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), Montral,
Qubec, 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 Editors 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). Editors 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). Editors 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.,
Saarbrcken, 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 Trummers 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, Vclav 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 Jrg-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),
Mlaga, 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, Malm Hgskola, 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, Malm Hgskola,
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 Bantre, 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-Recongurable 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-Recongurable Robots Between Arbitrary 2D
Congurations, 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: its 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 Bck, 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. Published as Sudhanshu
Garg, Nikhil
Gopalkrishnan, Harish Chandran,
Tianqi Song, Hieu Bui, Reem Mokhtar, and John Reif, An
Enzyme-free atalytic Self-Replicating DNA Nanodevice, in submission (2018).

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 Dwyer1, 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 in
book: Soft Nanomaterials (Edited by Ye Zhang), World Scientific, to appear
(2018).

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,
Tianqi Song, and John H Reif, Localized DNA Computation, Chapter in
book: From Parallel to Emergent Computing (Edited by Andrew Adamatzky), CRC Press, to appear (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

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 hairpinbased
logic circuits, submitted for journal publication, (2018)

268. Xin Song and
John H. Reif, Nucleic Acid Databases and Molecular-Scale Computing, invited
paper, Nature Nanotechnology, in submission, (2018)