1. John H.
Reif (Editor), VLSI Algorithms and Architectures, 3rd Aegean Workshop on
Computing, AWOC 88, Corfu, Greece, June 28 - July 1 1988, 476 pages, Springer-Verlag
Lecture Notes in Computer Science, Vol. 319
(1988).

2. John H.
Reif (Editor), Synthesis of Parallel Algorithms, 22 chapters, 1011 pages. Kluwer Academic
Publishers, San Mateo, California,
1993.

3. Robert
Paige, John H. Reif, and Ralph Wachter (Editors), Parallel Algorithm Derivation and Program
Transformation, 228 pages.
Published by Kluwer Academic Publishers, 1993.

4. Sanguthevar Rajasekaran, pp. M. Pardalos, John H. Reif and J. Rolim
(Editors), Handbook of Randomized Computing (Edited by), Kluwer Volume I and II, Academic
Press, London, 2001.

5.
Proceedings of the 34th ACM Symposium on Theory of
Computing (STOC2002), (Edited by John
H. Reif), Montréal, Québec, Canada, May 19-21, 2002.
Also, John H. Reif, Guest
Editor, Special Issue of Selected Papers from Proceedings of the Thirty-Fourth
Annual ACM Symposium on Theory of Computing (STOC2002) Journal of Computer and
System Sciences(JCSS), Volume 67, Issue 2, Page 211, (September 2003). Guest Editor’s Foreword, Page 211. [PDF]

6. Junghuei Chen and John H. Reif (Editors), Proceedings of the
Ninth International Meeting on DNA Based
Computers (DNA9), Madison, Wisconsin, June 1-3, 2003, 225
pages, Lecture Notes in Computer Science Vol. 2943, Springer-Verlag, New
York, (2004).

7. John H.
Reif (Editor), Proceedings of the First Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO04), Snowbird, Utah,
(April 21-23, 2004), Published by Sciencetechnica
(2004). Editor’s Foreword [PDF]

8. John H.
Reif (Editor), Proceedings of the Second Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO05), Snowbird, Utah,
(April 24-28, 2005), Published by Sciencetechnica
(2005). Editor’s Foreword [PDF]

9. John H.
Reif (Editor), Proceedings of the Third Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO06), Snowbird, Utah,
(April 23-27, 2006), Published by Sciencetechnica
(2006).

10. John H.
Reif (Editor), Proceedings of the Fourth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO07), Snowbird, Utah,
(April 18-22, 2007), Published by Sciencetechnica
(2007).

11. Sanguthevar Rajasekaran and John H. Reif (Editors), Handbook of Parallel Computing: Models, Algorithms
and Applications, Published by
Taylor & Francis, Boca Raton, FL. ISBN 978-1584886235
(December, 2007). [PDF]

12. John H.
Reif (Editor), Proceedings of the Fifth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices(FNANO08), Snowbird, Utah,
(April 21-25, 2008), Published by Sciencetechnica
(2008).

13. John H.
Reif and Marya Lieberman, editors, Proceedings of the
Sixth Conference on Foundations of Nanoscience: Self-Assembled Architectures
and Devices(FNANO09), Snowbird, Utah, Published by Sciencetechnica
(April 20-24, 2009).

14. Sudheer Sahu and John H. Reif, DNA-based Self-assembly and Nanorobotics, Published by VDM Verlag, Dr. Mueller e.K., Saarbrücken, Germany, 128
pages, (November 10, 2008) ISBN-10: 363909770X, ISBN-13: 978-3639097702.

15. John H.
Reif and Marya Lieberman, editors, Proceedings of the
Seventh Conference on Foundations of Nanoscience: Self-Assembled Architectures
and Devices(FNANO10), Snowbird, Utah, Published by Sciencetechnica
(April 27-30, 2010).

16. John H.
Reif and Marya Lieberman, editors, Proceedings of the
Eighth Conference on Foundations of Nanoscience: Self-Assembled Architectures
and Devices(FNANO11), Snowbird, Utah, Published by Sciencetechnica,
(April 11-15, 2011).

John H. Reif
and Marya Lieberman, editors, Proceedings of the
Ninth Conference on Foundations of Nanoscience: Self-Assembled Architectures
and Devices(FNANO12), Snowbird, Utah, Published by Sciencetechnica,
(April 16-19, 2012).

**Papers
**(most are downloadable)

1. John H. Reif, Combinatorial Aspects of Symbolic Program Analysis.
Ph.D. Thesis, Harvard University, July 1977. [PDF]
(Preface & Introductory Chapter 1:[PDF],
Chapter 2(pub. #3):[PDF],
Chapter 3:[PDF],
Chapter 4(pub. #5):[PDF],Chapter
5(pub. #4):[PDF])

2. Richard Barakat and John H. Reif, Numerical Solution of the
Fokker-Plank Equation via Chebyschev Approximations
with Reference to First Passage Time Probability Functions. *Journal of Computational Physics*, Vol. 23,
No. 4, April 1977, pp. 425-445. [PDF]

3. John H. Reif and Harry R. Lewis, Symbolic Evaluation and the Global
Value Graph. *4th ACM Symposium on
Principals of Programming Languages*,* *Los
Angeles, CA, January 1977, pp. 104-118. [PDF]
Published as Efficient Symbolic Analysis of Programs, in *Journal of Computer and System Sciences*,* *Vol. 32, No. 3, June 1986, pp. 280-314. [PDF]

4. John H. Reif, Code Motion. Presented at *Conference on Theoretical Computer Science*,* *University of Waterloo, Canada, 1977. Published in *SIAM Journal on Computing*, Vol. 9, No.
2, May 1980, pp. 375-395. [PDF]

5. John H. Reif, Symbolic Program Analysis in Almost Linear Time. *5th Annual ACM Symposium on Principals of
Programming Languages*, Tucson, AZ, January 1978, pp. 76-83. [PDF]
Published as John H. Reif and R.E. Tarjan, *SIAM Journal on Computing*, Vol. 11, No.
1, February 1982, pp. 81-93. [PDF]

6. John H. Reif, Data Flow Analysis of Communicating Processes. *6th Annual ACM Symposium on Principals of
Programming Languages*,* *San
Antonio, TX, January 1979, pp. 257-268. [PDF]
Published as John H. Reif and Scott A. Smolka, *International Journal of Parallel
Programming*, Vol. 19, No. 1, February 1990. [PDF]

7. John H. Reif, The Complexity of Extending a Graph Imbedding.
Computer Science Department, University of Rochester, TR-42, October 1978. [PDF]

8. Ion S. Filotti, Gary Miller, and John H. Reif, On Determining the
Genus of a Graph in 0(v^0(g)) Steps, *11th
Annual ACM Symposium on Theory of Computing(STOC79)*, Atlanta, GA, April
1979, pp. 27-37. [PDF]

9. John H. Reif, Universal Games of Incomplete Information. *11th Annual ACM Symposium on Theory of
Computing*, Atlanta, GA, April 1979, pp. 288-308. Harvard University
TR-35-81. [PDF]
Published as The Complexity of Two-Player Games of Incomplete Information. *Journal of Computer and System Sciences*,
Vol. 29, No. 2, October 1984, pp. 274-301. [PDF]

10. Gary L.
Peterson and John H. Reif, Multiple-Person Alternation. *20th Annual IEEE Symposium on Foundations of Computer Science*, San
Juan, Puerto Rico, October 1979, pp. 348-363. Published as Gary L. Peterson,
John H. Reif, and Selman Azhar, Lower Bounds for
Multiplayer Noncooperative Games of Incomplete Information, Computers and
Mathematics with Applications, Volume 41, April 2001, pp. 957-992. [PDF]

11. John H. Reif, Complexity of the Mover's Problem and
Generalizations. *20th Annual IEEE
Symposium on Foundations of Computer Science*, San Juan, Puerto Rico,
October 1979, pp. 421-427. [PDF]
Published as Complexity of the Generalized Mover's Problem, Chapter 11 in *Planning, Geometry and Complexity of Robot
Motion*, Jacob Schwartz, ed., Ablex Pub., Norwood,
NJ, 1987, pp. 267-281. [PDF]

12. Gary L. Peterson and John H. Reif, A Dynamic Logic of
Multiprocessing with Incomplete Information. *7th Annual ACM Symposium on Principles of Programming Languages*,* *Las Vegas, NV, January 1980, pp.
193-202. [PDF]

13. John H. Reif, Logics for Probabilistic Programming. *12th Annual ACM Symposium on Theory of
Computing*,* *Los Angeles, CA, April
1980, pp. 8-13. [PDF]

14. John H. Reif and Paul G. Spirakis,
Random Matroids. *12th Annual ACM
Symposium on Theory of Computing*,* *Los
Angeles, CA, April 1980, pp. 385-397. Revised as Probabilistic Analysis of Random
Extension-Rotation Algorithms, Harvard University TR-28-81, 1980. [PDF]

15. John H. Reif and Paul G. Spirakis,
Distributed Algorithms for Synchronizing Interprocess
Communication Within Real Time. *13th
Annual ACM Symposium on Theory of Computing*,* *Milwaukee, WI, 1981, pp. 133-145. Published as Real-Time
Synchronization of Interprocess Communications: *ACM Journal of Transactions on Programming
Languages and Systems*, Vol. 6, No. 2, April 1984, pp. 215-238. [PDF]

16. John H. Reif, Minimum s-t Cut of Planar Undirected Network in 0(n
log^2n) Time, 8th Colloquium on Automata, Languages and Programming, (Shimon
Even and Oded Kariv, editors) volume 115 of Lecture
Notes in Computer Science, pp. 56-67, Acre (Akko), Israel, 13-17 July 1981.
Springer-Verlag. Published in *SIAM
Journal on Computing*, Vol. 12, No. 1, February 1983, pp. 71-81. [PDF]

17. John H. Reif, Symmetric Complementation. *14th Annual ACM Symposium on Theory of Computing*,* *San Francisco, CA, May 1982, pp.
201-214. Presented at the NSF/AMS on *Probabilistic
Computational Complexity*,* *Durham,
NH, June 1982. Published in *Journal of
the ACM(JACM)*,* *Vol. 31, No. 2,
April 1984, pp. 401-421. [PDF]

18. Joseph Y. Halpern and John H. Reif, The Propositional Dynamic
Logic of Deterministic, Well-Structured Programs, *22nd Annual IEEE Symposium on Foundations of Computer Science*,* *Nashville, TN, October 1981, pp.
322-334. Published in *Journal of
Theoretical Computer Science*,* *Vol.
27, 1983, pp. 127-165. [PDF]

19. John H. Reif and Paul G. Spirakis,
Unbounded Speed Variability in Distributed Communication Systems. *9th Annual ACM Symposium on Principals of
Programming Languages(POPL80)*,* *Albuquerque,
NM, January 1982, pp. 46-56. [PDF]
Published in *SIAM Journal on Computing*,* *Vol. 14, No. 1, February 1985, pp.
75-92. [PDF]

20. Gary L. Peterson and John H. Reif, Decision Algorithms for
Multiplayer Games of Incomplete Information. Harvard University, TR-34-81.
Published as Gary L. Peterson, John H. Reif, and Selman Azhar,
Decision Algorithms for Multiplayer Non-Cooperative Games of Incomplete
Information. Computers and Mathematics with Applications, Vol. 43, Jan. 2002,
pp. 179-206. [PDF]

21. John H. Reif and Paul G. Spirakis,
K-connectivity in Random Undirected Graphs, *Discrete
Mathematics*,* *Vol. 54, No. 2,
April 1985, pp. 181-191. [PDF]
(Also, John H. Reif and Paul G. Spirakis, Strong
k-connectivity in Digraphs and Random Digraphs, Harvard University TR-25-81. [PDF])

22. John H. Reif and Paul G. Spirakis,
Strong k-connectivity in Digraphs and Random Digraphs, Harvard University
TR-25-81. [PDF]

23. John H. Reif, On the Power of Probabilistic Choice in Synchronous
Parallel Machines. Harvard University TR-30-81. *9th International Colloquium on Automata, Languages and Programming*,* *Aarhus, Denmark, 1982, pp. 442-450.
Published as On Synchronous Parallel Computations with Independent
Probabilistic Choice in *SIAM Journal on
Computing*, Vol. 13, No. 1, February 1984, pp. 46-56. [PDF]

24. John H. Reif and Paul G. Spirakis, Real
Time Resource Allocation in Distributed Systems, *ACM Symposium on Principals of Distributed Computing*,* *Ottawa, Canada, August 1982, pp. 84-94.
[PDF]

25. John H. Reif, Parallel Time *0*(log
*n*) Time Acceptance of Deterministic
CFLs. *23rd Annual IEEE Symposium on
Foundations of Computer Science*,* *Chicago,
IL, November 1982, pp. 290-296. Published as Phlip
Klein and John H. Reif, Parallel Time *0*(log
*n*) Time Acceptance of Deterministic
CFLs on an Exclusive-Write P-RAM, *SIAM
Journal on Computing*,* *Vol. 17,
No. 3, June 1988, pp. 463-485. [PDF]

26. John H. Reif and Paul G. Spirakis,
Expected Parallel Time and Sequential Space Complexity of Graph and Digraph
Problems, *Algorithmica*,
Special Issue on Graph Algorithms, Vol. 7, Numbers 5 & 7, pp. 597-630,
1992. [PDF]

27. Leslie G. Valiant and John H. Reif, A Logarithmic Time Sort for
Linear Size Networks. *15th Annual ACM
Symposium on Theory of Computing*,* *Boston,
MA, April 1983, pp. 10-16. [PDF]
Published in *Journal of the ACM(JACM)*,* *Vol. 34, No. 1, January 1987, pp.
60-76. [PDF]

28. John H. Reif and W.L. Scherlis, Deriving
Efficient Graph Algorithms. Logics of Programs
Workshop, Carnegie-Mellon University, Pittsburgh, PA, June 1983, Lecture Notes
in Computer Science, Vol. 164, 1984, pp. 421-441. Published in: Verification:
Theory and Practice: Essays Dedicated to Zohar Manna on the Occasion of His
64th Birthday (edited by Nachum Dershowitz), LNCS series Vol. 2772, pp.
645-681, 2004. [PDF]
or [PDF]

29. John H. Reif and A.P. Sistla, A Multiprocess Network Logic with Temporal and Spatial
Modalities, *10th International Colloquium
on Automata, Languages and Programming*, Barcelona, Spain, July 1983; *Lecture Notes in Computer Science*, Vol.
154, 1983, pp. 629-639. Published in *Journal
of Computer and System Sciences*,* *Vol.
30, No. 1, February 1985, pp. 41-53. [PDF]

30. John H. Reif, Logarithmic Depth Circuits for Algebraic Functions. *24th Annual IEEE Symposium on Foundations of
Computer Science*, Tucson, AZ, November 1983, pp. 138-145. Published in *SIAM Journal on Computing*,* *Vol. 15, No. 1, February 1986, pp.
231-242. [PDF]

31. John H. Reif, An n1+epsilon Processor, 0(log n) Time Probabilistic
Sorting Algorithm. *SIAM 2nd Conference on
the Applications of Discrete Mathematics*,* *Cambridge, MA, June 1983, pp. 27-29. [PDF]

32. John H. Reif, Probabilistic Parallel Prefix Computation, *13th Annual International Conference on
Parallel Processing*,* *Michigan,
1984. Published in *Computers and
Mathematics with Applications*, Vol. 26, Number 1, July 1993, pp. 101-110. [PDF]

33. John H. Reif and Paul G. Spirakis,
Probabilistic Bidding Gives Optimal Distributed Resource Allocation. *11th International Colloquium on Automata,
Languages and Programming*,* *Antwerp,
Belgium, July 1984. Published in *Lecture
Notes in Computer Science*, Vol. 172, pp. 391-402. [PDF]

34. John H. Reif, Depth-First Search is Inherently Sequential. *Information Processing Letters*,* *Vol. 20, No. 5, June 12, 1985, pp.
229-234. [PDF]

35. John H. Reif, A Topological Approach to Dynamic Graph
Connectivity. *Information Processing
Letters*,* *Vol. 25, No. 1, April
20, 1987, pp. 65-70. [PDF]

36. Gautam Kar, Christos N. holaou, and John
H. Reif, Assigning Processes to Processors: A Fault-Tolerant Approach, *14th International Conference on
Fault-Tolerant Computing*,* *Kissimmee,
FL, June 1984, pp. 306-309. [PDF]

37. Micheal Ben-Or, Dextor
Kozen, and John H. Reif, The Complexity of Elementary
Algebra and Geometry. *16th Annual
Symposium on Theory of Computing*, Washington, DC, April-May 1984,* *pp. 457-464. [PDF]
Published in *Journal of Computer and
Systems Sciences*,* *Vol. 32, No. 2,
April 1986, pp. 251-264. [PDF]

38. Ravi Nair, Anni Bruss, and John H. Reif, Linear Time Algorithms
for Optimal CMOS Layout, *International
Workshop on Parallel Computing and VLSI*, Amalfi, Italy, May 1984; *VLSI: Algorithms and Architectures*,* *North-Holland, pp. 327-338. [PDF]

39. John H. Reif and Doug Tygar, Efficient
Parallel Pseudo-random Number Generation. *CRYPTO-85,
Proceedings*, Vol. 218, H. Williams and E. Brickell, ed., Springer-Verlag,
New York, NY, 1986, pp. 433-446 Presented at the Mathematical Theory of
Security, Boston, MA, 1985. Published in *SIAM
Journal on Computing*, Vol. 17, No. 2, April 1988, pp. 404-411. [PDF]

40. Peter Gacs and John H. Reif, A Simple
Three-dimensional Real-time Reliable Cellular Array. *17th Annual ACM Symposium on Theory of Computing*, Providence, RI,
May 1985, pp. 388-395. [PDF]
Published in *Journal of Computer and
System Sciences*,* *Vol. 36, No. 2,
April 1990, pp. 125-147. [PDF]

41. Victor Y. Pan and John H. Reif, Efficient Parallel Solution of
Linear Systems. *17th Annual ACM Symposium
on Theory of Computing(STOC85)*, Providence, RI, (ACM Press, New York) May
1985,* *pp. 143-152. Presented at the
meeting on Efficient Algorithms, Mathematisches Forschungsinstitut, Oberwolfach,
W. Germany, November 1984. Presented at *2nd
SIAM Conference on Applied Linear Algebra*, Raleigh, NC, April 1985.
Published as Fast and Efficient Parallel Solution of Sparse Linear Systems. *SIAM Journal on Computing*, Vol 22, No.
6, pp. 1227-1250, December 1993. [PDF]
or [PDF]

42. Gary Miller and John H. Reif, Parallel Tree Contraction and its
Application. Harvard University TR-18-85. *26th
Annual IEEE Symposium on Foundations of Computer Science*, Portland, OR,
October 1985, pp. 478-489.

42a Portions
Published as Parallel Tree Contraction Part I: Fundamentals, Parallel Tree Contraction Part 1: Fundamentals. In
Randomness and Computation, (*Advances
in Computing Research*, Vol. 5., Silvio Micali, editor), pp. 47–72, JAI
Press, Greenwich, Connecticut, 1989. [PDF]

42b Portions
Published as Parallel Tree Contraction Part II: Further Applications, *SIAM Journal on Computing*, Vol. 20, No.
6, pp. 1128-1147, December 1991. [PDF]

43. Sanguthevar Rajasekaran
and John H. Reif, An Optimal Parallel Algorithm for Integer Sorting. *26th Annual IEEE Symposium on Foundations of
Computer Science*, Portland, OR, October 1985,* *pp. 496-503. Published as Optimal and Sublogarithmic
Time Randomized Parallel Sorting Algorithms, *SIAM Journal on Computing*, Vol. 18, No. 3, June 1989, pp. 594-607.
[PDF]
or [PostScript]
[PDF]

44. John H. Reif and M. Sharir, Motion
Planning in the Presence of Moving Obstacles, *26th Annual IEEE Symposium on Foundations of Computer Science*,
Portland, OR, October 1985,* *pp.
144-154. Published in Journal of the ACM (*JACM)*,
41:4, July 1994, pp. 764-790. [PDF]
or [PostScript]
[PDF]

45. John H. Reif, Probabilistic Algorithms in Group Theory.
Foundations of Computation Theory (FCT85), Cottbus, Democratic Republic of
Germany, September 1985; *Lecture Notes in
Computer Science*, Vol. 199, 1985, pp. 341-350. Also TR85-01, Dept. of
Computer Science, Harvard University, (1985). Published as Selman Azhar and John H. Reif, Efficient Algorithmic Learning of
the Structure of Permutation Groups by Examples, *Computers & Mathematics with Applications*, Volume 37, Issue 10,
May 1999, pp. 105-132. [PDF]

46. Victor Y. Pan and John H. Reif, Fast and Efficient Algorithms for
Linear Programming and for the Linear Least Squares Problem, *12th International Symposium on Mathematical
Programming*,* *MIT, Cambridge, MA,
pp. 283-295, August 1985. Abstract published as Efficient Parallel Linear
Programming, *Operations Research Letters*,* *Vol. 5, No. 3, August 1986, pp.
127-135. [PDF] Also presented as Fast and Efficient Parallel
Linear Programming and Least Squares Computations at Aegean Workshop on
Computing, Loutraki, Greece, July 1986; *Lecture Notes in Computer Science*,
Springer-Verlag, Vol. 227, 1986, pp. 283-295. Full Paper published as Fast and
Efficient Linear Programming and Linear Least-Squares Computations, *Computers and Mathematics with Applications*,* *Vol. 12A, No. 12, 1986, pp. 1217-1227.
[PDF]

47. John H. Reif, Parallel Interpolation Search. *23rd Annual Allerton Conference on Communication, Control and Computing*,* *Monticello, IL, October 1985. Published
as D.E. Willard and John H. Reif, Parallel Processing can be Harmful: the
Unusual Behavior of Interpolation Search, *Journal
of Information and Computation*, Vol. 81, No. 3, June 1989, pp. 364-379. [PDF]

48. John H. Reif and Scott A. Smolka, The
Complexity of Reachability in Distributed Communicating Processes, *Journal of Acta Informatica*,* *Vol. 25(3), April 1988, pp.333-354. [PDF]

49. Steve Homer and John H. Reif, Arithmetic Theories for
Computational Complexity Problems, *Journal
of Information and Control*, Vol. 69, nos. 1-3, April/May/June 1986, pp.
1-11. [PDF]

50. James A. Storer and John H. Reif, A Parallel Architecture for High
Speed Data Compression,* 3rd Symposium on
the Frontiers of Massively Parallel Computation*, College Park, MD, October
1990, pp. 238-243. Published in Journal of Parallel and Distributed
Computation, No. 13, 1991, pp. 222-227. [PDF]

51. Victor Y. Pan and John H. Reif, Fast and Efficient Parallel
Solution of Dense Linear Systems. *Computers
and Mathematics with Applications*, Vol. 17, No. 11, 1989, pp. 1481-1491. [PDF]

52. John H. Reif and James A. Storer, Shortest Paths in the plane with
polygonal obstacles, *Journal of the
ACM(JACM)* 41:5, September, 1994, pp. 982-1012. [PDF]

53. John H. Reif and James A. Storer, Minimizing Turns for Discrete
Movement in the Interior of a Polygon, *IEEE
Journal of Robotics and Automation*,* *Vol.
3, No. 3, June 1987, pp. 182-193. [PDF]

54. John H. Reif, Efficient VLSI Fault Simulation. *Computers and Mathematics with Applications*,
Vol 25, No. 2, Jan. 1993, pp. 15-32. [PDF]

55. Richard E. Ladner and John H. Reif, The Logic of Distributed
Protocols. *Conference on Theoretical
Aspects of Reasoning about Knowledge*, Los Altos, CA, March 1986, pp.
207-223. [PDF]

56. Victor Y. Pan and John H. Reif, Extension of the Parallel Nested
Dissection Algorithm to Path Algebra Problems. Presented at *6th Conference on Foundation of Software
Technology and Theoretical Computer Science*,* *New Delhi, India; *Lecture
Notes in Computer Science*, Springer Verlag, Vol. 241, pp. 470–487, 1986. An
abstract of this paper appears as Parallel Nested Dissection for Path Algebra
Computations, *Operations Research Letters*,* *Vol. 5, No. 4, October 1986,
pp. 177-184. [PDF]
Published as Fast and Efficient Solution of Path Algebra Problems, *Journal of Computer and Systems Sciences*,
Vol. 38, No. 3, June 1989, pp. 494-510. [PDF]

57. John Canny and John H. Reif, New Lower Bound
Techniques for Robot Motion Planning Problems. *28th Annual IEEE Symposium on Foundations of Computer Science*,* *Los
Angeles, CA, October 1987, pp. 49-60. [PDF]

58. Richard Barakat and John H. Reif, Lower Bounds on the
Computational Efficiency of Optical Computing Systems. *Journal of Applied Optics*,* *Vol.
26, No. 6, March 15, 1987, pp. 1015-1018. [PDF]

59. Richard Barakat and John H. Reif, Polynomial Convolution Algorithm
for Matrix Multiplication with Application for Optical Computing. Published in *Journal of Applied Optics*,* *Vol. 26, No. 14, July 15, 1987, pp.
2707-2711. [PDF]

60. John H. Reif, A Survey on Advances in the Theory of Computational
Robotics. Proceedings of the Fourth Workshop of Adaptive Systems Control
Theory, Princeton, NJ, 1986. Also as Chapter in Book: Adaptive and Learning
Systems: Theory and Applications, Princeton, NJ* (edited by *K.S. Narendra), Plenum Press, New York, NY, pp.
421--427 1986. [PDF]

61. Phlip Klein and John H. Reif, An
Efficient Parallel Algorithm for Planarity. *27th
Annual IEEE Symposium on Foundations of Computer Science*, Toronto, Canada, October
1986,* *pp.* *465-477. Published in *Journal
of Computer and System Sciences*,* *Vol.
37, No. 2, October 1988, pp. 190-246. [PDF]

62. Charles E. Leiserson, J.P. Mesirov, L. Nekludova, S.M. Omohundro, John H. Reif, and W. Taylor, Solving Sparse
Systems of Linear Equations on the Connection Machine. *Annual SIAM Conference*, Boston, MA, July 1986. [PDF]

63. T. Opsahl and John H. Reif, Solving Very Large, Sparse Linear
Systems on Mesh-Connected Parallel Computers. *First Symposium on Frontiers of Scientific Computing*,* *NASA, Goddard Space Flight Center,
Greenbelt, MD, September 1986, pp. 2241-2248. [PDF]

64. John H. Reif,
Simon Kasif, and Deepak Sherlekar, Formula Dissection: A
Parallel Algorithm for Constraint Satisfaction. *IEEE Workshop on Computer Architecture for Pattern Analysis and Machine
Intelligence*, Seattle, WA, October 1987, pp. 51-58. Published in Computers
and Mathematics with Applications, Vol. 5, (2008), pp. 1170-1177. [PDF] [PDF]

65. John H. Reif and Sandeep Sen, Optimal
Randomized Parallel Algorithms for Computational Geometry. *16th International Conference on Parallel Processing*, St. Charles,
IL, August 1987, pp. 270-276. Published in *Algorithmica*, Vol. 7, No. 1,
January 1992, pp. 91-117. [PDF]

66. John Canny, B. Donald, John H. Reif and Patrick G. Xavier. On the
Complexity of Kinodynamic Planning. *29th Annual IEEE Symposium on Foundations of
Computer Science*,* *White Plains,
NY, October 1988, pp. 306-316. Published as Kinodynamic
Motion Planning, *Journal of the ACM*,
Vol 40(5), November 1993, pp. 1048-1066. [PDF]

67. Sanguthevar Rajasekaran
and John H. Reif, Randomized Parallel Computation. Presented at *Foundations of Computation Theory Conference*,* *Kasan, USSR,* *June 1987;* Lecture Notes in Computer Science*,* *Vol. 278, 1987, pp. 364-376. Published in Chapter 11 of *Concurrent Computations: Algorithms,
Architecture and Technology*,* *S.K.* *Tewksbury, B.W. Dickinson and S.C.
Schwartz, ed., 1988, pp. 181-202. [PDF]

68. John H. Reif and Steve R. Tate, On Threshold Circuits and
Polynomial Computation. *2nd Structure in
Complexity Theory Conference*,* *Ithaca,
NY, June 1987. Published in *SIAM Journal
on Computing*, Vol.21, No. 5, October 1992, 896-908. [PDF]
or [PostScript]
[PDF]

69. Vijaya Ramachandran and John H. Reif, An Optimal Parallel
Algorithm for Graph Planarity. *30th
Annual IEEE Symposium on Foundations of Computer Science*, Research Triangle
Park, NC, October 1989, pp. 282-287. Published as Planarity Testing in Parallel*, Journal of Computer and System Sciences*,
**49**:3, December, 1994, pp. 517-561. [PostScript]
[PDF]

70. Sanguthevar Rajasekaran
and John H. Reif, Nested Annealing: A Provable Improvement to Simulated
Annealing. Presented at *Workshop on
Applications of Combinatorics and Graph Theory to Computer Science*,
Institute for Mathematics and its Applications, University of Minnesota,
December 1987. Presented at the *15th
International Colloquium on Automata, Languages and Programming*,* *Tampere, Finland, July 1988; *Lecture Notes in Computer Science*, Vol.
317, 1988, pp. 455-472. Published in *Journal
of Theoretical Computer Science*, 99(1):157-176, 1 June 1992. [PDF]

71. Victor Y. Pan and John H. Reif, Some Polynomial and Toeplitz
Matrix Computations. *28th Annual IEEE
Symposium on Foundations of Computer Science*, Los Angeles, CA, October
1987, (IEEE Computer Society Press)* *pp.
173-184. [PDF]

72. James A. Storer and John H. Reif, Real-time Compression of Video
on a Grid-connected Parallel Computer. *3rd International
Conference on Supercomputing*,* *Boston,
MA, May 1988. [PDF]

73. Edward W. Davis and John H. Reif, Architecture and Operation of
the BLITZEN Processing Element. *3rd International
Conference on Computing on Supercomputing*,* *Boston, MA, May 1988. Also revised as Donald W. Blevins, Edward W.
Davis, and John H. Reif, Processing Element and Custom Chip Architecture for
the BLITZEN Massively Parallel Processor, MCNC Technical Report TR87-22,
October 1987, revised June 1988. [PDF]

74. John H. Reif and Sandeep Sen, An Efficient Output-Sensitive
Hidden-Surface Removal Algorithm and its Parallelization. *4th Annual ACM Symposium on Computational Geometry*,* *Urbana, IL, June 1988,* *pp. 193-200. Published as An
Efficient Output-Sensitive Hidden-Surface Removal Algorithm for Polyhedral
Terrains, *Journal of Mathematical and
Computer Modeling*, Vol. 21, No. 5, pp. 89-104, 1995. [PDF]
or [PDF]

75. Lars S. Nyland and John H. Reif, An Algebraic Technique for
Generating Optimal CMOS Circuitry in Linear Time, *Computers and Mathematics with Applications *Vol 31, No. 1, Jan.
1996, pp.85-108. [PDF]

76. Donald W. Blevins, Edward W. Davis, Richard A. Heaton and John H.
Reif, BLITZEN: A Highly Integrated Massively Parallel Machine. *2nd Symposium on Frontiers of Massively
Parallel Computation*,* *Fairfax,
VA, October 1988. Published in *Journal of
Parallel and Distributed Computing*, Vol. 8, February 1990, pp. 150-160. [PDF]

77. John H. Reif and Steve R. Tate, Optimal Size Integer Division
Circuits. *21st Annual ACM Symposium on
Theory of Computing*, Seattle, WA, May 1989,* *pp. 264-273. Presented at meeting on Efficient Algorithms, Mathematisches Forschungsinstitut,
W. Germany, September 1989. Published in *SIAM
Journal on Computing*, Vol. 19, No. 5, October 1990, pp. 912-924. [PDF]
or [PostScript]
[PDF]
or [PostScript]

78. John H. Reif and Sandeep Sen, Polling: A New Randomized Sampling
Technique for Computational Geometry, *21st
Annual ACM Symposium on Theory of Computing*, Seattle, WA, May 1989, pp.
394-404. [PDF]
Revised as Optimal Parallel Randomized Algorithms for Three-Dimensional Convex
Hulls and Related Problems, Published in *SIAM
Journal on Computing*, Vol. 21, No. 3, June 1992, pp. 466-485. [PDF]
or [PDF]
(see also Erratum: Optimal parallel randomized algorithms for three-dimensional
convex hulls and related problems. SIAM Journal on Computing, 23(2):447-448,
April 1994. [PDF])

79. John
H. Reif and A. Tyagi, Energy Complexity of Optical Computations, *2nd IEEE Symposium on Parallel and
Distributed Processing*, Dallas, TX, December 1990, pp. 14-21. Revised
for Journal Publication in International Journal of Unconventional
Computing, 2016, Vol. 12 Issue 5/6, pp. 393-412. [PDF]

80. John H. Reif, Optical expanders give constant time holographic
routing using O(N log N) switches, 1988 [PDF].
Full paper appeared as E.S. Maniloff, K. Johnson, and
John H. Reif, Holographic Routing Network for Parallel Processing Machines *Holographic Optics II: Principals and Applications*,
G. Michael Morris; Ed.* *SPIE
Proceedings Series, Vol. 1136, EPS/EUROPTICA/SPIE International Congress on
Optical Science and Engineering, Paris, France, April 1989, pp. 283-289. [PDF]

81. John H. Reif,
Doug Tygar, and Akitoshi Yoshida, The Computability
and Complexity of Optical Beam Tracing. *31st
Annual IEEE Symposium on Foundations of Computer Science*, St. Louis, MO,
October 1990, pp. 106-114. Published as The Computability and Complexity of Ray
Tracing in *Discrete & Computational
Geometry*, 11: pp. 265-287 (December 1994). [PDF]

82. Selman Azhar, Andrew McLennan and John H. Reif, Computation of
Equilibria in Noncooperative Games, Duke University Technical Report
CS-1991-36. *Proc. Workshop for Computable
Economics*, Dec. 1992. Published in Computers
& Mathematics with Applications, Volume 50, Issues 5-6, September 2005, pp.
823-854. [PDF]

83. R. Paturi, Sanguthevar
Rajasekaran, and John H. Reif, Efficient and Robust
Learning Using Statistical Bootstrap, *Proceedings
of the 2nd Annual Workshop on Computational Learning Theory*, Santa Cruz,
CA, August 1989. [PostScript]
[PDF]
Published as The Light Bulb Problem, *Information
and Computation*, 117(2):187-192, March 1995. [PDF]

84. John H. Reif and Sandeep Sen, Randomized Parallel Algorithms. *IBM Workshop on Capabilities and Limitations
of Parallel Computing*, San Jose, CA, December 1988. *Information Processing* *89*,
G. Ritter, ed., Elsevier Science Publishers, North Holland, 1989, pp. 455-458.
[PDF] A
Case for Randomized Parallel Algorithms in *Opportunities
and Constraints of Parallel Computing*, J.L.C. Sanz (ed.), Springer-Verlag New York, 1989, pp. 101-105. Also
presented as Randomization in Parallel Algorithms and its Impact on
Computational Geometry, in *Optimal Algorithms;Lecture
Notes in Computer Science*, Vol. 401, 1989, pp. 1-8. [PDF]
Also presented as C. Pandurangan, Sanguthevar
Rajasekaran, John H. Reif, Sandeep Sen, Studies on
Sequential and Parallel Randomized Algorithms, Indo-US Workshop on Cooperative
Research in Computer Science, Bangalore, India, August 4-6, 1992. [PDF]

85. Victor Y. Pan and John H. Reif, On the Bit-Complexity of Discrete
Approximations to PDEs.* International
Colloquium on Automata, Languages, and Programming(ICALP 90)*, Warwich, England, Springer Lecture Notes in Computer
Science 443, pp. 612-625, July 1990. [PDF]
Published as The Bit-Complexity of Discrete Solutions of Partial Differential
Equations: Compact Multigrid, *Computers
and Mathematics with Applications,* Vol. 20, No. 2, 1990, pp. 9-16. [PDF].

86. John H. Reif and A. Tyagi, Efficient Algorithms for Optical
Computing with the DFT Primitive, Presented at *10th Conference on Foundations of Software Technology and Theoretical
Computer Science*, Bangalore, India, *Lecture
Notes in Computer Science, pp. 149-160 (*December 1990). Published as
Efficient Algorithms for Optical Computing with the discrete Fourier transform
(DFT) primitive, *Journal of Applied
Optics*, Vol. 36, 1997, pp. 7327-7340. [PDF]
or [PostScript]
[PDF]

87. John Canny, A. Rege, and John H. Reif,
An Exact Algorithm for Kinodynamic Planning in the
Plane. *6th Annual ACM Symposium on
Computational Geometry*, Berkeley, CA, June 1990, pp. 271-280. [PDF]
Published in *Discrete and Computational
Geometry*, Vol. 6, 1991, pp. 461-484. [PDF]

88. John H. Reif
and Sandeep Sen, Randomized Algorithms for Binary Search and Load Balancing on
Fixed Connection Networks with Geometric Applications. *2nd Annual ACM Symposium on Parallel Algorithms and Architectures*,
Crete, Greece, July 1990, pp. 327-337. Published in *SIAM Journal of Computing* 23:3, June, 1994, pp.633-651. [PDF]

89. John H. Reif, Efficient Parallel Algorithms: Theory and Practice. *SIAM 35th Anniversary Meeting*, Denver,
CO, October 1987. *XI World Computer
Congress*, IFIP 89, San Francisco, CA, 1989.

90. Hristo Djidjev
and John H. Reif, An Efficient Algorithm for the Genus Problem with Explicit
Construction of Forbidden Subgraphs. *23rd
Annual ACM Symposium on Theory of Computing*, New Orleans, LA, May 1991, pp.
337-347. [PDF]

91. Hillel Gazit and John H. Reif, A
Randomized Parallel Algorithm for Planar Graph Isomorphism. *2nd Annual ACM Symposium on Parallel
Algorithms and Architectures*, Crete, Greece, July 1990, pp. 210-219. Published
in* Journal of Algorithms, *Vol. 28,
No. 2, pp. 290-314, August 1998. [PostScript]
[PDF]

92. Victor Y. Pan and John H. Reif, The Parallel Computation of
Minimum Cost Paths in Graphs by Stream Contraction, *Information Processing Letters*, Vol. 40, October 25,1991, pp.
79-83. [PDF]

93. John H. Reif and Steve R. Tate, Approximate Kinodynamic
Planning Using *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(log2 n) Time Efficient Parallel Factorization of
Dense, Sparse Separable, and Banded Matrices. *5th Annual ACM Symposium on Parallel Algorithms and Architectures
(SPAA'94)*, Cape May, NJ, June 1994, pp. 114-121.** **[PostScript]
[PDF]

112. John H. Reif, An *O*(*n* log^3 *n*) Algorithm for the Real Root Problem. *34th Annual IEEE Conference on Foundations of Computer Science (FOCS
'93) Proceedings*, November 1993, Palo Alto, CA, pp. 626-635. Revised as An
Efficient Algorithm for the Real Root and Symmetric Tridiagonal Eigenvalue
Problems, 1994. [PostScript]
[PDF]
and [PostscriptFigures]

113. Tassos Markas
and John H. Reif, Memory-Shared Parallel Architectures for Vector Quantization
Algorithms, 1992. Picture Coding Symposium, Lusanne
Switzerland, March, 1993.

114. Peter H. Mills, Lars S. Nyland, Jan Prins,
and John H. Reif, Prototyping N-body Simulation in *Proteus*, *Sixth International
Parallel Processing Symposium*, IEEE, Beverly Hills, CA, pp. 476-482, 1992.
[PostScript]
[PDF]

115. Deganit Armon and John H. Reif, Space and time efficient implementations of parallel
nested dissection, *4th Annual ACM Symposium on Parallel Algorithms and
Architectures*, San Diego, CA,
July 1992. Submitted for journal publication as Space and
Time Efficient Implementations of a Parallel Direct Solver using Nested
Dissection. [__PDF__]

116. Peter H. Mills, Lars S. Nyland, Jan Prins,
and John H. Reif, Prototyping High-Performance Parallel Computing Applications
in *Proteus*. *DARPA Software Technology Conference*, May, 1992. [PostScript]
[PDF]

117. Victor Y. Pan, John H. Reif, Steve R. Tate. The Power of
Combining the Techniques of Algebraic and Numerical Computing: Improved Approximate Multipoint
Polynomial Evaluation and Improved Multipole Algorithms, 32th Annual IEEE
Symposium on Foundations of Computer Science (FOCS'92), Pittsburgh, PA, Oct.
1992, pp. 703-713. Rewritten as John H. Reif and Steve R. Tate, "N-body
simulation I: Fast algorithms for potential field evaluation and Trummer's problem". Tech. Report. #N-96-002, Univ. of
North Texas, Dept. of Computer Science (1996). [PostScript]
[PDF] Submitted for journal
publication as as John H. Reif and Steve R. Tate, Efficient
N-body Simulation: Fast Algorithms for Potential Field Evaluation and Trummer’s Problem [PDF].

118. William L. Hightower, Jan Prins, and
John H. Reif, Implementations of Randomized Sorting on Large Parallel Machines.
*4th Annual ACM Symposium on Parallel
Algorithms and Architectures (SPAA'92)*, San Diego, CA, pp. 158-167, July
1992. [PDF]

119. Yijie Han, Victor Y. Pan, and John H.
Reif, Efficient Parallel Algorithms for Computing All Pair Shortest Paths in
Directed Graphs. University of Kentucky Technical Report 204-92. *4th Annual ACM Symposium on Parallel
Algorithms and Architectures*, San Diego, CA, July 1992, pp. 353-362.
Published in Algorithmica, Vol 17, pp. 399-415, 1997.
[PDF]

120. John H. Reif and Hongyan Wang, Social
Potential Fields: A Distributed Behavioral Control for Autonomous Robots, *Workshop on Algorithmic Foundations of
Robotics (WAFR'94)*, San Francisco, California, February, 1994; The
Algorithmic Foundations of Robotics, A.K.Peters,
Boston, MA. 1995, pp. 431-459. Published in Robotics and Autonomous Systems,
Vol. 27, no.3, pp.171-194, (May 1999). [PostScript]
[PDF]

121. John H. Reif and Steve R. Tate, Dynamic Algebraic Algorithms, *Proceedings of the* *5th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'94),* TX,
Jan. 1994. pp.290-301. Published as On Dynamic Algorithms for Algebraic
Problems, Journal of Algorithms, Volume 22, Number 2, pp. 347-371, February
1997. [PostScript]
[PDF]

122. John H. Reif and Steve R. Tate, Dynamic Parallel Tree
Contraction, *5th Annual ACM Symposium on
Parallel Algorithms and Architectures (SPAA'94)*, Cape May, NJ, June 1994.
pp.114-121. Revised version submitted for journal publication. [PDF]

123. Deganit Armon and John H. Reif, A
Dynamic Separator Algorithm with Applications to Computational Geometry and
Nested Dissection, *3rd Annual Workshop on
Algorithms and Data Structures (WADS '93)*, Montreal, Quebec, Canada,
August, 1993, pp. 107-118. [PDF]

124. Selman Azhar, Greg J. Badros, Arman Glodjo, Ming Kao,
and John H. Reif, Data Compression Techniques for Stock Market Prediction, *Proceedings: IEEE Data Compression
Conference (DCC'94)*, Snowbird, UT, IEEE Computer Society Press, James A.
Storer, Martin Cohn (Eds.), March 1994, pp. 72-82. [PDF]

125. Joseph Cheriyan and John H. Reif,
Parallel and Output Sensitive Algorithms for Combinatorial and Linear Algebra
Problems, 1992. *4th Annual ACM Symposium
on Parallel Algorithms and Architectures (SPAA'93*), Velon,
Germany, July 1993, p.50-56. Published as John H. Reif, Parallel Output
Sensitive Algorithms for Combinatorial and Linear Algebra Problems, *Journal of Computer and System Sciences*,
Vol. 62, May 2001, pp. 398-412. [PostScript] [PDF]

126. Sotiris E. Nikoletseas, John H. Reif,
Paul G. Spirakis, Moti Yung, Stochastic Graphs Have
Short Memory: Fully Dynamic Connectivity in Poly-Log Expected Time. *Proceedings of the 22nd Annual Colloquium on
Automata, Languages and Programming (ICALP'95)*, Szeged, Hungary, July 1995,
pp. 159-170. [PDF]

127. Steve R. Tate and John H. Reif, The Complexity of N-body
Simulation, *Proceedings of the 20th
Annual Colloquium on Automata, Languages and Programming (ICALP'93)*, Lund,
Sweden, July, 1993, pp. 162-176. [PostScript]
[PDF]

128. Tassos Markas
and John H. Reif, Multispectral Image Compression Algorithms, *Proceedings: IEEE Data Compression
Conference* *(DCC'93)*, Snowbird,
UT, IEEE Computer Society Press, James A. Storer, Martin Cohn (Eds.), pp.
391-400, March 1993. [PDF]

129. Peter H. Mills, Jan Prins, and John H.
Reif, Rate Control as a Language Construct for Parallel and Distributed
Programming, Proc. IEEE Workshop on Parallel and Distributed Real-Time Systems
(IPPS'93), pp. 164-170, 1993. [PostScript]
[PDF]

130. Richard Barakat and John H. Reif, Diffraction Realization of an
Optical Expander, (1993). [PDF]

131. Lars S. Nyland, Jan F. Prins, and John
H. Reif, A Data Parallel Implementation of the Adaptive Fast Multipole
Algorithm. *Dartmouth Institute for
Advanced Graduate Studies (DAGS '93),* Hanover, NH, June, 1993, pp. 111-123.
[PostScript]
[PDF]

132. Sefeng Chen and John H. Reif, Using
difficulty of prediction to decrease computation: fast sort, priority queue and
convex hull on entropy bounded inputs, *34th
Annual IEEE Conference on Foundations of Computer Science (FOCS '93)
Proceedings*, November 1993, Palo Alto, CA, pp. 104-112. [PDF]

133. Andrew Neff and John H. Reif, An *O*(*n^{*1+epsilon} log *b*) Algorithm for the Complex Roots
Problem. *35th Annual IEEE Conference on
Foundations of Computer Science (FOCS '94) Proceedings*, Santa Fe, NM,
November 1994. pp. 540-547. Improved Paper Published as An Efficient Algorithm
for the Complex Roots Problem, Journal of Complexity, 12(2) pp. 81-115, (June
1996). [PostScript]
[PDF]

134. Andrew Goldberg, Jan Prins,
Rickard Faith, Zhiyong Li, Peter H. Mills, Lars S.
Nyland, Daniel Palmer, John H. Reif, James Riely, and
Stephen Westfold, The Proteus System for the
Development of Parallel Applications. Prototyping and Software Development
(Malcolm C. Harrison, ed.), Chapter 6, pp. 151-190, Digital Book, 1996. [PostScript] [PDF]

135. Peter H. Mills, Lars S. Nyland, J.F. Prins,
and John H. Reif, Software Issues in High-Performance Computing and a Framework
for the Development of HPC Applications. In *Developing
a Computer Science Agenda for High Performance Computing* (U. Vishkin, ed.) pp. 110-117, ACM, 1994. [PostScript]
[PDF]

136. Andrew Goldberg, Peter H. Mills, Lars S. Nyland, Jan F. Prins, John H. Reif, and J. Riely,
Specification and Development of Parallel Algorithms with the Proteus System,
Specification of Parallel Algorithms, *DIMACS
Series in Discrete Mathematics and Theoretical Computer Science*, AMS Press,
Vol. 18, 1994, pp. 383-399. [PostScript]
[PDF]

137. Victor Y. Pan and John H. Reif, Generalized Compact Multi-grid, *Computers Math Applications, Volume *25,
Number 9, pp. 3-5, May 1993. [PDF]

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

139. Sefeng Chen and John H. Reif, Fast
Pattern Matching for Entropy Bounded Text. *Proceedings:
IEEE Data Compression Conference (DCC'95)* Snowbird, UT, IEEE Computer Society
Press, James A. Storer, Martin Cohn (Eds.), March 1995, pp. 282-301. [PDF]

140. John H. Reif, Efficient Parallel Solution of Sparse Eigenvalue
and Eigenvector Problems, *Proceedings of
the 36th Annual IEEE Symposium on Foundations of Computer Science (FOCS'95)*
Milwaukee, WI, October 23-25, 1995, pp. 123-132. Published as Efficient
Parallel Computation of the Characteristic Polynomial of a Sparse, Separable
Matrix, Algorithmica, 29: 487-510 (2001). [PDF]

141. Akitoshi Yoshida, Jannick P. Rolland and John H.
Reif, Design and Applications of a High Resolution Insert Head-Mounted Display.
*IEEE Virtual Reality Annual International
Symposium (VRAIS'95)*, Research Triangle Park, NC, March 11-15, 1995, pp.
84-93. [PostScript] [PDF] Also, Jannick P. Rolland
and Akitoshi Yoshida, and John H. Reif, Optical design and analysis of a
head-mounted display with a high-resolution insert, (Novel Optical Systems
Design and Optimization, Jose M. Sasian; Ed.,), Proc.
SPIE Vol. 2537, pp. 71-82, Aug. 1995. Published as Jannick P. Rolland, Akitoshi Yoshida, Larry D. Davis, and John H. Reif, High
resolution inset head-mounted display, Applied Optics: Optical Technology and
Biomedical Optics, 37(19), 4183-4193 (1998). [PDF]

142. Sandeep K. S. Gupta, Zhiyong Li, and
John H. Reif, Generating Efficient Programs for Two-Level Memories from
Tensor-Products. *Proceedings of the 7th
IASTED/ISMM International Conference on Parallel and Distributed Computing and
Systems* Washington DC, October 1995, pp. 510-513. [PostScript]
[PDF]

143. John H. Reif, Parallel Biomolecular Computation: Models and
Simulations. *Proceedings: 7th Annual ACM
Symposium on Parallel Algorithms and Architectures (SPAA'95)* Santa Barbara,
CA, July 1995, pp. 213-223. Published in Algorithmica,
special issue on Computational Biology, Vol. 25, No. 2, 142-176, 1999. [PDF] [PostScript] and [PostScriptFigures]

144. John H. Reif, Work Efficient Parallel Solution of Toeplitz
Systems and Polynomial GCD. *Proc. of the
27th ACM Symposium on Theory of Computing (STOC 95)*, Las Vegas, NV, May
29-June 1, 1995, pp. 751-761. Revised as Efficient Parallel Factorization and
Solution of Structured and Unstructured Linear Systems, *Journal of Computer and System Sciences*, *Vol. 71, Issue 1 (July 2005), pp. 86 - 143*. [PDF] [PDF]

145. Sandeep K. S. Gupta, Zhiyong Li, and
John H. Reif, Synthesizing Efficient Out-of-Core Programs for Block Recursive
Algorithms using Block-Cyclic Data Distributions. P*roceedings of the 1996 International Conference on Parallel Processing*,
Bloomingdale, IL, Vol. II, pp. 142-149, (August 1996). Published in *IEEE Transactions on Parallel and
Distributed Systems*, Vol. 10, No. 3, March 1999, pp. 297-315. [PDF]
or [PDF]

146. Lars S. Nyland, Jan Prins, Andrew
Goldberg, Peter H. Mills, John H. Reif, and Robert Wagner. A Refinement
Methodology for Developing Data-Parallel Applications, Second International
Euro-Par Conference (Euro-Par'96 Parallel Processing), Lyon, France, Springer
Lecture Notes in Computer Science, pp.145-150, 1996. [PDF]

147. Sefeng Chen and John H. Reif,
Compression of Trees and Digraphs, Abstract, *Proceedings: IEEE Data Compression Conference (DCC'96),* Snowbird,
UT, James A. Storer, Martin Cohn (Eds.), IEEE Computer Society Press, March
1996. [PDF]

148. John H. Reif and Hongyan Wang, Nonuniform Discretization for Kinodynamic
motion planning and its applications, *Workshop
on Foundations of Robotics,* Toulouse, France, July 1996, pp. 97-112.
Published in SIAM Journal of Computing (SICOMP), Volume 30, No. 1, pp. 161-190,
(2000). [PostScript]
[PDF]

149. Zhiyong Li, Peter H. Mills, and John H.
Reif, Models and Resource Metrics for Parallel and Distributed Computation, *Proc. 28th Annual Hawaii International
Conference on System Sciences* (HICSS-28 Parallel Algorithms Software
Technology Track), Wailea, Maui, Hawaii, pp. 133-143, January 3-6, 1995.
Published in *Parallel Algorithms and
Applications*, Vol. 8, pp. 35-59, 1996. [PostScript]
[PDF]

150. Erol Gelenbe, Nestor Schmajuk, John Staddon, and John H. Reif, Autonomous Search
and the Search for Robots and Mines: A Survey, Robotics and Autonomous Systems,
Vol. 22, pp. 23-33. (November 1997). [PostScript]
[PDF]

151. John H. Reif, Approximate Complex Polynomial Evaluation in Near
Constant Work Per Point. Proc. 29th ACM Symposium on Theory of Computing
(STOC97), El Paso, Texas, pp. 30-39 (May 4-6, 1997). Published in *SIAM Journal of Computing (SICOMP),* Vol. 28, Number 6, pp. 2059-2089, 1999. [PostScript] [PDF]

152. John H. Reif, Efficient Approximate Solution of Sparse Linear
Systems, Published in *Computers and
Mathematics with Applications*, Vol. 36, No. 9, Nov. 1998, pp. 37-58. [PostScript] [PDF]
(Also, see errata, Computers and Mathematics with Applications, Vol. 38, No. 9,
1999, pp. 141-141. [PDF])

153. John H. Reif and Steve R. Tate, Fast spatial decomposition and
closest pair computation for limited precision input, Journal of Algorithmica, Volume 28, Number 3, pp. 271-287 (2000). [PDF]
or [PostScript]
[PDF]

154. Sefeng Chen and John H. Reif, Fast and
Compact Fast and Compact Volume Rendering in the Compressed Transform, *Proceedings: IEEE Data Compression
Conference (DCC'97)* Snowbird, UT, James A. Storer, Martin Cohn (Eds.), IEEE
Computer Society Press, March 1997, pp. 271-280. [PDF]

155. John H. Reif and Doreen Yen, Derivation of Parallel Graph
Connectivity Algorithms via Stream Contraction, Duke University Technical
Report, 1989. [PDF]

156. John H. Reif, Local Parallel Biomolecular Computation, Proc.
DNA-Based Computers, III: University of Pennsylvania, June 23-26, 1997. DIMACS
Series in Discrete Mathematics and Theoretical Computer Science, H. Rubin and
D. H. Wood, editors. American Mathematical Society, Providence, RI, vol. 48,
1999, pp. 217-254. [PDF]
Revised as invited paper of special issue "Biomolecular Computing
- From Theory to Practical Applications"** **of** ***International Journal
of Unconventional Computing*, Vol.
8, pp. 459-507 (2014). [PDF]
or [PDF]

157. John H. Reif, On the Impossibility of Interaction-Free Quantum
Sensing for Small I/O Bandwidth, *Information
and Computation,* Jan 2000, pp. 1-20. [PDF]

158. John H. Reif, (Yin, Guo et al. 2004)s: Robust, Adaptive and
Dynamic Motion, 19th NSF Design and Manufacturing Grantees Conference,
Monterrey, Mexico, Jan 1998. [PostScript]
[PDF]

159. John H. Reif and Sandeep Sen, Parallel Computational Geometry: An
approach using randomization. Published as Chapter 8 in *Handbook of Computational Geometry,* Edited by Jorge Urrutia and Jörg-Rudiger Sack, Elsevier Science Publishing, Amsterdam,
the Netherlands, pp. 765-828. 1999. [PDF]
or [PDF]

160. John H. Reif, Paradigms for Biomolecular Computation, *First International Conference on Unconventional
Models of Computation*, Auckland, New Zealand, January 5-9, 1998. Published *in Unconventional Models of Computation*,
(edited by C.S. Calude, J. Casti,
and M.J. Dinneen), DMTCS Series, Springer-Verlag,
Singapore, January 1998, pp. 72-93. [PostScript] [PDF]

161. John H. Reif and James A. Storer, Optimal Lossless Compression of
a Class of Dynamic Sources, Data Compression Conference (DCC'98), Snowbird, UT,
James A. Storer, Martin Cohn (Eds.), IEEE Computer Society Press, pp. 501-510,
March, 1998. Published as Optimal Encoding of Non-stationary Sources, Special
Issue of Information Sciences, Volume 135, pp. 87-105 (2001). [PDF]

162. John H. Reif and Hongyan Wang, The
Complexity of the Two Dimensional Curvature-Constrained Shortest-Path Problem, *Third International Workshop on Algorithmic
Foundations of Robotics* *(WAFR98), *Pub.
by A. K. Peters Ltd, Houston, Texas, pp. 49-57, June, 1998. [PostScript]
[PDF]

163. John H. Reif and Zheng Sun, The Computational Power of Frictional
Mechanical Systems, *Third International
Workshop on Algorithmic Foundations of Robotics*, *(WAFR98),* Pub. by A. K. Peters Ltd, Houston, Texas, pp. 223-236,
Mar. 5-7 1998. Published as On Frictional Mechanical
Systems and Their Computational Power, SIAM Journal of Computing
(SICOMP), Vol. 32, No. 6, pp. 1449-1474, (2003). [PDF]
or [PDF].
Talk: [HTML]

164. A. Gehani and John H. Reif, Micro Flow
Bio-Molecular Computation, 4th DIMACS Workshop on DNA Based Computers,
University of Pennsylvania, June 15-19, 1998. *DNA Based Computers, IV, DIMACS Series in Discrete Mathematics and
Theoretical Computer Science,* (ed. H. Rubin), American Mathematical
Society, 1999. Also in a special issue of Biosystems, Journal of Biological and
Informational Processing Sciences, Vol. 52, Nos. 1-3, (Edited By L. Kari, H.
Rubin, and D. H. Wood), pp. 197-216, (October 1999). [PostScript]
[PDF]
or [PDF]
Talk: [PDF]

165. John H. Reif, Alternative Computational Models: A Comparison of
Biomolecular and Quantum Computation, Invited paper, 18th *International Conference on Foundations of Software Technology and Theoretical
Computer Science (FSTTCS1998),* Chennai, India (December, 17-19, 1998). [PDF]

166. John H. Reif and Zheng Sun, Nano-Robotics Motion Planning and Its
Applications in Nanotechnology and Biomolecular Computing, *NSF Design and Manufacturing Grantees Conference, *Jan 5-8, 1999. [HTML]

167. Thomas H. LaBean, Hao Yan, Jens Kopatsch, Furong Liu, Erik
Winfree, John H. Reif and Nadrian C. Seeman, The
construction, analysis, ligation and self-assembly of DNA triple crossover
complexes, *Journal of American Chemistry
Society(JACS)* 122, pp. 1848-1860 (2000). [PDF]

168. John H. Reif and Sukhendu Chakraborty,
Efficient and Exact Quantum Compression, Journal of Information and
Computation, Vol. 205, pp. 967-981 (2007). [PDF] [PDF]

169. John H. Reif, Quantum Computing. In book “Bio-inspired and Nanoscale
Integrated Computing”, Chapter 3, pp. 67-110 (edited by Mary Mehrnoosh Eshaghian-Wilner),
Publisher: Wiley, Hoboken, NJ, USA, (February 2009). [PDF]

170. John Fischer and John H. Reif, Nonparametric Multiscale
Multimodal Model for Detection/Recognition, Multi-Modality Image Fusion
Conference, Rochester, NY, Oct 6-7, 1999. [PDF]

171. A. Gehani, Thomas H. LaBean, and John H. Reif, DNA-based Cryptography, Proc. DNA
Based Computers V: Cambridge, MA, June 14-16, 1999. Published in DIMACS Series
in Discrete Mathematics and Theoretical Computer Science, Volume 54, edited by
Erik Winfree and D.K. Gifford, American Mathematical Society, Providence, RI,
pp. 233-249, (2000). [PDF]
Talk: [PDF]. Published
as an invited chapter in "Aspects of Molecular
Computing - Essays dedicated to Tom Head on the occasion of his 70th
Birthday", Springer Verlag series in Natural Computing (edited by N. Jonoska, G. Paun and G. Rozenberg) LNCS 2950 Festschrift, Springer, pp. 167-188,
(2004). [PDF]

172. Thomas H. LaBean, Erik Winfree, and
John H. Reif, Experimental Progress in Computation by Self-Assembly of DNA Tilings, Proceeding of DNA Based Computers V: Cambridge,
MA, June 14-16, 1999. Published in DIMACS Series in Discrete Mathematics and
Theoretical Computer Science, Volume 54, edited by Erik Winfree and D.K.
Gifford, American Mathematical Society, Providence, RI, pp. 123-140, (2000). [PostScript]
[PDF]
Talk: [HTML Lecture]

173. John H. Reif and Zheng Sun. An efficient approximation algorithm
for weighted region shortest path problem. In *Proceedings of the 4th
Workshop on Algorithmic Foundations of Robotics **(WAFR2000),* A. K. Peters Ltd Publishers, Hanover, New Hampshire,
pp. 191-203, Mar. 16-18 2000. [PDF] [PostScript].
Published as Zheng Sun and John H. Reif, On Finding Approximate Optimal Paths in Weighted Regions,
Journal of Algorithms, Volume 58, Number 1, pp. 1-32, January 2006. [PDF]

174. John H. Reif and Zheng Sun. Movement planning in the presence of
flows. In *Proceedings of the 7th International Workshop on Algorithms and
Data Structures* (WADS2001), volume 2125 of *Lecture Notes in Computer
Science*, pp. 450-461, Brown University, Providence, RI, August 8-10,
(2001). Published in Algorithmica, Volume 39, Number
2, pp. 127-153, February 2004. [PDF]
or [PDF].
Talk: [PDF]

175. John H. Reif and Thomas H. LaBean,
Computationally Inspired Biotechnologies: Improved DNA Synthesis and
Associative Search Using Error-Correcting Codes and Vector-Quantization, Sixth
International Meeting on DNA Based Computers (DNA6)*, Leiden, The Netherlands (June 2000). *DIMACS Series in Discrete
Mathematics and Theoretical Computer Science, Edited by A. Condon and G. Rozenberg. Lecture Notes in Computer Science,
Springer-Verlag, Berlin Heidelberg, vol. 2054,
pp. 145-172 (2001) [PostScript]
[PDF]
Talk: [PDF]

176. John H. Reif, Thomas H. LaBean, and Nadrian C. Seeman, Challenges and Applications for
Self-Assembled DNA Nanostructures, Proc. Sixth International Workshop on
DNA-Based Computers, Leiden, The Netherlands, June 13-17, 2000. Published in
DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Edited
by A. Condon and G. Rozenberg. Lecture Notes in
Computer Science, Springer-Verlag, Berlin Heidelberg, vol. 2054, 2001, pp. 173-198. [PostScript]
[PDF]
Talk: [PDF] [PPT]

177. Chengde Mao, Thomas H. LaBean, John H. Reif, Nadrian C.
Seeman, Logical Computation Using Algorithmic Self-Assembly of DNA
Triple-Crossover Molecules, Nature, vol. 407, pp. 493-495 (Sept. 28 2000); C.
Erratum: Nature 408, 750-750 (2000). [PDF]
or [PDF]

178. John H. Reif and Thomas H. LaBean, and Nadrian C. Seeman. Programmable Assembly at the Molecular
Scale: Self-Assembly of DNA Lattices, Invited paper, 2001 IEEE International
Conference on Robotics and Automation (ICRA2001)*,* Seoul, Korea, ed. Lee Beom, pp. 966-971
(May, 2001). [PDF]

179. Zheng Sun and John H. Reif. BUSHWHACK: An approximation algorithm
for minimal paths through pseudo-Euclidean spaces. In *Proceedings of the
12th Annual International Symposium on Algorithms and Computation*(ISAAC01), Christchurch, New Zealand, Dec 19-21,
2001, Volume 2223 of *Lecture Notes in Computer Science*, pp. 160-171,
Dec, 2001. Published in IEEE Transactions on Systems, Man, and Cybernetics
(SMC), Part B: Cybernetics, Vol. 37, No. 4, pp. 925-936 (2007). [PDF] [PDF]

180. John H. Reif, Thomas H. LaBean, M. Pirrung, V. Rana, B. Guo, K. Kingsford, and G. Wickham,
Experimental Construction of Very Large Scale DNA Databases with Associative
Search Capability, Seventh International Meeting on DNA Based Computers (DNA7)*, *Tampa, FL, June 11-13, 2001. Lecture Notes in Computer Science, Springer-Verlag, New
York, Volume 2340, pp. 231-247, (2002). [PostScript] [PDF] Talk: [PDF] [PPT]. Also published as John H. Reif, Michael Hauser,
Michael Pirrung, and Thomas LaBean,
Application of Biomolecular Computing to Medical
Science: A Biomedical Database System for Storage and Retrieval of Genetic
Information and Material, Chapter 3 of Complex Systems Science in
Biomedicine (Edited by Thomas S. Deisboeck and J. Yasha Kresh), International
Topics in Biomedical Engineering Series, Springer Publishers, New York, Chapter 3, pp. 701-735, (2005). ISBN: 0-387-30241-7. [PDF] or [PDF]. Talk: [PDF][PPT]

181. John H.
Reif, DNA Lattices: A Method for Molecular Scale
Patterning and Computation, special issue on Bio-Computation, Computer and
Scientific Engineering Magazine, IEEE Computer Society, Vol. 4, No. 1, February
2002, pp. 32-41. [PostScript][PDF]

182. John H.
Reif, The Emerging Discipline of Biomolecular Computation in the US, invited paper to the special issue on Biomolecular
Computing, New Generation Computing, edited by Masami Hagiya, Masayuki Yamamura, and Tom Head, Vol. 20, No. 3,
pp. 217-236, (2002). [PostScript][PDF]
or [PDF]

183. John H.
Reif, Molecular Assembly and Computation: From Theory to Experimental
Demonstrations, plenary paper, Twenty Ninth International Colloquium on
Automata, Languages, and Programming(ICALP), Málaga, Spain (July 8, 2002).
Lecture Notes in Computer Science, New York, Volume 2380, pp. 1-21, (2002). [PostScript][PDF]
Talk: [PDF] [PPT]

184. John H. Reif, The Design of Autonomous DNA
Nanomechanical Devices: Walking and Rolling DNA. DNA Based Computers (DNA8),
Sapporo, Japan, June 10-13, 2002, (Edited by Masami Hagiya
and Azuma Ohuchi), Lecture Notes in Computer Science, No. 2568,
Springer-Verlag, New York, (2003), pp. 22-37. Published in Natural Computing,
DNA8 special issue, Vol. 2, p 439-461, (2003). [PDF] or [PostScript][PDF] Talk: [__PDF__]

185. Dage Liu, John H.
Reif, Thomas H. LaBean, DNA Nanotubes, Construction
and Characterization of Filaments Composed of TX-tile Lattice. DNA Based
Computers (DN**A**8), Sapporo, Japan,
June 10-13, 2002, (Edited by Masami Hagiya and Azuma
Ohuchi), Lecture Notes in Computer Science, No. 2568, Springer-Verlag, New
York, (2003), pp. 10-21. Published as DNA nanotubes self-assembled from
triple-crossover tiles as templates for conductive nanowires, Proceedings of the National Academy of Science(PNAS),
Vol. 101, No. 3, pp. 717-722, (January 20, 2004). PubMed PMID: 14709674. [PDF]

186. John H. Reif, DNA Computation - Perspectives:
Successes and Challenges, Science, 296: 478-479, April 19, 2002. PubMed PMID: 11964464. [PostScript][PDF]

187. Zheng Sun and John H. Reif, On Finding
Energy-minimizing Paths on Terrains for a Mobile Robot, 2003 IEEE International
Conference on Robotics and Automation(ICRA2003), Taipei, Taiwan, pp. 3782-3788, May 12-17, 2003. Published in IEEE Transaction on Robotics, Volume: 21, Issue: 1,
February 2005, pp. 102-114. [PDF]

188. D. Hsu, T. Jiang, John H. Reif, and Zheng Sun, The
Bridge Test for Sampling Narrow Passages with Probabilistic Roadmap Planners,
2003 IEEE International Conference on Robotics and Automation(ICRA2003),
Taipei, Taiwan, Vol.3, pp. 4420 – 4426, Sept. 14-19, 2003. Published as Zheng Sun, D. Hsu, T. Jiang, H. Kurniawati, and J.H.Reif, Narrow
Passage Sampling for Probabilistic Roadmap Planning, IEEE Transactions on
Robotics, Volume 21, No. 6, Dec. 2005. pp. 1105–1115. [PDF]

189. John H. Reif and Zheng Sun, On
Boundaries of Highly Visible Spaces and Applications, 14th Symposium on
Fundamentals of Computation Theory, Malmö Högskola,
Sweden, August 12-15, 2003, Springer-Verlag Lecture Notes in Computer Science,
2003. Invited paper published in Theoretical Computer Science, Volume 354,
Issue 3, (4 April 2006), pp. 379-390. [PDF] [PDF]

190. Hao Yan,
Thomas H. LaBean, Liping
Feng, and John H. Reif, Directed Nucleation Assembly of Barcode Patterned DNA
Lattices, Proceedings of the National Academy of
Science(PNAS), Volume 100, No. 14, pp. 8103-8108, July 8, (2003). PubMed PMID: 12821776. [PostScript] [PDF]

191. Hao Yan, Liping Feng, Thomas H. LaBean,
and John H. Reif, DNA Nanotubes, *Parallel Molecular Computation of Pair-Wise XOR Using DNA
String Tile,* Ninth International Meeting
on DNA Based Computers (DNA9), Madison, Wisconsin, June 2-4, 2003,
(Edited by Junghuei Chen and John H. Reif), Abstract in Lecture Notes
in Computer Science, Springer-Verlag, New York, (2003). Published as Parallel Molecular Computations of Pairwise Exclusive-Or
(XOR) Using DNA "String Tile" Self-Assembly in Journal of
American Chemistry Society (JACS), Vol. 125, No. 47,
pp. 14246-14247, 2003. PubMed PMID: 14624551.
[PDF] or [PDF]; Supporting Information: [PDF]

192. Hao Yan,
Sung Ha Park, Liping Feng, John H. Reif, and Thomas
H. LaBean, *4x4 DNA Tile and Lattices: Characterization, Self-Assembly
and Metallization of a Novel DNA Nanostructure Motif*, Ninth International Meeting on DNA Based Computers
(DNA9), Madison, Wisconsin, June 2-4, 2003, (Edited by Junghuei Chen and John
H. Reif), Lecture Notes in Computer Science, Springer-Verlag, New York, (2003).
Published as Hao Yan, Sung Ha Park, Gleb Finkelstein,
John H. Reif, and Thomas H. LaBean, DNA-Templated
Self-Assembly of Protein Arrays and Highly Conductive Nanowires, Science, Vol.
301, pp. 1882-1884, Sep 26 2003. PubMed PMID: 14512621.
[PDF] Supporting Materials: [PDF] Supplemental Information: [PDF]

193. Liping Feng, Sung Ha
Park, John H. Reif, and Hao Yan, A Two-State DNA Lattice Switched by DNA
Nanoactuator, Angewandte Chemie [International Edition], Vol. 42, pp. 4342-4346,
Sept. 2003. PubMed PMID: 14502706. [PDF] Supplemental Information: [PDF]

194. Zheng Sun and John H. Reif, Adaptive and Compact Discretization
for Weighted Region Optimal Path Finding. 14th Symposium on Fundamentals of
Computation Theory, Malmö Högskola, Sweden, August
12-15, 2003, Springer-Verlag Lecture Notes in Computer Science, Vol. 2751, pp.
258-270, 2003. [PostScript] [*PDF*].

195. Tinging Jiang and John H. Reif, Efficient Methods for Stochastic Simulations of
Biomolecular Motions, submitted for publication, July, 2003. [PDF]

196. H. Li, S.H. Park, John H. Reif, Thomas H. LaBean,
Hao Yan, DNA-Templated Self-Assembly of Protein and Nanoparticle Linear Arrays,
Journal of American Chemistry Society (JACS), Vol.
126, No. 2, pp. 418-419, 2004. PubMed PMID: 14719910. [PDF]. Supporting Information: [PDF]

197. Hao Yan,
Peng Yin, Sung Ha Park, Hanying Li, Liping Feng, Xiaoju Guan, Dage Liu, John H. Reif, & Thomas H. LaBean
(2004) Self-Assembled DNA Structures for Nanoconstruction.
International Symposium on DNA-Based Molecular Electronics, Jena, Germany, May,
2004. Fritzsche, W. eds. AIP Conference Proceedings,
725, American Institute of Physics. pp. 43-52. [PDF]

198. John H.
Reif, Sudheer Sahu, Peng Yin, Compact Error-Resilient
Computational DNA Tiling Assemblies, Tenth
International Meeting on DNA Based Computers (DNA10), Milano, Italy,
June 7-10, 2004. Lecture Notes in Computer Science (Edited by C Ferretti, G.
Mauri and C. Zandron), Vol.
3384, Springer-Verlag, New York, (2005), pp. 293-307. Published as an invited chapter in text "Nanotechnology: Science and Computation”, Springer
Verlag series in Natural Computing (edited by J. Chen; N. Jonoska and
G. Rozenberg),
Springer-Verlag Berlin, Germany, pp. 79-104, 2006. [PDF] Talk: [PDF] [PPT]

199. Peng Yin,
Andrew J. Turberfield, Sudheer Sahu,
John H. Reif, Designs for Autonomous Unidirectional Walking DNA Devices, Tenth International Meeting on DNA Based Computers
(DNA10), Milano, Italy, June 7-10, 2004. Lecture Notes in Computer Science
(Edited by C Ferretti, G. Mauri and C. Zandron), Vol. 3384, Springer-Verlag, New York, (2005), pp.
410-425. [PDF] Talk: [PDF] [PPT]

200. Peng Yin, Hao Yan, Xiaoju
G. Daniel, Andrew J. Turberfield, John H. Reif, A
Unidirectional DNA Walker Moving Autonomously Along a Linear Track, Angewandte Chemie [International
Edition], Volume 43, Number 37, Sept. 20, 2004, pp. 4906-4911. PubMed PMID: 15372637. [PDF] or [PDF] Supplemental Information: [PDF] Abstract: [PDF] Talk: [PDF] [PPT]

201. Peng Yin, Andrew J. Turberfield, John
H. Reif, Design of an Autonomous DNA Nanomechanical Device Capable of Universal
Computation and Universal Translational Motion, Tenth
International Meeting on DNA Based Computers (DNA10), Milano, Italy,
June 7-10, 2004. Lecture Notes in Computer Science (Edited by C Ferretti, G.
Mauri and C. Zandron), Vol.
3384, Springer-Verlag, New York, (2005), pp. 426-444. [PDF] Talk: [PDF] [PPT]

202. Peng Yin, Bo
Guo, Christina Belmore, Will Palmeri, Erik Winfree,
Thomas H. LaBean, John H. Reif, TileSoft:
Sequence Optimization Software For Designing DNA Secondary Structures, Duke
University Computer Science Department Technical Report TR-CS-2004-09. [PDF] Talk: [PDF] [PPT]

203. John H.
Reif, DNA-Based Nano-Engineering: DNA and its Enzymes as the Engines of
Creation at the Molecular Scale, Invited Talk, Abstract, Preliminary
Proceedings, Tenth International Meeting on DNA Based Computers (DNA10),
Milano, Italy, (June 7-10, 2004). Abstract: [PDF] Talk: [PDF] [PPT]

204. John H. Reif, Thomas LaBean, Sudheer Sahu, Hao Yan, Peng Yin, Design, Simulation, and
Experimental Demonstration of Self-Assembled DNA Nanostructures and DNA Motors,
Unconventional Programming Paradigms: International Workshop UPP 2004, Le Mont
Saint Michel, France, September 15-17, 2004. Published by Springer-Verlag
Berlin Heidelberg, edited by Jean-Pierre Banâtre,
Pascal Fradet, Jean-Louis Giavitto,
Olivier Michel, Lecture Notes for Computer Science (LNCS) 3566, pp. 173-187,
(2005). [PDF] Talk: [PDF] [PPT]

205. Sung Ha Park, Hao Yan, John H. Reif,
Thomas H LaBean, and Gleb
Finkelstein, Electronic nanostructures templated on self-assembled DNA
scaffolds, Nanotechnology 15 pp. S525–S527 (2004). [PDF]

206. Sung Ha Park, Peng Yin, Yan Liu, John
H. Reif, Thomas LaBean, and Hao Yan, Programmable DNA
Self-assemblies for Nanoscale Organization of Ligands and Proteins, *Nano Letters *(Communication), Volume *5*, Number 4, pp. 729-733, (2005). PubMed
PMID: 15826117. [PDF]; Supplemental Information: [PDF]

207. Sung Ha Park, Robert Barish,
Hanying Li, John H. Reif, Gleb
Finkelstein, Hao Yan and Thomas LaBean, Three-Helix
Bundle DNA Tiles Self-Assemble into 2D Lattice or 1D Templates for Silver
Nanowires, Nano Letters (Communication), Volume 5, Number 4, pp. 693-696
(2005). PubMed PMID: 15826110. [PDF] Supplemental Information: [*PDF*]

208. Sung Ha Park, Constantin Pistol, Sang Jung Ahn,
John H. Reif, Alvin R. Lebeck, Chris Dwyer, and
Thomas H. LaBean, Finite-Size,
Fully Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures, Angewandte Chemie
[International Edition], Volume 45, Issue 5, pp. 735-739, January 23, 2006.
DOI: 10.1002/anie.200503797. [PDF]

209. John H. Reif, Sudheer Sahu, and Peng Yin,
Complexity of Graph Self-Assembly in Accretive Systems and Self-Destructible
Systems, Eleventh International Meeting on DNA
Based Computers (DNA11), London, Ontario, Canada (June, 2005). Springer-Verlag
Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Alessandra Carbone and Niles Pierce), Vol. 3892,
Springer-Verlag, New York, (2006), pp. 257-274 [PDF]. Talk: [PPT]. Published in
Theoretical Computer Science, Volume 412, pp 1592-1605, (2011). DOI
information: 10.1016/j.tcs.2010.10.034 [PDF].

210. Peng Yin, Andrew J. Turberfield, John
H. Reif, Design of Autonomous DNA Cellular Automata, Eleventh
International Meeting on DNA Based Computers (DNA11), London, Ontario,
Canada (June, 2005). Springer-Verlag Lecture Notes for Computer Science (LNCS),
NYC, NY, (edited by Alessandra Carbone and Niles
Pierce), Vol. 3892, Springer-Verlag, New York,
(2006), pp. 399-416 [PDF].

211. Sudheer Sahu, Peng Yin and
John H. Reif, A Self-Assembly Model of
Time-Dependent Glue Strength, Eleventh International
Meeting on DNA Based Computers (DNA11), London, Ontario, Canada (June,
2005). Springer-Verlag Lecture Notes for Computer Science (LNCS), NYC, NY,
(edited by Alessandra Carbone and Niles Pierce), Vol.
3892, Springer-Verlag, New York, pp.
290-304 (2006). Invited Chapter in "Algorithmic
Bioprocesses" (edited by A.Condon, D.Harel, J.N.Kok, A.Salomaa, and E.Winfree), Published by Springer-Verlag, ISBN:
978-3-540-88868-0, pp. 185-204 (2009). [PDF] [PDF] Talk: [PPT]

212. Peng Yin,
Sudheer Sahu, Rizal Hariadi,
Harry M. T. Choi, Sung Ha Park, Bethany Walters, Thomas H. LaBean,
John H. Reif, On Constructing Tile-less DNA Ribbons and Tubes, Abstract,
Preliminary Proceedings, 12th International Meeting on DNA Computing (DNA12),
Seoul, Korea (June 5-9, 2006). [PDF] Published as: Peng
Yin, Rizal F. Hariadi, Sudheer Sahu,
Harry M.T.Choi, Sung Ha Park, Thomas H. LaBean, John H. Reif, Programming DNA Tube Circumferences,
Science, Vol. 321. no. 5890, pp. 824–826 (August 8, 2008). DOI:
10.1126/science.1157312. [PDF] Supplemental Information: [PDF]

213. Sudheer Sahu and John H. Reif, Capabilities and Limits of Compact
Error Resilience Methods for Algorithmic Self-Assembly in Two and Three
Dimensions, 12th International Meeting on DNA Computing (DNA 12), Seoul, Korea,
June 5-9, 2006. Published in DNA Computing: DNA12, Springer-Verlag Lecture
Notes for Computer Science (LNCS), Volume 4287 (edited by Chengde Mao and
Takashi Yokomori), Springer, Berlin Heidelberg, pp.
223-238 (2006). DNA12 Version: [PDF]. Talk: [PPT]. Published
in Algorithmica, Volume 56, Issue 4, pp. 480-504,
Springer New York (April 2010), Full Paper: [PDF] [PDF].

214. Sudheer Sahu, Bei Wang, Peng Yin, John H. Reif, A Framework for Modeling DNA based Molecular Systems,
12th International Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9,
2006. Published in DNA Computing: DNA12, Springer-Verlag Lecture Notes for
Computer Science (LNCS), Volume 4287 (edited by Chengde
Mao and Takashi Yokomori), Springer, Berlin Heidelberg, pp. 250-265 (2006). DNA12
Version: [PDF]. Published as Sudheer
Sahu, Bei Wang, John H. Reif, A Framework for
Modeling DNA based Molecular Systems. Computational and Theoretical
Nanoscience, Volume 5, Number 11, pp. 2124-2134(11) (November 2008). Full Paper: [PDF] Presentation: [PPT]

215. Urmi Urmi
Majumder, Sudheer Sahu, Thomas LaBean,
and John H. Reif, Design and Simulation of self-repairing DNA Lattices, 12th
International Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006,
DNA Computing: DNA12, Springer-Verlag Lecture Notes for Computer Science
(LNCS), Volume 4287 (edited by Chengde Mao and
Takashi Yokomori), Springer, Berlin Heidelberg, pp. 195–214, (2006). DNA12
Version: [PDF] Poster: [PDF]. Revised paper: Urmi
Majumder, Sudheer Sahu, Thomas LaBean,
and John H. Reif, Toward Compact Inherently Self-Repairing DNA Lattices Using
Reversibility, submitted for journal publication (2014). [PDF]

216. John H. Reif and Sam Slee,
Asymptotically Optimal Kinodynamic Motion Planning
for Self-Reconfigurable Robots, Seventh International Workshop on the
Algorithmic Foundations of Robotics (WAFR2006), NYC, New York, July 16-18,
2006. Published in Algorithmic Foundation of Robotics VII, Springer Tracts in
Advanced Robotics (Edited by S. Akella, N.M. Amato,
W.H. Huang, B. Mishra), Volume 47, Springer-Verlag Berlin, pp. 457–472, (Aug
2008). [PDF] Published as Asymptotically
Optimal Kinodynamic Motion Planning for a Class of
Lattice-Style Modular Self-Reconﬁgurable Robots, International Journal of
Computational Geometry & Applications (IJCGA), Vol. 21, No. 2, pp. 131-155 (2011). DOI: 10.1142/S0218195911003585 [PDF]

217. Thomas H. LaBean, Kurt V. Gothelf, and John H. Reif, Self-assembling
DNA Nanostructures for Patterned Molecular Assembly, invited chapter 5 in
Nanobiotechnology II: More Concepts and Applications, (edited by Chad A. Mirkin and Christof M. Niemeyer), John Wiley & Sons
Publishers, pp. 79-97, (2007). [PDF] DOI: 10.1002/9783527610389.ch5

218. John H. Reif
and Thomas H. LaBean, Autonomous Programmable Biomolecular
Devices Using Self-Assembled DNA Nanostructures, invited paper, Fourteenth Workshop on Logic, Language, Information and
Computation (WoLLIC'2007), Rio de Janeiro, Brazil, July 2-5, 2007, Springer-Verlag
Lecture Notes for Computer Science (LNCS), Volume 4576 - 0297, pp. 297-306. Published in
Communications of the ACM (CACM), Special Section entitled “New
Computing Paradigms (edited by Toshinori Munakata), Volume 50, Issue 9,
pp. 46-53 (Sept 2007). Short version [PDF] Extended version [PDF] Talk: [PPT] [PDF]

219. Urmi Majumder and John H. Reif, A
Framework for Designing Novel Magnetic Tiles Capable of Complex
Self-Assemblies, Conference on Unconventional Computation, Vienna, Austria, Aug
25-26, 2008, Unconventional Computing, Lecture Notes in Computer Science number
105633, Springer, Berlin Heidelberg. Conference Version: [PDF]. Revised paper submitted for journal publication as Barcoded Magnetic Tiles for Complex Programmable Assemblies (2012). Full Paper: [PDF]

220. John H. Reif and Thomas H. LaBean, DNA
Nanotechnology and its Biological Applications. In book “Bio-inspired and
Nanoscale Integrated Computing”, Chapter 13, pp. 349-375 (edited by Mary Mehrnoosh Eshaghian-Wilner),
Publisher: Wiley, Hoboken, NJ, USA, (February 2009). [PDF]

221. Ashish Gehani and John H. Reif,
Parameterizing Super-resolution Forensic Analysis of Video, 3rd IFIP
International Conference on Digital Forensics, Orlando, FL, Jan 28-31, 2007.
Published as Super-Resolution Video Analysis for Forensic Investigations,
Advances in Digital Forensics, Chapter 20, Volume 32007, pp. 228-229. [PDF]

222. John H. Reif and Sam Slee, Optimal Kinodynamic Motion Planning for Self-Reconﬁgurable Robots
Between Arbitrary 2D Conﬁgurations, Robotics: Science and Systems Conference,
Georgia Institute of Technology, Atlanta, GA, June 27-30, 2007. [PDF]

223. John H. Reif and Sudheer Sahu, Autonomous Programmable DNA Nanorobotic Devices Using
DNAzymes, 13th International Meeting on DNA
Computing (DNA 13), Memphis, Tennessee, June
4-8, 2007. In DNA Computing: DNA13 (edited by Max
Garzon and Hao Yan), Springer-Verlag Lecture Notes for Computer Science
(LNCS), Springer, Berlin Heidelberg, Volume 4848, pp.
66-78 (2008). DNA13 Version: [PDF] Talk: [PDF]. Published in Special Journal Issue on Self-Assembly, Theoretical
Computer Science (TCS), Vol 410, Issue 15, pp. 1428-1439 (April 2009). Full Paper: [PDF] [PDF].

224. Urmi
Majumder, Thomas H LaBean, and John H. Reif,
Activatable Tiles for Compact Error-Resilient Directional Assembly. 13th
International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8,
2007. Conference Version: Activatable Tiles: Compact, Robust Programmable
Assembly and Other Applications, in DNA Computing: DNA13 (edited by Max Garzon
and Hao Yan), Springer-Verlag Lecture Notes for Computer Science (LNCS),
Springer, Berlin Heidelberg, Volume 4848, pp. 15-25, (2008). [PDF] Talk: [PPT]. Published as: Urmi Majumder, Sudhanshu Garg, Thomas H LaBean,
and John H. Reif, Activatable
Tiles for Compact Robust Programmable Molecular Assembly and Other Applications,
Natural Computing, Volume 15, Issue
4, pp 611–634 (December 2016). DOI 10.1007/s11047-015-9532-3 [PDF] [PDF]

225. Urmi Majumder, John H. Reif, and
Sudheer Sahu, Stochastic Analysis of Reversible
Self-Assembly. Journal of Computational and Theoretical Nanoscience, Volume 5,
Number 7, pp. 1289-1305, July 2008. Full Paper: [PDF] [PDF].

226. John
H. Reif, Mechanical Computation: it’s Computational Complexity and
Technologies, invited chapter, Encyclopedia of Complexity and System Science
(edited by Robert A. Meyers), in section:
Unconventional Computing (section editor: Andrew Adamatzky),
Springer-Verlag,
New York (2009), pp. 1821-1836, ISBN: 978-0-387-75888-6. DOI: 10.1007/978-0-387-30440-3_325. [HTML] [PDF] [PDF]. A
revised version also appears as Mechanical Computing: The Computational Complexity of
Physical Devices, invited chapter, Encyclopedia of Complexity and System Science
(edited by Andrew Spencer), Springer-Verlag, Heidelberg, Germany. Springer-Verlag, Heidelberg, Germany. Published online (2013)
and in print in pp. 5466-5482 (2014). [HTML] [PDF] [PDF] [PDF] A further
revised version also appears as Mechanical Computing: The
Computational Complexity of Physical Devices, invited chapter, pp. 1-21, Encyclopedia of
Complexity and System Science (edited by R.A.),
Springer-Verlag, Heidelberg, Germany. Springer-Verlag, Heidelberg, Germany.
Published online (April 2017). [PDF] [PDF] DOI: 10.1007/978-3-642-27737-5_325-4.

227. John H. Reif and Urmi Majumder,
Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular
Computation, Fourteenth International Meeting on DNA
Based Computers (DNA14), Prague, Czech Republic
(June, 2008). Lecture Notes for Computer Science (LNCS), NYC, NY, (edited by Ashish Goel and Friedrich C. Simmel), Springer-Verlag,
New York, (2009). Conference Version: [PDF] Talk: [PDF] [PPT]. Invited Paper,
Special issue in Natural Computing, Vol. 9, Number 1, pp. 183-206, (March
2010). Springer Netherlands, ISSN: 1567-7818 (Online), DOI:
10.1007/s11047-009-9148-6. Full Paper: [PDF] [PDF]

228. Sudheer Sahu, Thomas H. LaBean and John H. Reif, A DNA Nanotransport
Device Powered by Polymerase ϕ29,
Nano Letters, 2008, 8 (11), pp 3870–3878, (October, 2008) DOI:
10.1021/nl802294d. [PDF] [PDF] supplementary material: [PDF]

229. Thomas H. LaBean,
Geetha Shetty, Peng Yin, Erik A. Schultes, Harish
Chandran, John H. Reif, A Dendritic Nanostructure for
DNA Detection, abstract, Proceedings of the Sixth Conference on
Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO09),
Snowbird, Utah, Sciencetechnica, pp. 82-83 (April
2009). [PDF] Thomas H. LaBean, Geetha
Shetty, Hao Yan, Erik A. Schultes, Harish Chandran, John H.
Reif, Target DNA Detection by Strand Displacement and Deoxyribozymogen
Amplification, abstract, Proceedings of the Sixth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices (FNANO09),
Snowbird, Utah, Sciencetechnica, pp. 60-61 (April
2009). [PDF] Bishop Morgan A.,
Clare D. Thiem, Thomas E. Renz, Erik A. Schultes, Harish Chandran, John H Reif, Structural
Optimization of Dendritic DNA Self-Assembly, abstract, Proceedings of the Sixth
Conference on Foundations of Nanoscience: Self-Assembled Architectures and
Devices (FNANO09), Snowbird, Utah, Sciencetechnica,
pp. 147-148 (April 2009). [PDF] *Final Publication:*
Harish Chandran, Abhijit Rangnekar, Geetha Shetty,
Erik A Schultes, John H Reif, Thomas H LaBean, An Autonomously Self‐Assembling Dendritic DNA
Nanostructure for Target DNA Detection, Biotechnology Journal, Wiley-VCH Verlag, Vol. 8, Number 2, pp. 221-227, (Feb, 2013). PMID: 22965937.
DOI: 10.1002/biot.201100499. [PDF] (also published online Oct, 2012)

230. Nikhil Gopalkrishnan, Harish
Chandran and John Reif, 2D and 3D DNA Lattices Via Staggered Assembly of the
Double-Decker Tile, abstract, Digital
Proceedings of the Ninth Conference on Foundations of Nanoscience:
Self-Assembled Architectures and Devices (FNANO12), Snowbird, Utah, pp. 108
(April 2012)

231. Harish Chandran, Nikhil Gopalkrishnan, and John Reif, The Tile Complexity of Linear
Assemblies, 36th International Colloquium on Automata, Languages and
Programming (ICALP 2009), July 5 - 12, 2009, Rhodes, Greece, Proceedings Part I
(edited by Susanne Albers, Alberto Marchetti-Spaccamela,
Yossi Matias, Sotiris Nikoletseas, and Wolfgang
Thomas), Lecture Notes in Computer Science, Springer-Verlag, Berlin, pp.
235-253 (2009). Published in SIAM Journal of Computation (SICOMP), Society for
Industrial Mathematics, Vol. 41, No, 4, pp. 1051-1073, (2012). [PDF]
[PDF]
Talk: [PPT]
[PDF]

232. John H. Reif and Thomas H. LaBean, Engineering Natural Computation by
Autonomous DNA-Based Biomolecular Devices, Invited
Chapter, Handbook of Natural Computing, Chapter 39, Volume III, edited by Grzegor Rozenberg, Thomas Bäck, Joost Kok, Springer-Verlag,
Heidelberg, Germany, pp.1314-1354 (July, 2012),
3540929096 978-3-540-9-2909-3. [PDF] [PDF]

233. John H. Reif and Urmi Majumder, Design
of a Biomolecular Device that Executes Process Algebra, Fifteenth International Meeting on DNA Computing and Molecular
Programming (DNA15), Fayetteville, Arkansas
(June 8-11, 2009). Lecture Notes for Computer Science (LNCS), Vol 5877, NYC,
NY, (edited by Russell Deaton and Jin-Woo
Kim), Springer-Verlag, New York, pp 107-105, (2010)
[PDF] [PDF]. Published in
Natural Computing, Vol 10, No. 1. pp 447-466 (2011). Talk:
[PDF] [PPT] [Keynote].

234. John Reif, Harish Chandran, Nikhil Gopalkrishnan,
and Thomas LaBean, Self-assembled DNA Nanostructures
and DNA Devices. Invited Chapter 14, Nanofabrication Handbook (Edited by
Stefano Cabrini and Satoshi Kawata),
pages 299-328, CRC Press, Taylor and Francis Group, New York, NY,
ISBN13:9781420090529, ISBN10: 1420090526 (2012). [PDF] [PDF]

235. Harish Chandrann, Nikhil Gopalkrishnan and John Reif, Tile Complexity of Approximate Squares and Lower
Bounds for Arbitrary Shapes, Algorithmica, Volume 66, Issue
1 (2013), Page 1-17 (2013)
(also published online Feb 22, 2012). ISSN
0178-4617, DOI 10.1007/s00453-012-9620-z. [PDF] [PDF]

236. Nikhil Gopalkrishnan, Harish Chandran
and John Reif, High-Fidelity DNA Hybridization using
Programmable Molecular DNA Devices,** International Conference on DNA Computing and Molecular Programming**,
(DNA16), Hong Kong University of Science and Technology. Hong Kong, China, **June 14-17th, 2010**. Lecture Notes
for Computer Science (LNCS), Vol. 6516, NYC, NY, (edited by Yasubumi
Sakakibara and Mi Yongli), Springer-Verlag, LNCS
6518, New York, (Feb 2011), pp 59-70. ISBN: 978-3-642-18304-1 [PDF] [PDF] Talk: [PDF] [PPT]

237. Sam Slee and Sam
Slee and John H. Reif, Robomotion:
Scalable, Physically Stable Locomotion for Self-Reconfigurable Robots, Workshop
on the Algorithmic Foundations of Robotics (WAFR 2010), Singapore, Springer
(Dec. 13-15 2010). [PDF]

238. Urmi Majumder, Abhijit Rangnekar, Kurt V. Gothelf, John H Reif and Thomas H LaBean, Design and Construction of Double-Decker Tile as a
Route to Three-Dimensional Periodic Assembly of DNA, Journal American Chemical
Society (JACS), Vol. 133, no. 11, pp. 3843—3845 (Feb. 2011) [PDF] Supplementary Info: [PDF]

239. Harish
Chandran, Nikhil Gopalkrishnan, and John Reif, DNA NanoRobotics, Chapter, Nanorobotics: Current Approaches and
Techniques, (edited by Constantinos Mavroidis and Antoine Ferreira), Springer-Verlag, New York,
NY, pp. 355-382 (Jan. 31, 2013). ISBN 13**:** 9781461421184, ISBN 10**:** 1461421187
[PDF] [PDF]

240. John H. Reif, Perspectives:
Biochemistry: Scaling Up DNA Computation,
Science, Vol. 332, pp. 1156-1157 (June 3, 2011). DOI:
10.1126/science.1208068 [PDF]

241 Harish Chandran,
Nikhil Gopalkrishnan, Andrew Philips and John Reif,
Localized Hybridization Circuits, International Conference on DNA Computing and
Molecular Programming, (DNA17), California Institute of Technology, Pasadena,
California, Sept 19-23, 2011, pp. 64-83. Lecture Notes for Computer Science
(LNCS), NYC, NY, (edited by Luca Cardelli and William
Shih), Springer-Verlag, LNCS, Berlin, Heidelberg,
(2011). ISBN:
978-3-642-23637-2 [PDF] Revised as
Neil Dalchau, Harish Chandran, Nikhil Gopalkrishnan, Andrew Philips and John Reif, Probabilistic Analysis of
Localized DNA Hybridization Circuits, ACS Synthetic Biology, Vol. *4*, Issue 8, pp 898–913, (July, 2015). DOI:10.1021/acssynbio.5b00044 [PDF] [PDF] Supporting
Info: [PDF]

242. Harish Chandran, Nikhil Gopalkrishnan, Sudhanshu Garg, and John Reif, Biomolecular
Computing Systems - From Logic Systems to Smart Sensors and Actuators, Invited
Chapter 11, Molecular and Biomolecular Information Processing (Editor: Evgeny Katz),
Published by Wiley-VCH, Verlag GmbH & Comp. KGaA, Weinheim, Germany,
pp. 199-224, July 2012. ISBN 978-3-527-33228-1 Online ISBN: 9783527645480 DOI: 10.1002/9783527645480 [PDF]
[PDF]

243. Harish Chandran, Nikhil Gopalkrishnan,
Bernard Yurke,
John Reif, Meta-DNA: Synthetic Biology via DNA Nanostructures and
Hybridization Reactions, Journal
of the Royal Society Interface, (published
online Jan., 2012), pp. 1742-5662 doi: 10.1098/rsif.2011.0819 [PDF]
[PDF] [Supplement]. An expanded version appears as Meta-DNA: A DNA-Based Approach to Synthetic
Biology, Chapter 7 in Book: A Systems Theoretic Approach to Systems and Synthetic Biology II:
Analysis and Design of Cellular Systems, edited by* *Vishwesh V. Kulkarni, Guy-Bart
Stan, and Karthik
Raman*,*
published by Springer, New York (2014). ISBN:
978-94-017-9046-8 (Print) 978-94-017-9047-5 (Online) DOI 10.1007/978-94-017-9047-5 [PDF] [PDF] Talk: [PDF] [PPT]

244. Harish Chandran,
Sudhanshu Garg, Nikhil Gopalkrishnan and John H Reif,
Activatable Tiles: Demonstration of Linear and Directed Self Assembly,
abstract, Digital Proceedings of the Ninth Conference on Foundations of
Nanoscience: Self-Assembled Architectures and Devices (FNANO12), Snowbird,
Utah, pp. 109 (April 2012). Also, Sudhanshu Garg, Harish Chandran, Nikhil Gopalkrishnan, and John Reif, One-Time, Directed and
Catalytic Activation of 1-D DNA Tiles, Poster Abstract DNA19, Tempe, AZ, Sept,
22-27, 2013. Journal publication: Sudhanshu Garg, Harish Chandran, Nikhil Gopalkrishnan, Thomas H. LaBean,
and John Reif, Directed Enzymatic Activation of 1-D DNA Tiles, ACS Nano, Volume
9, Issue 2, pages 1072-1079, January 27, 2015. [PDF] [PDF]
Supplementary [PDF] DOI: 10.1021/nn504556v

245. Hieu Bui,
Harish Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan,
Reem Mokhtar, Tianqi Song and John H Reif, DNA Computing, Chapter
in Section 3: Architecture and Organization, Volume I: Computer
Science and Software Engineering (Edited by
Teofilo F. Gonzalez, Jorge Diaz-Herrera, Allen
Tucker), The Computer Science Handbook, Third Edition (Editor-In-Chief
Allen B. Tucker), Taylor & Francis Group, (2013). ISBN 9781439898529 [PDF]

246. Sudhanshu
Garg, Nikhil Gopalkrishnan, Harish Chandran, and John
Reif, Self-Replicating DNA Nanostructures: Autocatalytic Nanodevices derived from
Catalytic Nanodevices, FNANO 2013, Snowbird, Utah, April 15-18, 2013.

247.
Reem Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu
Bui, Tianqi Song, and John Reif, Kinetic Digraph Rewrite Systems:
Coarse-Grained Models for Dynamic DNA Nanodevices, Poster Abstract, FNANO 2013,
Snowbird, Utah, April 15-18, 2013. Also, A Python Implementation
of a DNA Graph Rewriting System (DAGR), poster abstract, FNANO2015, p148, April
2015. Published as Reem
Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu Bui,
Tianqi Song, and John Reif, Modeling
DNA Nanodevices Using Graph Rewriting Systems, invited Chapter, Advances in Unconventional Computing, Volume 2:
Prototypes, Models and Algorithms (Edited by Andrew Adamatzky), Springer,
pp. 347-396 (2017). ISBN 978-3-319-33921-4
[PDF] [PDF]

248. Hieu
Bui, Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, and John Reif,
Local Hybridization Chain-Reactions on the Surface of DNA Origami, Poster
Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013. Also Design DNA
Hairpin Systems for Localized DNA Hybridization Reactions, poster abstract,
FNANO2015, p169, April 2015. Expanded paper rewritten for journal publication
as: Hieu Bui, Sudhanshu Garg, Reem Mokhtar, Harish
Chandran, Vincent Miao and John
Reif, Design and Analysis of Localized DNA
Hybridization Chain Reactions, Small (2017), 1602983. [PDF] [PDF]

249.
John H. Reif and Tianqi Song, Complexity and Computability of Temperature-1 Tilings, Poster Abstract, FNANO 2013, Snowbird, Utah, April
15-18, 2013. Poster Abstract DNA19, Tempe, AZ, Sept, 22-27, 2013. Submitted for journal publication, (2015). [PDF]

250.
John H. Reif and
Wadee Alhalabi, Advancing Attention
Control Using VR-Induced Artificial Synesthesia, submitted for journal publication, (2014). [PDF]

251.
John H. Reif and Wadee
Alhalabi, Design and Analysis of a High-Efficiency, Cost-Effective Solar
Concentrator, submitted
for journal publication, (2014). [PDF]

252. John
H. Reif and Wadee
Alhalabi, Solar-Powered
Desalination: Its Significant Challenges and Potential, Renewable and Sustainable
Energy Reviews, Volume 48, Pages 152-165, (August
2015). [PDF] [PDF]

253. Hiba Shahid, Wadee Alhalabi, and John H. Reif, Real-time operating system
(RTOS) with application to play models, International Journal of Computing
Engineering Research, Vol.5(2), pp. 9-16, October 2014, DOI:
10.5897/IJCER2013.0202, ISSN: 2141-6494, (Oct, 2014). [PDF]

254. Wadee
Alhalabi, John Reif, Zeineb
Elsheikh, Heba Felimban, Majda
Fallata, Khalid Thabit, Abdullah Abusorrah, The Co-learning in the Design, Simulation and
Optimization of a Solar Concentrating System, Computers in Human Behavior, Vol
51, Part B, pp. 857-866 (December 2014). [PDF] https://dx.doi.org/10.1016/j.chb.2014.10.043

255. Tianqi Song, Sudhanshu Garg, Hieu Bui, Reem Mokhtar, and John H. Reif, Analog Computation by DNA Strand Displacement Circuits, ACS
Synthetic Biology, 5, 898−912 (July, 2016). DOI: 10.1021/acssynbio.6b00144 [PDF] [PDF]

256. Hieu
Bui, Sudhanshu Garg, Vincent Miao, Tianqi Song,
Reem Mokhtar, and John Reif, Design and Analysis of Linear Cascade DNA
Hybridization Chain Reactions Using DNA Hairpins, Special Issue, Journal of New
Physics, Vol. 19, (2017) 015006. doi:10.1088/1367-2630/aa53d0 [PDF] [PDF]

257. Sudhanshu
Sudhanshu
Garg, Shalin
Shah, Hieu Bui, Tianqi Song, Reem Mokhtar, and John
Reif, Renewable Time‐Responsive DNA Circuits, Small *14*, 1801470(July
18, 2018). [PDF] [PDF] DOI: 10.1002/smll.201801470
https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201801470

258. Hieu Bui, Shalin Shah, Reem Mokhtar, Tianqi Song, Sudhanshu
Garg, John Reif, Localized DNA Hybridization Chain Reactions on DNA Origami, ACS Nano, Volume *12*, Num. 2, pp 1146–1155(January 22, 2018). DOI: 10.1021/acsnano.7b06699

259. Danie** **Daniel
Fu, Shalin Shah, Tianqi Song and John H Reif,
DNA-based Analog Computing, Chapter in book: Synthetic Biology: Methods
and Protocols, Edited by Jeffrey C.
Braman), In Series Methods in Molecular Biology, published
by Springer, pp. 411-417 (2018). ISBN: [PDF] [PDF]

260. Tianqi Song, Sudhanshu Garg, Hieu Bui,
Reem Mokhtar, and John H Reif, Design
and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation
Using Autocatalytic Amplifiers, ACS Synthetic Biology (Dec
2017). DOI: 10.1021/acssynbio.6b00390

261. Xin Song, Abeer Eshra, Chris Dwyer, and
John Reif, Renewable DNA Seesaw
Logic Circuits Enabled by Photoregulation of
Toehold-Mediated Strand Displacement, RSC Advances, Volume 7, Issue 45,
pp. 28130-28144 (March, 2017). DOI: 10.1039/C7RA02607B [PDF]
(supplementary: [PDF])

262. Sudhanshu
Garg, H Hieu Bui,
Abeer Eshra, Shalin
Shah and John H Reif, Nucleic Acid Hairpins: A Robust and Powerful
Motif for Molecular Devices, Chapter 7 in book: “Soft Nanomaterials” (Edited
by Ye Zhang and Bing Xu), World Scientific Series in Nanoscience and Nanotechnology, World Scientific,
Volume 19, pp. 175-199 (2019). ISBN: 978-981-120-102-8, DOI:
10.1142/9789811201035_0007

263. John H. Reif, DNA robots sort as they
walk,
Prospective, Science, Vol. 357, Issue 6356, pp. 1095-1096 (September, 2017).
DOI: 10.1126/science.aao5125

264. Hieu Bui
and John H Reif, Localized DNA Computation, Chapter 19
in book: “From Parallel to Emergent Computing” (Edited by Andrew Adamatzky, Selim Akl,
and Georgios Ch. Sirakoulis), CRC Press (February 18, 2019). Taylor & Francis Group of CRC Press. ISBN: 9781138054011

265. Shalin Shah and John H. Reif,
Temporal DNA Barcodes: A Time-Based Approach for Single-Molecule Imaging, 24th
International Conference, DNA 24, Jinan, China, Also, Chapter 5 of
DNA Computing and Molecular Programming (DNA 2018), edited by D. Doty and
H. Dietz, LNCS 11145, published by Springer Nature Switzerland AG, pp.71-86, (2018).
DOI: 10.1007/978-3-030-00030-1_5 Also published as Shah, Shalin, Abhishek
Dubey, and John Reif. "Improved optical multiplexing with temporal DNA
barcodes." ACS Synthetic Biology 8.5 (2019): 1100-1111. DOI: 10.1021/acssynbio.9b00010

266. Tianqi
Song, Nikhil Gopalkrishnan, Abeer
Eshra, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, Harish Chandran and John Reif, Improving the
Performance of DNA Strand Displacement Circuits by Shadow Cancellation, ACS
Nano, (Oct 29, 2018). DOI: 10.1021/acsnano.8b07394 https://doi.org/10.1021/acsnano.8b07394

267. Abeer Eshra, Shalin Shah, Tianqi Song, John Reif, Renewable DNA hairpin-based logic circuits, IEEE Transactions on Nanotechnology,
Vol. 18, pp. 252-259, (2019). DOI: 10.1109/TNANO.2019.2896189

268. Shalin Shah, Dubey Abhishek and John H.
Reif, Programming temporal DNA barcodes for single-molecule
fingerprinting, Nano letters, 19 (4), pp 2668–2673 (March
2019). DOI: 10.1021/acs.nanolett.9b00590

269. Xin
Song and John H Reif, Nucleic Acid Databases and Molecular-Scale
Computing, ACS Nano, Vol 13, Issue 6, pp 6256-6268 (May 2019).
DOI: 10.1021/acsnano.9b02562

270. Tianqi
Song, Abeer Eshra, Shalin
Shah, Hieu Bui, Daniel Fu, Ming Yang, Reem Mokhtar,
and John Reif, Fast and Compact DNA Logic Circuits Based on Single-Stranded
Gates Using Strand-Displacing Polymerase, Nature Nanotechnology (Sept 2019).
DOI: 10.1038/s41565-019-0544-5

271. Tianqi Song, Shalin Shah, Hieu Bui, Sudhanshu Garg, Abeer Eshra, Ming Yang, and John Reif, Programming DNA-Based
Biomolecular Reaction Networks on Cancer Cell Membranes, Journal of the
American Chemical Society (JACS), Vol. 141, No. 42, pp. 16539-16543. (Oct
2019). DOI: 10.1021/jacs.9b05598
https://doi.org/10.1021/jacs.9b05598

272. Shalin Shah., Tianqi Song,
Xin Song, Ming Yang, John H. Reif,
Implementing Arbitrary CRNs Using Strand Displacing Polymerase. In: Thachuk C., Liu Y. (eds) DNA Computing and Molecular
Programming. International Conference on DNA
Computing and Molecular Programming (DNA
2019). Lecture Notes in Computer Science, vol 11648. Springer, Cham, pp 21-36 (2019). DOI: 10.1007/978-3-030-26807-7_2. Published
as Chapter in: DNA Computing and Molecular Programming (edited by Chris Thachuk and Yan Liu), Volume 11648, Springer, Switzerland
AG, pp 21-36, (2019). ISBN: 978-3-030-26807-7. [PDF]

273. Xin Song, Shalin Shah, and John
Reif, An Overview of DNA-Based Digital Data Storage, Chapter 18, DNA- and RNA-Based
Computing Systems (Evgeny Katz, editor), Wiley-VCH
Verlag GmbH Publishers, Weinheim, Germany, pp. 345-350 (Dec., 2020). ISBN:
978-3-527-82541-7

274. Reem Mokhtar, Tianqi
Song, Daniel Fu, Shalin Shah, Xin Song, Ming Yang, and John Reif, DNA Origami
Transformers, Chapter, Chapter 16, DNA-
and RNA-Based Computing Systems (Evgeny Katz,
editor), Wiley-VCH Verlag GmbH Publishers, Weinheim, Germany, pp. 307-322
(Dec., 2020). ISBN: 978-3-527-82541-7 [PDF]

275. Xin Song, Daniel Fu, Shalin
Shah, John Reif, UV-Micropatterned
Miniaturization: Rapid In-Situ Photopatterning and Miniaturization of
Microscale Features on Shrinkable Thermoplastics, Advanced Materials, Vol. 5, Issue
6 (May 4,2020).

DOI: 10.1002/admt.202000146 https://doi.org/10.1002/admt.202000146

276. Shalin Shah, Jasmine Wee, Tianqi Song, Luis Ceze, Karin Strauss, Yuan-Jyue
Chen, John Reif, Using strand displacing polymerase to program chemical
reaction networks, Journal of the American Chemical Society (JACS), Vol.
142, Issue. 21, pp. 9587–9593 (May 4, 2020). DOI: 10.1021/jacs.0c02240 https://pubs.acs.org/doi/10.1021/jacs.0c02240
(Supporting Information https://pubs.acs.org/doi/10.1021/jacs.0c02240).

277. Xin Song and John Reif, Optics-Free Imaging with DNA
Microscopy: An Overview, Chapter 6. Handbook of Unconventional Computing:
Volume 2: Implementations (edited by Andrew Adamatzky),
WSPC Book Series in Unconventional Computing, World Scientific Publishers
(WSPC), pp. 181-191 (2021). DOI: 10.1142/12232 DOI: 10.1142/9789811235740_0006.
[PDF] ISBN: 978-981-123-527-6 (ebook), 978-981-123-503-0 (hardcover).

278. Shalin Shah, Ming Yang, Tianqi Song, and John Reif,
Molecular computation via polymerase strand displacement reactions, Chapter 5.
Handbook of Unconventional Computing: Volume 2: Implementations (edited by
Andrew Adamatzky), WSPC Book Series in Unconventional
Computing, World Scientific Publishers, pp. 165-197 (2021) [PDF] DOI: 10.1142/9789811235740_0005. ISBN:
978-981-123-527-6 (ebook), 978-981-123-503-0
(hardcover).

279. Daniel Fu, Raghu Narayanan
Pradeep, Fei Zhang, John Schreck, Hao Yan and John Reif, Automated Design of
Curved DNA Origami Nano-Capsules with Specific Shape and Variable
Multilayer-Reinforced Rigidity, International Conference on DNA Computing and
Molecular Programming (DNA 2019), Seattle, WA (Aug, 2019).

281. Daniel Fu and John H Reif, 3D DNA Nanostructures: The Nanoscale Architect. special
issue (Mechanical Design in DNA Nanotechnology) of Applied Sciences, Volume 11, No. 6, eLocator-ID
2624, (2021). DIO: https://doi.org/10.3390/app11062624

282. Xin Song, Shalin Shah, John
Reif, Multidimensional Data Organization and Random Access in Large-Scale DNA
Storage Systems, special issue of Natural Computing (Theoretical Computer
Science – track C), Vol. 894, pp. 190–202 (2021).
DIO: https://doi.org/10.1016/j.tcs.2021.09.021

283. Xin Song, Felicity Coulter, Ming
Yang, Fikadu Tafesse,
William Messer, John Reif, Lyophilized
Colorimetric RT-LAMP Test Kit for Rapid, Low-Cost, At-Home Molecular
Testing of SARS-CoV-2 and Other Pathogens, Scientific Reports,12: 7043 (April
2022). DOI: 10.1038/s41598-022-11144-5.

284. Ming Yang, and John H. Reif,
Social DNA Nanorobots, Invited Chapter for Book on DNA Nanotechnology at
40, (accepted, 2021).