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
n^{1+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 *L*2-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(log^{2} 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]

- John H. Reif and James A. Storer,
3-Dimensional Shortest Paths in the Presence of Polygonal Obstacles. 13th
*Symposium on Mathematical Foundations of Computer Science*,*(Edited by*Michal Chytil, Ladislav Janiga, Václav Koubek) Czechoslovakia, August 29-September 2, 1988, pp. 85-92. Published as A Single-Exponential Upper Bound for Finding Shortest Paths in Three Dimensions.*Journal of the ACM(JACM*), Vol. 41, No. 5, Sept. 1994, pp. 1013-1019. [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.
P*roceedings 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
(DN**A**8), 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]

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, Poster Abstract, 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] http://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] https://doi.org/10.1002/smll.201801470258. DOI: 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, 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 (2019). ISBN: 978-981-120-102-8

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.

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

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), to appear (2020).

272. Shah S., Song
T., Song X., Yang M., Reif J. (2019) 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 DOI: https://doi.org/10.1007/978-3-030-26807-7_2

273. Xin Song, Shalin Shah, and John Reif, An Overview of DNA-Based Digital Data Storage, Chapter, DNA- and RNA-Based Computing Systems (Evgeny Katz, editor),
Wiley Publishers, to appear (2020).

274. Reem Mokhtar, Tianqi
Song, Daniel Fu, Shalin Shah, Xin Song, Ming Yang, and John Reif, DNA Origami
Transformers, Chapter, DNA- and RNA-Based
Computing Systems (Evgeny Katz, editor), Wiley Publishers, to appear (2020).