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] http://dx.doi.org/10.1016/j.chb.2014.10.043

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

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

257. Sudhanshu
Sudhanshu Garg, Shalin Shah, Hieu Bui, Tianqi Song, Reem Mokhtar, and John Reif,
Renewable Time‐Responsive DNA Circuits, Small *14*, 1801470(July 18, 2018). [PDF] [PDF] 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. Shah S., Song T., Song X., Yang M., Reif J.
(2019) Implementing Arbitrary CRNs Using Strand Displacing Polymerase. In:
Thachuk C., Liu Y. (eds) DNA Computing and Molecular Programming. International
Conference on DNA Computing and Molecular Programming (DNA 2019).
Lecture Notes in Computer Science, vol 11648. Springer, Cham, pp 21-36 DOI: 10.1007/978-3-030-26807-7_2

273. Xin Song, Shalin Shah, and John
Reif, An Overview of DNA-Based Digital Data Storage, Chapter, DNA- and
RNA-Based Computing Systems (Evgeny Katz, editor), Wiley-VCH Verlag GmbH Publishers, Weinheim,
Germany, to appear (March, 2021).
ISBN10: 3527347208 ISBN13: 9783527347209

274. Reem Mokhtar, Daniel Fu, Shalin Shah, Xin Song, Ming Yang, and John Reif, DNA
Origami Transformers, Chapter, DNA- and RNA-Based Computing Systems (Evgeny
Katz, editor), Wiley-VCH Verlag GmbH
Publishers, Weinheim, Germany, to appear
(March, 2021). ISBN10: 3527347208 ISBN13: 9783527347209 [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 11, Vol 2. Implementations, Alternative
Computing, (edited by Andrew Adamatzky), World Scientific (to appear, 2021). [PDF]

278. Shalin Shah, Ming Yang, Tianqi Song, and John Reif,
Molecular computation via polymerase strand displacement reactions, Chapter 12,
Vol 2. Implementations, Alternative Computing, (edited by Andrew Adamatzky), World
Scientific (to appear, 2021). [PDF]

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).

280. Shah S., Song T., Song X., Yang
M., Reif J, Implementing Arbitrary CRNs Using Strand Displacing Polymerase.
International Conference on DNA Computing and Molecular Programming (DNA 2019),
Seattle, WA (Aug, 2019). 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]

281. Dan Fu and John H Reif, Design of Shaped 3D DNA
Nanostructures, invited submission to special issue (Mechanical Design in DNA
Nanotechnology) of Applied Sciences, (2021).

282. Xin Song, Shalin Shah, John Reif, Multidimensional Data
Organization and Random Access in Large-Scale DNA Storage Systems, invited
submission to special issue of Natural Computing (Theoretical Computer Science
– track C), (2021). DIO: https://doi.org/10.1101/743369

283. Xin
Song, Felicity Coulter, Ming Yang, Fikadu Tafesse, William Messer, John Reif, Rapid
At-Home Testing of COVID-19 with an Accurate, Inexpensive, Lyophilized
Molecular Test Kit, manuscript in preparation, April 2021).