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. Nikolaou, 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 (July 18, 2018). [PDF] [PDF] https://doi.org/10.1002/smll.201801470258.

258. Hieu Bui, Shalin Shah, Reem Mokhtar, Tianqi Song, Sudhanshu
Garg, John Reif, Localized
DNA Hybridization Chain Reactions on DNA Origami,
ACS Nano
(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 (2018).