas S. Deisboeck and J. Yasha Kresh), International Topics in Biomedical
Engineering Series, Springer Publishers, New York,
Chapter 3, pp. 701-735, (2005). ISBN: 0-387-30241-7.
[PDF] or [PDF]. Talk: [PDF][PPT]
181. John H.
Reif, DNA Lattices: A Method for Molecular Scale
Patterning and Computation, special issue on Bio-Computation, Computer and
Scientific Engineering Magazine, IEEE Computer Society, Vol. 4, No. 1, February
2002, pp. 32-41. [PostScript][PDF]
182. John H.
Reif, The Emerging Discipline of Biomolecular Computation in the US, invited paper to the special issue on Biomolecular
Computing, New Generation Computing, edited by Masami Hagiya, Masayuki
Yamamura, and Tom Head, Vol. 20, No. 3, pp. 217-236, (2002). [PostScript][PDF] or [PDF]
183. John H.
Reif, Molecular Assembly and Computation: From Theory to Experimental
Demonstrations, plenary paper, Twenty Ninth International Colloquium on
Automata, Languages, and Programming(ICALP), Málaga, Spain (July 8, 2002).
Lecture Notes in Computer Science, New York, Volume 2380, pp. 1-21, (2002). [PostScript][PDF] Talk: [PDF] [PPT]
184. John H. Reif,
The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA.
DNA Based Computers (DNA8), Sapporo, Japan, June 10-13, 2002, (Edited by Masami
Hagiya and Azuma Ohuchi), Lecture Notes in Computer Science, No. 2568, Springer-Verlag,
New York, (2003), pp. 22-37. Published in Natural Computing, DNA8 special
issue, Vol. 2, p 439-461, (2003). [PDF]
or [PostScript][PDF]
Talk: [PDF]
185. Dage Liu,
John H. Reif, Thomas H. LaBean, DNA Nanotubes, Construction and
Characterization of Filaments Composed of TX-tile Lattice. DNA Based Computers
(DNA8), Sapporo, Japan, June 10-13,
2002, (Edited by Masami Hagiya and Azuma Ohuchi), Lecture Notes in Computer
Science, No. 2568, Springer-Verlag, New York, (2003), pp. 10-21. Published as
DNA nanotubes self-assembled from triple-crossover tiles as templates for
conductive nanowires, Proceedings of the National
Academy of Science(PNAS), Vol. 101, No. 3, pp. 717-722, (January 20,
2004). PubMed PMID: 14709674. [PDF]
186. John H. Reif,
DNA Computation - Perspectives: Successes and Challenges, Science, 296:
478-479, April 19, 2002. PubMed PMID: 11964464. [PostScript][PDF]
187. Zheng Sun and
John H. Reif, On Finding Energy-minimizing Paths on Terrains for a Mobile
Robot, 2003 IEEE International Conference on Robotics and Automation(ICRA2003),
Taipei, Taiwan, pp. 3782-3788, May 12-17, 2003. Published in IEEE Transaction on Robotics, Volume: 21, Issue: 1,
February 2005, pp. 102-114. [PDF]
188. D. Hsu, T.
Jiang, John H. Reif, and Zheng Sun, The Bridge Test for Sampling Narrow
Passages with Probabilistic Roadmap Planners, 2003 IEEE International
Conference on Robotics and Automation(ICRA2003), Taipei, Taiwan, Vol.3, pp.
4420 – 4426, Sept. 14-19, 2003. Published as Zheng Sun, D. Hsu, T.
Jiang, H. Kurniawati, and J.H.Reif, Narrow Passage Sampling for Probabilistic
Roadmap Planning, IEEE Transactions on Robotics, Volume 21, No. 6, Dec. 2005.
pp. 1105–1115. [PDF]
189. John
H. Reif and Zheng Sun, On Boundaries of Highly Visible Spaces and Applications,
14th Symposium on Fundamentals of Computation Theory, Malmö Högskola,
Sweden, August 12-15, 2003, Springer-Verlag Lecture Notes in Computer Science,
2003. Invited paper published in Theoretical Computer Science, Volume 354,
Issue 3, (4 April 2006), pp. 379-390. [PDF]
[PDF]
190. Hao Yan,
Thomas H. LaBean, Liping Feng, and John H. Reif, Directed Nucleation Assembly
of Barcode Patterned DNA Lattices, Proceedings of the
National Academy of Science(PNAS), Volume 100, No. 14, pp. 8103-8108,
July 8, (2003). PubMed PMID: 12821776. [PostScript] [PDF]
191. Hao Yan,
Liping Feng, Thomas H. LaBean, and John H. Reif, DNA Nanotubes, Parallel Molecular
Computation of Pair-Wise XOR Using DNA String Tile, Ninth International Meeting on DNA Based Computers
(DNA9), Madison, Wisconsin, June 2-4, 2003, (Edited by Junghuei
Chen and John H. Reif), Abstract in Lecture Notes in Computer Science,
Springer-Verlag, New York, (2003). Published as Parallel
Molecular Computations of Pairwise Exclusive-Or (XOR) Using DNA "String
Tile" Self-Assembly in Journal of American Chemistry Society (JACS), Vol. 125, No. 47, pp. 14246-14247, 2003. PubMed
PMID: 14624551. [PDF]
or [PDF];
Supporting Information: [PDF]
192. Hao Yan,
Sung Ha Park, Liping Feng, John H. Reif, and Thomas H. LaBean, 4x4 DNA Tile and
Lattices: Characterization, Self-Assembly and Metallization of a Novel DNA
Nanostructure Motif, Ninth International
Meeting on DNA Based Computers (DNA9), Madison, Wisconsin, June 2-4,
2003, (Edited by Junghuei Chen and John H.
Reif), Lecture Notes in Computer Science, Springer-Verlag, New York, (2003).
Published as Hao Yan, Sung Ha Park, Gleb Finkelstein, John H. Reif, and Thomas
H. LaBean, DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive
Nanowires, Science, Vol. 301, pp. 1882-1884, Sep 26 2003. PubMed PMID:
14512621. [PDF]
Supporting Materials: [PDF]
Supplemental Information: [PDF]
193. Liping Feng,
Sung Ha Park, John H. Reif, and Hao Yan, A Two-State DNA Lattice Switched by
DNA Nanoactuator, Angewandte Chemie [International
Edition], Vol. 42, pp. 4342-4346, Sept. 2003. PubMed PMID: 14502706. [PDF]
Supplemental Information: [PDF]
194. Zheng
Sun and John H. Reif, Adaptive and Compact
Discretization for Weighted Region Optimal Path Finding. 14th Symposium on
Fundamentals of Computation Theory, Malmö Högskola, Sweden, August 12-15, 2003,
Springer-Verlag Lecture Notes in Computer Science, Vol. 2751, pp. 258-270,
2003. [PostScript] [PDF].
195. Tinging
Jiang and John H. Reif, Efficient Methods for
Stochastic Simulations of Biomolecular Motions, submitted for publication,
July, 2003. [PDF]
196. H. Li, S.H. Park, John H.
Reif, Thomas H. LaBean, Hao Yan, DNA-Templated Self-Assembly of Protein and
Nanoparticle Linear Arrays, Journal of American Chemistry Society (JACS), Vol. 126, No. 2, pp. 418-419, 2004. PubMed PMID:
14719910. [PDF].
Supporting Information: [PDF]
197. Hao Yan,
Peng Yin, Sung Ha Park, Hanying Li, Liping Feng, Xiaoju Guan, Dage Liu, John H.
Reif, & Thomas H. LaBean (2004) Self-Assembled DNA Structures for
Nanoconstruction. International Symposium on DNA-Based Molecular Electronics,
Jena, Germany, May, 2004. Fritzsche, W. eds. AIP Conference Proceedings, 725,
American Institute of Physics. pp. 43-52. [PDF]
198. John H.
Reif, Sudheer Sahu, Peng Yin, Compact Error-Resilient Computational DNA Tiling
Assemblies, Tenth International Meeting on DNA
Based Computers (DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in
Computer Science (Edited by C Ferretti, G. Mauri and C. Zandron), Vol. 3384, Springer-Verlag, New York, (2005), pp.
293-307. Published as an invited chapter in
text "Nanotechnology: Science and Computation”, Springer
Verlag series in Natural Computing (edited by J. Chen; N. Jonoska and G. Rozenberg), Springer-Verlag Berlin, Germany, pp. 79-104, 2006. [PDF]
Talk: [PDF]
[PPT]
199. Peng Yin,
Andrew J. Turberfield, Sudheer Sahu, John H. Reif, Designs for Autonomous
Unidirectional Walking DNA Devices, Tenth
International Meeting on DNA Based Computers (DNA10), Milano, Italy,
June 7-10, 2004. Lecture Notes in Computer Science (Edited by C Ferretti, G.
Mauri and C. Zandron), Vol. 3384,
Springer-Verlag, New York, (2005), pp. 410-425. [PDF]
Talk: [PDF]
[PPT]
200. Peng Yin, Hao
Yan, Xiaoju G. Daniel, Andrew J. Turberfield, John H. Reif, A Unidirectional
DNA Walker Moving Autonomously Along a Linear Track, Angewandte Chemie
[International Edition], Volume 43, Number 37, Sept. 20, 2004, pp. 4906-4911. PubMed PMID:
15372637. [PDF]
or [PDF]
Supplemental Information: [PDF]
Abstract:
[PDF]
Talk: [PDF]
[PPT]
201. Peng Yin, Andrew J.
Turberfield, John H. Reif, Design of an Autonomous DNA Nanomechanical Device
Capable of Universal Computation and Universal Translational Motion, Tenth International Meeting on DNA Based Computers
(DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science
(Edited by C Ferretti, G. Mauri and C. Zandron), Vol.
3384, Springer-Verlag, New York, (2005), pp. 426-444. [PDF]
Talk: [PDF]
[PPT]
202. Peng Yin, Bo
Guo, Christina Belmore, Will Palmeri, Erik Winfree, Thomas H. LaBean, John H.
Reif, TileSoft: Sequence Optimization Software For Designing DNA Secondary
Structures, Duke University Computer Science Department Technical Report
TR-CS-2004-09. [PDF]
Talk: [PDF]
[PPT]
203. John H.
Reif, DNA-Based Nano-Engineering: DNA and its Enzymes as the Engines of
Creation at the Molecular Scale, Invited Talk, Abstract, Preliminary
Proceedings, Tenth International Meeting on DNA Based Computers (DNA10),
Milano, Italy, (June 7-10, 2004). Abstract: [PDF]
Talk: [PDF]
[PPT]
204. John H. Reif, Thomas LaBean, Sudheer Sahu, Hao Yan, Peng Yin, Design,
Simulation, and Experimental Demonstration of Self-Assembled DNA Nanostructures
and DNA Motors, Unconventional Programming Paradigms: International Workshop
UPP 2004, Le Mont Saint Michel, France, September 15-17, 2004. Published by
Springer-Verlag Berlin Heidelberg, edited by Jean-Pierre Banâtre, Pascal
Fradet, Jean-Louis Giavitto, Olivier Michel, Lecture Notes for Computer Science
(LNCS) 3566, pp. 173-187, (2005). [PDF]
Talk: [PDF]
[PPT]
205. Sung
Ha Park, Hao Yan, John H. Reif, Thomas H LaBean, and Gleb Finkelstein,
Electronic nanostructures templated on self-assembled DNA scaffolds,
Nanotechnology 15 pp. S525–S527 (2004). [PDF]
206. Sung
Ha Park, Peng Yin, Yan Liu, John H. Reif, Thomas LaBean, and Hao Yan,
Programmable DNA Self-assemblies for Nanoscale Organization of Ligands and
Proteins, Nano Letters (Communication),
Volume 5, Number 4, pp. 729-733,
(2005). PubMed PMID: 15826117. [PDF];
Supplemental Information: [PDF]
207. Sung Ha Park,
Robert Barish, Hanying Li, John H. Reif, Gleb
Finkelstein, Hao Yan and Thomas LaBean, Three-Helix Bundle DNA Tiles
Self-Assemble into 2D Lattice or 1D Templates for Silver Nanowires, Nano
Letters (Communication), Volume 5, Number 4, pp. 693-696 (2005). PubMed
PMID: 15826110. [PDF]
Supplemental Information: [PDF]
208. Sung Ha Park, Constantin
Pistol, Sang Jung Ahn, John H. Reif, Alvin R. Lebeck, Chris Dwyer, and Thomas
H. LaBean, Finite-Size, Fully Addressable DNA
Tile Lattices Formed by Hierarchical Assembly Procedures, Angewandte Chemie [International Edition], Volume 45, Issue 5, pp.
735-739, January 23, 2006. DOI: 10.1002/anie.200503797. [PDF]
209. John H. Reif, Sudheer
Sahu, and Peng Yin, Complexity of Graph Self-Assembly in Accretive Systems and
Self-Destructible Systems, Eleventh International
Meeting on DNA Based Computers (DNA11), London, Ontario, Canada (June,
2005). Springer-Verlag Lecture Notes for Computer Science (LNCS), NYC, NY,
(edited by Alessandra Carbone and Niles Pierce), Vol.
3892, Springer-Verlag, New York, (2006),
pp. 257-274 [PDF].
Talk: [PPT].
Published
in Theoretical Computer Science, Volume 412, pp 1592-1605, (2011). DOI
information: 10.1016/j.tcs.2010.10.034 [PDF].
210. Peng Yin, Andrew J.
Turberfield, John H. Reif, Design of Autonomous DNA Cellular Automata, Eleventh International Meeting on DNA Based
Computers (DNA11), London, Ontario, Canada (June, 2005). Springer-Verlag
Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Alessandra Carbone and Niles Pierce), Vol. 3892,
Springer-Verlag, New York, (2006), pp. 399-416
[PDF].
211. Sudheer Sahu,
Peng Yin and John H. Reif, A Self-Assembly Model of Time-Dependent Glue Strength, Eleventh International Meeting on DNA Based
Computers (DNA11), London, Ontario, Canada (June, 2005). Springer-Verlag
Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Alessandra Carbone and Niles Pierce), Vol. 3892,
Springer-Verlag, New York, pp. 290-304 (2006).
Invited Chapter in "Algorithmic
Bioprocesses" (edited by A.Condon, D.Harel, J.N.Kok, A.Salomaa, and
E.Winfree), Published by Springer-Verlag,
ISBN: 978-3-540-88868-0, pp. 185-204 (2009). [PDF]
[PDF]
Talk: [PPT]
212. Peng Yin,
Sudheer Sahu, Rizal Hariadi, Harry M. T. Choi, Sung Ha Park, Bethany Walters,
Thomas H. LaBean, John H. Reif, On Constructing Tile-less DNA Ribbons and
Tubes, Abstract, Preliminary Proceedings, 12th International Meeting on DNA
Computing (DNA12), Seoul, Korea (June 5-9, 2006). [PDF]
Published as: Peng Yin, Rizal F. Hariadi, Sudheer Sahu, Harry M.T.Choi,
Sung Ha Park, Thomas H. LaBean, John H. Reif, Programming DNA Tube
Circumferences, Science, Vol. 321. no. 5890, pp. 824–826 (August 8, 2008). DOI:
10.1126/science.1157312. [PDF]
Supplemental Information: [PDF]
213. Sudheer Sahu
and John H. Reif, Capabilities and Limits of Compact Error Resilience Methods
for Algorithmic Self-Assembly in Two and Three Dimensions, 12th International
Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006. Published in
DNA Computing: DNA12, Springer-Verlag Lecture Notes for Computer Science
(LNCS), Volume 4287 (edited by Chengde Mao and Takashi Yokomori), Springer,
Berlin Heidelberg, pp. 223-238 (2006). DNA12 Version: [PDF]. Talk: [PPT]. Published
in Algorithmica, Volume 56, Issue 4, pp. 480-504, Springer New York (April
2010), Full Paper: [PDF] [PDF].
214. Sudheer
Sahu, Bei Wang, Peng Yin, John H. Reif, A Framework
for Modeling DNA based Molecular Systems, 12th International Meeting on
DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006. Published in DNA
Computing: DNA12, Springer-Verlag Lecture Notes for Computer Science (LNCS),
Volume 4287 (edited by Chengde Mao and Takashi
Yokomori), Springer, Berlin Heidelberg,
pp. 250-265 (2006). DNA12 Version: [PDF].
Published as Sudheer
Sahu, Bei Wang, John H. Reif, A Framework for Modeling DNA based Molecular
Systems. Computational and Theoretical Nanoscience, Volume 5, Number 11,
pp. 2124-2134(11) (November 2008). Full Paper: [PDF]
Presentation: [PPT]
215. Urmi Urmi Majumder,
Sudheer Sahu, Thomas LaBean, and John H. Reif, Design and Simulation of
self-repairing DNA Lattices, 12th International Meeting on DNA Computing (DNA
12), Seoul, Korea, June 5-9, 2006, DNA Computing: DNA12, Springer-Verlag Lecture
Notes for Computer Science (LNCS), Volume 4287 (edited by Chengde Mao and Takashi Yokomori), Springer, Berlin Heidelberg, pp. 195–214, (2006). DNA12
Version: [PDF]
Poster: [PDF].
Revised paper: Urmi Majumder, Sudheer Sahu, Thomas LaBean, and John H.
Reif, Toward Compact Inherently Self-Repairing DNA Lattices Using
Reversibility, submitted for journal publication (2014). [PDF]
216. John H. Reif and Sam Slee,
Asymptotically Optimal Kinodynamic Motion Planning for Self-Reconfigurable
Robots, Seventh International Workshop on the Algorithmic Foundations of
Robotics (WAFR2006), NYC, New York, July 16-18, 2006. Published in Algorithmic
Foundation of Robotics VII, Springer Tracts in Advanced Robotics (Edited by S.
Akella, N.M. Amato, W.H. Huang, B. Mishra), Volume 47, Springer-Verlag Berlin,
pp. 457–472, (Aug 2008). [PDF]
Published as Asymptotically
Optimal Kinodynamic Motion Planning for a Class of Lattice-Style Modular
Self-Reconfigurable Robots, International Journal of Computational Geometry
& Applications (IJCGA), Vol. 21, No. 2, pp. 131-155 (2011). DOI: 10.1142/S0218195911003585 [PDF]
217. Thomas H.
LaBean, Kurt V. Gothelf, and John H. Reif, Self-assembling DNA Nanostructures
for Patterned Molecular Assembly, invited chapter 5 in Nanobiotechnology II:
More Concepts and Applications, (edited by Chad A. Mirkin and Christof M.
Niemeyer), John Wiley & Sons Publishers, pp. 79-97, (2007). [PDF]
DOI:
10.1002/9783527610389.ch5
218. John H. Reif
and Thomas H. LaBean, Autonomous Programmable Biomolecular Devices Using
Self-Assembled DNA Nanostructures, invited paper, Fourteenth
Workshop on Logic, Language, Information and Computation (WoLLIC'2007), Rio de
Janeiro, Brazil, July 2-5, 2007, Springer-Verlag Lecture Notes for
Computer Science (LNCS), Volume 4576 - 0297, pp. 297-306. Published in Communications of the
ACM (CACM), Special Section entitled “New Computing Paradigms (edited by
Toshinori Munakata), Volume 50, Issue 9, pp. 46-53
(Sept 2007). Short version [PDF]
Extended version [PDF]
Talk: [PPT]
[PDF]
219. Urmi Majumder and John H.
Reif, A Framework for Designing Novel Magnetic Tiles Capable of Complex
Self-Assemblies, Conference on Unconventional Computation, Vienna, Austria, Aug
25-26, 2008, Unconventional Computing, Lecture Notes in Computer Science number
105633, Springer, Berlin Heidelberg. Conference Version: [PDF].
Revised paper submitted for journal publication as Barcoded Magnetic Tiles for Complex
Programmable Assemblies (2012). Full Paper: [PDF]
220. John H. Reif and Thomas H.
LaBean, DNA Nanotechnology and its Biological Applications. In book
“Bio-inspired and Nanoscale Integrated Computing”, Chapter 13, pp. 349-375
(edited by Mary Mehrnoosh Eshaghian-Wilner), Publisher: Wiley, Hoboken, NJ, USA,
(February 2009). [PDF]
221. Ashish Gehani and John H.
Reif, Parameterizing Super-resolution Forensic Analysis of Video, 3rd IFIP International
Conference on Digital Forensics, Orlando, FL, Jan 28-31, 2007. Published as
Super-Resolution Video Analysis for Forensic Investigations, Advances in
Digital Forensics, Chapter 20, Volume 32007, pp. 228-229. [PDF]
222. John H. Reif and Sam Slee,
Optimal Kinodynamic Motion Planning for Self-Reconfigurable Robots Between
Arbitrary 2D Configurations, Robotics: Science and Systems Conference, Georgia
Institute of Technology, Atlanta, GA, June 27-30, 2007. [PDF]
223. John
H. Reif and Sudheer Sahu, Autonomous Programmable DNA Nanorobotic Devices Using
DNAzymes, 13th International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8, 2007. In DNA
Computing: DNA13 (edited by Max Garzon and Hao Yan),
Springer-Verlag Lecture Notes for Computer Science (LNCS), Springer, Berlin
Heidelberg, Volume 4848, pp. 66-78 (2008). DNA13 Version: [PDF]
Talk: [PDF].
Published
in Special Journal Issue on Self-Assembly, Theoretical
Computer Science (TCS), Vol 410, Issue 15, pp. 1428-1439 (April 2009). Full Paper: [PDF]
[PDF].
224. Urmi Majumder, Thomas H
LaBean, and John H. Reif, Activatable Tiles for Compact Error-Resilient
Directional Assembly. 13th International Meeting on DNA Computing (DNA 13),
Memphis, Tennessee, June 4-8, 2007. Conference Version: Activatable Tiles:
Compact, Robust Programmable Assembly and Other Applications, in DNA Computing:
DNA13 (edited by Max Garzon and Hao Yan), Springer-Verlag Lecture Notes for
Computer Science (LNCS), Springer, Berlin Heidelberg, Volume 4848, pp. 15-25,
(2008). [PDF] Talk: [PPT]. Published as: Urmi
Majumder, Sudhanshu Garg, Thomas H LaBean, and John H. Reif, Activatable Tiles for
Compact Robust Programmable Molecular Assembly and Other Applications, Natural Computing, Volume 15, Issue
4, pp 611–634 (December 2016). DOI
10.1007/s11047-015-9532-3 [PDF] [PDF]
225. Urmi Majumder, John H.
Reif, and Sudheer Sahu, Stochastic Analysis of Reversible Self-Assembly.
Journal of Computational and Theoretical Nanoscience, Volume 5, Number 7, pp.
1289-1305, July 2008. Full Paper: [PDF]
[PDF].
226. John
H. Reif, Mechanical Computation: it’s Computational Complexity and
Technologies, invited chapter, Encyclopedia of Complexity and System Science
(edited by Robert A. Meyers), in section: Unconventional Computing (section
editor: Andrew Adamatzky), Springer-Verlag,
New York (2009), pp. 1821-1836, ISBN: 978-0-387-75888-6. DOI: 10.1007/978-0-387-30440-3_325. [HTML]
[PDF] [PDF]. A revised version also appears as Mechanical Computing: The Computational Complexity of
Physical Devices, invited chapter, Encyclopedia
of Complexity and System Science (edited by Andrew
Spencer), Springer-Verlag, Heidelberg, Germany.
Springer-Verlag,
Heidelberg, Germany. Published online (2013) and
in print in pp. 5466-5482 (2014). [HTML]
[PDF] [PDF] [PDF] A further revised
version also appears as Mechanical
Computing: The Computational Complexity of Physical Devices, invited chapter, pp. 1-21, Encyclopedia
of Complexity and System Science
(edited by R.A.),
Springer-Verlag, Heidelberg, Germany. Springer-Verlag, Heidelberg, Germany.
Published online (April 2017). [PDF] [PDF] DOI: 10.1007/978-3-642-27737-5_325-4.
227. John H. Reif and Urmi
Majumder, Isothermal Reactivating Whiplash PCR for Locally Programmable
Molecular Computation, Fourteenth International
Meeting on DNA Based Computers (DNA14),
Prague, Czech Republic (June, 2008). Lecture Notes for Computer Science
(LNCS), NYC, NY, (edited by Ashish Goel and Friedrich
C. Simmel), Springer-Verlag, New York, (2009).
Conference Version: [PDF]
Talk: [PDF]
[PPT]. Invited
Paper, Special issue in Natural Computing, Vol. 9, Number 1, pp. 183-206,
(March 2010). Springer Netherlands, ISSN: 1567-7818 (Online), DOI:
10.1007/s11047-009-9148-6. Full Paper: [PDF]
[PDF]
228. Sudheer Sahu, Thomas H.
LaBean and John H. Reif, A DNA Nanotransport Device Powered by Polymerase ϕ29, Nano
Letters, 2008, 8 (11), pp 3870–3878, (October, 2008) DOI: 10.1021/nl802294d. [PDF]
[PDF]
supplementary material: [PDF]
229. Thomas
H. LaBean, Geetha Shetty, Peng Yin, Erik A. Schultes, Harish Chandran, John H. Reif, A Dendritic Nanostructure for DNA
Detection, abstract, Proceedings of the Sixth Conference on Foundations
of Nanoscience: Self-Assembled Architectures and Devices (FNANO09), Snowbird,
Utah, Sciencetechnica, pp. 82-83 (April 2009). [PDF]
Thomas H. LaBean, Geetha Shetty, Hao Yan, Erik A. Schultes, Harish
Chandran, John H. Reif, Target DNA Detection by
Strand Displacement and Deoxyribozymogen Amplification, abstract,
Proceedings of the Sixth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO09),
Snowbird, Utah, Sciencetechnica, pp. 60-61 (April 2009). [PDF] Bishop Morgan A., Clare D.
Thiem, Thomas E. Renz, Erik A. Schultes, Harish Chandran, John H Reif,
Structural Optimization of Dendritic DNA Self-Assembly, abstract, Proceedings
of the Sixth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices (FNANO09), Snowbird, Utah, Sciencetechnica, pp.
147-148 (April 2009). [PDF]
Final Publication: Harish Chandran,
Abhijit Rangnekar, Geetha Shetty, Erik A Schultes, John H Reif, Thomas H
LaBean, An
Autonomously Self‐Assembling Dendritic DNA Nanostructure for Target DNA
Detection, Biotechnology Journal, Wiley-VCH
Verlag, Vol. 8, Number 2, pp. 221-227, (Feb,
2013). PMID: 22965937.
DOI: 10.1002/biot.201100499. [PDF]
(also published online Oct, 2012)
230. Nikhil Gopalkrishnan,
Harish Chandran and John Reif, 2D and 3D DNA Lattices Via Staggered Assembly of
the Double-Decker Tile, abstract, Digital Proceedings of
the Ninth Conference on Foundations of Nanoscience: Self-Assembled
Architectures and Devices (FNANO12), Snowbird, Utah, pp. 108 (April 2012)
231. Harish
Chandran, Nikhil Gopalkrishnan, and John Reif, The Tile Complexity of Linear
Assemblies, 36th International Colloquium on Automata, Languages and
Programming (ICALP 2009), July 5 - 12, 2009, Rhodes, Greece, Proceedings Part I
(edited by Susanne Albers, Alberto Marchetti-Spaccamela, Yossi Matias, Sotiris
Nikoletseas, and Wolfgang Thomas), Lecture Notes in Computer Science,
Springer-Verlag, Berlin, pp. 235-253 (2009). Published in SIAM Journal of
Computation (SICOMP), Society for Industrial Mathematics, Vol. 41, No, 4, pp.
1051-1073, (2012). [PDF] [PDF] Talk: [PPT] [PDF]
232. John
H. Reif and Thomas H. LaBean, Engineering Natural Computation by
Autonomous DNA-Based Biomolecular Devices, Invited
Chapter, Handbook of
Natural Computing, Chapter 39, Volume III, edited by Grzegor Rozenberg,
Thomas Bäck, Joost Kok, Springer-Verlag, Heidelberg, Germany, pp.1314-1354
(July, 2012), 3540929096 978-3-540-9-2909-3. [PDF]
[PDF]
233. John H. Reif and Urmi
Majumder, Design of a Biomolecular Device that Executes Process Algebra, Fifteenth International Meeting on DNA Computing and
Molecular Programming (DNA15), Fayetteville,
Arkansas (June 8-11, 2009). Lecture Notes for Computer Science (LNCS),
Vol 5877, NYC, NY, (edited by Russell Deaton and
Jin-Woo Kim), Springer-Verlag, New York, pp
107-105, (2010) [PDF]
[PDF]. Published
in Natural Computing, Vol 10, No. 1. pp 447-466 (2011). Talk: [PDF]
[PPT]
[Keynote].
234. John Reif, Harish
Chandran, Nikhil Gopalkrishnan, and Thomas LaBean, Self-assembled DNA
Nanostructures and DNA Devices. Invited Chapter 14, Nanofabrication Handbook
(Edited by Stefano Cabrini and Satoshi Kawata), pages
299-328, CRC Press, Taylor and Francis Group, New York, NY,
ISBN13:9781420090529, ISBN10: 1420090526 (2012). [PDF]
[PDF]
235. Harish Chandrann, Nikhil
Gopalkrishnan and John Reif, Tile
Complexity of Approximate Squares and Lower Bounds for Arbitrary Shapes,
Algorithmica, Volume 66, Issue 1 (2013), Page 1-17 (2013) (also published
online Feb 22,
2012). ISSN 0178-4617, DOI 10.1007/s00453-012-9620-z. [PDF]
[PDF]
236. Nikhil Gopalkrishnan,
Harish Chandran and John Reif, High-Fidelity DNA
Hybridization using Programmable Molecular DNA Devices, International Conference on DNA Computing and
Molecular Programming, (DNA16), Hong Kong University of Science
and Technology. Hong Kong, China, June
14-17th, 2010. Lecture Notes for Computer Science (LNCS), Vol.
6516, NYC, NY, (edited by Yasubumi Sakakibara and Mi
Yongli), Springer-Verlag, LNCS 6518, New York, (Feb
2011), pp 59-70. ISBN: 978-3-642-18304-1 [PDF]
[PDF]
Talk: [PDF]
[PPT]
237. Sam Slee and Sam
Slee and John H. Reif, Robomotion: Scalable, Physically Stable Locomotion for
Self-Reconfigurable Robots, Workshop on the Algorithmic Foundations of Robotics
(WAFR 2010), Singapore, Springer (Dec. 13-15 2010). [PDF]
238. Urmi Majumder, Abhijit
Rangnekar, Kurt V. Gothelf, John H Reif and Thomas H LaBean, Design and
Construction of Double-Decker Tile as a Route to Three-Dimensional Periodic
Assembly of DNA, Journal American Chemical Society (JACS), Vol. 133, no. 11, pp.
3843—3845 (Feb. 2011) [PDF]
Supplementary Info: [PDF]
239. Harish Chandran, Nikhil Gopalkrishnan, and John Reif, DNA NanoRobotics,
Chapter, Nanorobotics: Current Approaches and Techniques, (edited by
Constantinos Mavroidis and Antoine Ferreira), Springer-Verlag, New York, NY,
pp. 355-382 (Jan. 31, 2013). ISBN 13: 9781461421184, ISBN
10: 1461421187 [PDF] [PDF]
240. John
H. Reif, Perspectives: Biochemistry: Scaling Up DNA Computation, Science, Vol. 332, pp. 1156-1157 (June 3, 2011).
DOI: 10.1126/science.1208068 [PDF]
241 Harish Chandran, Nikhil Gopalkrishnan, Andrew
Philips and John Reif, Localized Hybridization Circuits, International
Conference on DNA Computing and Molecular Programming, (DNA17), California
Institute of Technology, Pasadena, California, Sept 19-23, 2011, pp. 64-83.
Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Luca Cardelli
and William Shih), Springer-Verlag, LNCS, Berlin,
Heidelberg, (2011). ISBN: 978-3-642-23637-2 [PDF] Revised as Neil
Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Philips and John Reif, Probabilistic
Analysis of Localized DNA Hybridization Circuits, ACS Synthetic Biology, Vol. 4, Issue 8, pp 898–913, (July, 2015). DOI:10.1021/acssynbio.5b00044 [PDF] [PDF] Supporting Info:
[PDF]
242. Harish
Chandran, Nikhil Gopalkrishnan, Sudhanshu Garg, and John Reif, Biomolecular
Computing Systems - From Logic Systems to Smart Sensors and Actuators, Invited
Chapter 11, Molecular
and Biomolecular Information Processing (Editor: Evgeny Katz),
Published by Wiley-VCH, Verlag GmbH & Comp.
KGaA, Weinheim, Germany, pp. 199-224,
July 2012. ISBN 978-3-527-33228-1
Online ISBN: 9783527645480 DOI: 10.1002/9783527645480
[PDF] [PDF]
243. Harish
Chandran, Nikhil Gopalkrishnan, Bernard Yurke, John Reif, Meta-DNA: Synthetic Biology via DNA Nanostructures and
Hybridization Reactions, Journal
of the Royal Society Interface, (published
online Jan., 2012), pp. 1742-5662 doi: 10.1098/rsif.2011.0819 [PDF] [PDF] [Supplement].
An expanded version appears as Meta-DNA:
A DNA-Based Approach to Synthetic Biology,
Chapter 7 in Book: A Systems Theoretic Approach to Systems and Synthetic
Biology II: Analysis and Design of Cellular Systems, edited by Vishwesh V. Kulkarni, Guy-Bart
Stan, and Karthik
Raman, published by
Springer, New
York (2014).
ISBN:
978-94-017-9046-8 (Print) 978-94-017-9047-5 (Online)
DOI
10.1007/978-94-017-9047-5 [PDF]
[PDF]
Talk: [PDF]
[PPT]
244. Harish Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan
and John H Reif, Activatable Tiles: Demonstration of Linear and Directed Self
Assembly, abstract, Digital Proceedings of the Ninth Conference on Foundations
of Nanoscience: Self-Assembled Architectures and Devices (FNANO12), Snowbird,
Utah, pp. 109 (April 2012). Also, Sudhanshu Garg, Harish Chandran, Nikhil
Gopalkrishnan, and John Reif, One-Time, Directed and Catalytic Activation of
1-D DNA Tiles, Poster Abstract DNA19, Tempe, AZ, Sept, 22-27, 2013. Journal
publication: Sudhanshu Garg, Harish Chandran, Nikhil Gopalkrishnan, Thomas H.
LaBean, and John Reif, Directed Enzymatic Activation of 1-D DNA Tiles, ACS
Nano, Volume 9, Issue 2, pages 1072-1079, January 27, 2015. [PDF] [PDF] Supplementary [PDF] DOI: 10.1021/nn504556v
245. Hieu Bui, Harish
Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan, Reem Mokhtar, Tianqi Song
and John H Reif, DNA Computing, Chapter in Section 3: Architecture
and Organization, Volume I: Computer Science and Software Engineering
(Edited by Teofilo F. Gonzalez, Jorge Diaz-Herrera, Allen Tucker), The Computer
Science Handbook, Third Edition (Editor-In-Chief Allen B. Tucker), Taylor
& Francis Group, (2013). ISBN 9781439898529 [PDF]
246. Sudhanshu Garg, Nikhil Gopalkrishnan, Harish Chandran,
and John Reif, Self-Replicating DNA Nanostructures: Autocatalytic Nanodevices
derived from Catalytic Nanodevices, FNANO 2013, Snowbird, Utah, April 15-18,
2013.
247. Reem Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu
Bui, Tianqi Song, and John Reif, Kinetic Digraph Rewrite Systems:
Coarse-Grained Models for Dynamic DNA Nanodevices, Poster Abstract, FNANO 2013,
Snowbird, Utah, April 15-18, 2013. Also, A Python Implementation
of a DNA Graph Rewriting System (DAGR), poster abstract, FNANO2015, p148, April
2015. Published as Reem
Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu Bui, Tianqi Song, and John Reif,
Modeling
DNA Nanodevices Using Graph Rewriting Systems, invited Chapter, Advances in Unconventional Computing, Volume 2: Prototypes, Models and Algorithms (Edited by Andrew Adamatzky), Springer, pp. 347-396 (2017). ISBN 978-3-319-33921-4 [PDF] [PDF]
248.
Hieu Bui, Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, and John
Reif, Local Hybridization Chain-Reactions on the Surface of DNA Origami, Poster
Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013. Also Design DNA
Hairpin Systems for Localized DNA Hybridization Reactions, poster abstract,
FNANO2015, p169, April 2015. Expanded paper rewritten for journal publication
as: Hieu Bui, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, Vincent Miao and
John Reif, Design and Analysis of Localized DNA
Hybridization Chain Reactions, Small
(2017), 1602983.
[PDF]
[PDF]
249. John H. Reif and Tianqi Song, Complexity and
Computability of Temperature-1 Tilings, Poster Abstract, FNANO 2013, Snowbird,
Utah, April 15-18, 2013. Poster Abstract DNA19, Tempe, AZ, Sept, 22-27, 2013. Submitted
for journal publication, (2015). [PDF]
250. John H. Reif and Wadee
Alhalabi, Advancing Attention Control Using
VR-Induced Artificial Synesthesia, submitted for journal
publication, (2014). [PDF]
251. John H. Reif and Wadee
Alhalabi, Design
and Analysis of a High-Efficiency, Cost-Effective Solar Concentrator, submitted
for journal publication, (2014). [PDF]
252. John
H. Reif and Wadee Alhalabi, Solar-Powered Desalination: Its
Significant Challenges and Potential, Renewable
and Sustainable Energy Reviews, Volume 48, Pages 152-165, (August 2015). [PDF] [PDF]
253. Hiba
Shahid, Wadee Alhalabi, and John H. Reif, Real-time operating system (RTOS)
with application to play models, International Journal of Computing Engineering
Research, Vol.5(2), pp. 9-16, October 2014, DOI: 10.5897/IJCER2013.0202, ISSN:
2141-6494, (Oct, 2014). [PDF]
254. Wadee Alhalabi, John Reif, Zeineb Elsheikh, Heba Felimban,
Majda Fallata, Khalid Thabit, Abdullah Abusorrah,
The Co-learning in the Design, Simulation and Optimization of a Solar
Concentrating System, Computers in Human Behavior, Vol 51, Part B, pp. 857-866
(December 2014). [PDF]
https://dx.doi.org/10.1016/j.chb.2014.10.043
255. Tianqi Song, Sudhanshu Garg,
Hieu Bui, Reem Mokhtar, and John H. Reif, Analog
Computation by DNA Strand Displacement Circuits, ACS Synthetic Biology, 5, 898−912 (July, 2016).
DOI: 10.1021/acssynbio.6b00144 [PDF] [PDF]
256. Hieu Bui, Sudhanshu Garg,
Vincent Miao, Tianqi
Song, Reem Mokhtar, and John Reif, Design and
Analysis of Linear Cascade DNA Hybridization Chain Reactions Using DNA
Hairpins, Special Issue, Journal of New Physics, Vol. 19, (2017) 015006. doi:10.1088/1367-2630/aa53d0 [PDF]
[PDF]
257. Sudhanshu Sudhanshu Garg, Shalin Shah,
Hieu Bui, Tianqi Song, Reem Mokhtar, and John Reif, Renewable Time‐Responsive
DNA Circuits, Small 14, 1801470(July 18, 2018). [PDF] [PDF] DOI:
10.1002/smll.201801470 https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201801470
258. Hieu
Bui, Shalin Shah, Reem Mokhtar, Tianqi Song, Sudhanshu Garg, John Reif, Localized DNA Hybridization Chain Reactions on DNA Origami, ACS Nano, Volume 12, Num. 2, pp 1146–1155(January 22, 2018). DOI: 10.1021/acsnano.7b06699
259. Danie Daniel Fu, Shalin Shah,
Tianqi Song and
John H Reif, DNA-based Analog Computing, Chapter in book: Synthetic Biology: Methods
and Protocols, Edited by Jeffrey C.
Braman), In Series
Methods in Molecular Biology, published by Springer,
pp. 411-417 (2018). ISBN: [PDF] [PDF]
260. Tianqi Song, Sudhanshu Garg, Hieu Bui, Reem
Mokhtar, and
John H Reif, Design
and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation
Using Autocatalytic Amplifiers, ACS Synthetic Biology (Dec
2017). DOI: 10.1021/acssynbio.6b00390
261. Xin
Song, Abeer Eshra, Chris Dwyer, and John Reif, Renewable
DNA Seesaw Logic Circuits Enabled by Photoregulation of Toehold-Mediated Strand
Displacement, RSC Advances, Volume 7,
Issue 45, pp. 28130-28144 (March, 2017). DOI: 10.1039/C7RA02607B [PDF] (supplementary: [PDF])
262. Sudhanshu Garg, H Hieu Bui, Abeer Eshra, Shalin Shah and John
H Reif, Nucleic Acid Hairpins: A Robust and Powerful Motif for Molecular
Devices, Chapter 7 in book: “Soft Nanomaterials” (Edited by Ye Zhang and Bing Xu), World Scientific Series in Nanoscience and Nanotechnology,
World Scientific, Volume 19, pp. 175-199 (2019). ISBN: 978-981-120-102-8, DOI:
10.1142/9789811201035_0007
263. John H.
Reif, DNA
robots sort as they walk, Prospective,
Science, Vol. 357, Issue 6356, pp. 1095-1096 (September, 2017). DOI:
10.1126/science.aao5125
264. Hieu Bui and John H Reif, Localized DNA Computation,
Chapter 19 in book: “From Parallel to Emergent Computing” (Edited by Andrew Adamatzky, Selim Akl, and Georgios Ch.
Sirakoulis), CRC
Press (February 18, 2019). Taylor & Francis Group of CRC Press. ISBN: 9781138054011
265.
Shalin Shah and John H. Reif, Temporal DNA Barcodes: A Time-Based Approach for
Single-Molecule Imaging, 24th
International Conference, DNA 24, Jinan, China, Also, Chapter 5 of DNA Computing and Molecular Programming (DNA
2018), edited by D. Doty and H. Dietz, LNCS 11145, published by Springer
Nature Switzerland AG, pp.71-86, (2018). DOI: 10.1007/978-3-030-00030-1_5 Also published
as Shah, Shalin, Abhishek Dubey, and John Reif. "Improved optical
multiplexing with temporal DNA barcodes." ACS Synthetic Biology 8.5
(2019): 1100-1111. DOI:
10.1021/acssynbio.9b00010
266. Tianqi Song, Nikhil Gopalkrishnan, Abeer Eshra,
Sudhanshu Garg, Reem Mokhtar, Hieu Bui, Harish Chandran and John Reif,
Improving the Performance of DNA Strand Displacement Circuits by Shadow
Cancellation, ACS Nano, (Oct 29, 2018). DOI: 10.1021/acsnano.8b07394 https://doi.org/10.1021/acsnano.8b07394
267. Abeer Eshra, Shalin Shah, Tianqi Song, John Reif, Renewable DNA hairpin-based logic circuits, IEEE Transactions on Nanotechnology, Vol. 18, pp. 252-259, (2019). DOI: 10.1109/TNANO.2019.2896189
268. Shalin Shah,
Dubey Abhishek and John H.
Reif, Programming temporal DNA
barcodes for single-molecule fingerprinting,
Nano letters, 19 (4), pp 2668–2673 (March 2019). DOI: 10.1021/acs.nanolett.9b00590
269. Xin Song and John H Reif, Nucleic Acid Databases and
Molecular-Scale Computing, ACS Nano, Vol 13,
Issue 6, pp 6256-6268 (May
2019). DOI: 10.1021/acsnano.9b02562
270. Tianqi Song,
Abeer Eshra, Shalin Shah, Hieu Bui, Daniel Fu, Ming Yang, Reem Mokhtar, and
John Reif, Fast and Compact DNA Logic Circuits Based on Single-Stranded Gates
Using Strand-Displacing Polymerase, Nature Nanotechnology (Sept 2019). DOI:
10.1038/s41565-019-0544-5
271. Tianqi Song, Shalin Shah, Hieu Bui,
Sudhanshu Garg, Abeer Eshra, Ming Yang, and John Reif, Programming DNA-Based
Biomolecular Reaction Networks on Cancer Cell Membranes, Journal of the
American Chemical Society (JACS), Vol. 141, No. 42, pp. 16539-16543. (Oct 2019).
DOI: 10.1021/jacs.9b05598 https://doi.org/10.1021/jacs.9b05598
272. Shalin
Shah., Tianqi
Song, Xin Song, Ming Yang, John H. Reif,
Implementing Arbitrary CRNs Using Strand Displacing Polymerase. In: Thachuk C.,
Liu Y. (eds) DNA Computing and Molecular Programming. International Conference on DNA Computing and Molecular
Programming (DNA 2019). Lecture Notes in
Computer Science, vol 11648. Springer, Cham, pp 21-36 (2019). DOI: 10.1007/978-3-030-26807-7_2.
Published as Chapter in: DNA Computing and Molecular Programming (edited by
Chris Thachuk and Yan Liu), Volume 11648, Springer, Switzerland AG, pp 21-36,
(2019). ISBN: 978-3-030-26807-7. [PDF]
273.
Xin Song, Shalin Shah, and John Reif, An Overview of DNA-Based Digital Data
Storage, Chapter 18, DNA- and RNA-Based Computing Systems (Evgeny Katz,
editor), Wiley-VCH Verlag GmbH Publishers, Weinheim, Germany, pp. 345-350
(Dec., 2020). ISBN: 978-3-527-82541-7
274.
Reem Mokhtar, Tianqi Song, Daniel Fu, Shalin Shah, Xin Song, Ming
Yang, and John Reif, DNA Origami Transformers, Chapter, Chapter 16, DNA- and RNA-Based Computing Systems
(Evgeny Katz, editor), Wiley-VCH Verlag GmbH Publishers, Weinheim, Germany, pp.
307-322 (Dec., 2020). ISBN: 978-3-527-82541-7 [PDF]
275.
Xin Song, Daniel Fu, Shalin Shah, John Reif, UV-Micropatterned
Miniaturization: Rapid In-Situ Photopatterning and Miniaturization of
Microscale Features on Shrinkable Thermoplastics, Advanced Materials, Vol. 5, Issue
6 (May 4,2020).
DOI:
10.1002/admt.202000146 https://doi.org/10.1002/admt.202000146
276.
Shalin Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin Strauss,
Yuan-Jyue Chen, John Reif, Using strand displacing polymerase to program
chemical reaction networks, Journal of the American Chemical Society (JACS), Vol.
142, Issue. 21, pp. 9587–9593 (May 4, 2020). DOI: 10.1021/jacs.0c02240 https://pubs.acs.org/doi/10.1021/jacs.0c02240
(Supporting Information https://pubs.acs.org/doi/10.1021/jacs.0c02240).
277.
Xin Song and John Reif, Optics-Free Imaging with DNA Microscopy:
An Overview, Chapter 6. Handbook of Unconventional Computing: Volume 2: Implementations
(edited by Andrew Adamatzky), WSPC Book Series in Unconventional Computing,
World Scientific Publishers (WSPC), pp. 181-191 (2021). DOI: 10.1142/12232 DOI:
10.1142/9789811235740_0006. [PDF] ISBN: 978-981-123-527-6 (ebook),
978-981-123-503-0 (hardcover).
278.
Shalin Shah, Ming Yang, Tianqi Song, and John Reif, Molecular
computation via polymerase strand displacement reactions, Chapter 5. Handbook
of Unconventional Computing: Volume 2: Implementations (edited by Andrew
Adamatzky), WSPC Book Series in Unconventional Computing, World Scientific
Publishers, pp. 165-197 (2021) [PDF] DOI: 10.1142/9789811235740_0005. ISBN:
978-981-123-527-6 (ebook), 978-981-123-503-0 (hardcover).
279.
Daniel Fu, Raghu Narayanan Pradeep, Fei Zhang, John Schreck, Hao Yan and John
Reif, Automated Design of Curved DNA Origami Nano-Capsules with Specific Shape
and Variable Multilayer-Reinforced Rigidity, International Conference on DNA
Computing and Molecular Programming (DNA 2019), Seattle, WA (Aug, 2019).
281.
Daniel Fu and John H Reif, 3D DNA
Nanostructures: The Nanoscale Architect. special
issue (Mechanical Design in DNA Nanotechnology) of Applied Sciences, Volume 11, No. 6, eLocator-ID 2624, (2021). DIO: https://doi.org/10.3390/app11062624
282.
Xin Song, Shalin Shah, John Reif, Multidimensional Data Organization and Random
Access in Large-Scale DNA Storage Systems, special issue of Natural Computing
(Theoretical Computer Science – track C), Vol. 894, pp. 190–202 (2021). DIO:
https://doi.org/10.1016/j.tcs.2021.09.021
283.
Xin Song, Felicity Coulter, Ming Yang,
Fikadu Tafesse, William Messer, John Reif, Lyophilized
Colorimetric RT-LAMP Test Kit for Rapid, Low-Cost, At-Home Molecular Testing of SARS-CoV-2 and Other
Pathogens, Scientific Reports,12: 7043 (April 2022). DOI:
10.1038/s41598-022-11144-5.
284.
Yang, and John H. Reif, Social DNA
Nanorobots, pp 371-396, Invited
Chapter for Book on DNA Nanotechnology at 40 for the next 40 - A Tribute to
Nadrian C. Seeman, (edited by Natasha Jonoska and Erik Winfree, book series
Natural Computing, Springer (2023).
285.
Daniel Fu, Raghu Pradeep Narayanan, Abhay Prasad, Fei Zhang, Dewight Williams, John
S. Schreck, Hao Yan, John Reif, Automated Design of 3D DNA Origami with
Non-Rasterized 2D Curvature, Science Advances, Volume 8, Issue 51, (2022). DOI:
10.1126/sciadv.ade4455
286.
Rajiv Teja Nagipogu Daniel Fu and John Reif, Molecular scale learning using DNA
circuits” Nanoscale (2022).
A survey on molecular-scale learning systems
with relevance to DNA computing, Nanoscale, Royal Society of Chemistry (2023), DOI: 10.1039/d2nr06202j
287.
Daniel Fu and John Reif, A Biomimetic Branching Signal-Passing Tiling Model
with Dynamic Assembly and Disassembly. Submitted for publication, Dec 2023.
288.
Rajiv Teja Nagipogu and John H. Reif, Leak-resilient Nucleic Acid Dynamical
Systems through Shadow Cancellation. Submitted for publication, Dec 2023.
289.
Grayson York and John Reif, Nondeterministic Temperature 1 Self Assembly in 2
Dimensions is Undecidable. Submitted for publication, Dec 2023.