CURRICULUM VITAE

John H. Reif

Personal

John Henry Reif

Born: 1951

Madison, Wisconsin

U.S. Citizen 

Current Position

Hollis Edens Distinguished Professor, Trinity College of Arts and Sciences, Duke University since 2003.

Professor of Computer Science at Duke University, since 1986.

Secondary appointment in Department of Electrical and Computer Engineering, Pratt School of Engineering, Duke University since June, 2016.

Academic Address                              Home Address

D223 LSRC Building                            3112 Devon Road

Dept. of Computer Science                          Durham, NC 27707

Duke University

Box 90129

Durham, NC 27708-0129

U.S.A.

Office phone:                                 home phone:

(919) 660-6568                                (919) 493-7978

Email address:

Reif DNA Nanoscience Lab: Room 3245, French Family Science Center

Homepage: http://www.cs.duke.edu/~reif

Research Interests - DNA nanostructures, Molecular Computation, Efficient Algorithms, Parallel Computation, Robotic Motion Planning, and Optical Computing.

Recreational Interests - skiing and cross-country skiing, wind surfing, canoeing and hiking

Education

Ph.D. in Applied Mathematics (Division of Applied Sciences, Harvard University, Cambridge, MA, July 1977) Thesis title: Combinatorial Aspects of Symbolic Program Optimization. Thesis advisor: Harry R. Lewis (Previously Dean of Harvard College)

M.S. in Applied Mathematics (Division of Applied Sciences, Harvard University, Cambridge, MA, Spring 1975)

B.S., magna cum laude, in Applied Mathematics and Computer Science, (Tufts University, Medford, MA, Spring 1973)

Enrolled in independent study in mathematics, computation and optics during Fall 1970 - Spring 1973, funded by a grant from the Sloan Foundation's Unified Science Study Program.

Note: While an undergraduate Fall 1970 - Spring 1973 at Tufts U., Reif was in the Unified Science Study Program(USSP), an interdisciplinary independent study program (spanning mathematics, computer science, physics, and engineering disciplines) funded by a grant from the Sloan Foundation. His undergraduate projects were funding under this program and included: stochastic analysis and computer simulations of neural nets, design of computer made holograms, software for structural analysis of geodesic domes, and a computer generated a short animated movie. Reif was given a full scholarship and graduated from Tufts in 3 Years, Magna cum laude.

Wellesley High School, Wellesley, MA, Spring 1970

Faculty Positions

A. Hollis Edens Distinguished Professor of Computer Science in Trinity College of Arts and Sciences, Duke University, September 1, 2003 to present.

Professor, Duke University, Summer 1986 to present

Distinguished Adjunct Professor, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University (KAU), Jeddah, Saudi Arabia (10/2011-9/2014).

Visiting Professor (Sabbatical), Carnegie Mellon University, Spring 1994.

Visiting Scientist, Mathematical Sciences Research Institute, Berkeley, CA, Spring 1986

Associate Professor, Harvard University, Spring 1983 to Spring 1986

Visiting Scientist (Sabbatical), Laboratory for Computer Science at M.I.T., Fall 1984

Assistant Professor, Harvard University, Fall 1979 to Spring 1983

Assistant Professor, University of Rochester, New York, Fall 1978 to Spring 1979

Research Associate, University of Rochester, New York, Fall 1977 to Fall 1978

(Research Assistant, Harvard University, Spring 1975 to Spring 1977)

Memberships, Awards and Prizes

Awarded: Tufts Notable, Tufts University, 2010.

Fellow: Association for the Advancement of Science (AAAS), since 2003.

Fellow: Association for Computing Machinery (ACM), since 1997.

Fellow: Institute of Electrical and Electronics Engineers (IEEE) since 1993.

Fellow: Institute of Combinatorics and its Applications, since 1991.

Awarded: Rozenberg Tulip Award in DNA Computing (Tulip Prize) International Society for Nanoscale Science, Computation and Engineering (ISNSCE), 2005

Awarded: Harvard University Thomas Hoopes Prize for directing the undergraduate honors thesis, by Philip N. Klein (now Full Professor, Brown University), June 1984.

Member: Faculty of 1000, since 2005

Member: International Society for Nanoscale Science, Computation and Engineering (ISNSCE) Chair of Scientific Advisory Committee of ISNSCE since 2004.

Member: Society of Industrial and Applied Mathematicians (SIAM)

Member: American Mathematics Society (AMS)

Member: Sigma Xi Scientific Research Society

Listed: ISI (Thomson Reuters) Highly Cited Researcher, Computer Science

Listed: Who's Who in America, Who's Who in the World, Who's Who in Emerging Leaders in America, Who's Who in Science and Engineering, Who's Who in American Education.

Postdoc Supervision

Xiaoju Guan (jointly supervised with Hao Yan), 2003-2005 (now Inner Mongolia Medical University, China).

Sang Jung Ahn (jointly supervised with Thom LaBean), 2003-2004. (Later postdoctoral fellow at the California Institute of Technology. Currently Research Scientist, Korea Research Institute of Standards and Science, Daejeon, South Korea)

Dage Liu, Postdoc 2001-2004 (Later Research Associate at North Carolina State University, University of Wisconsin-Madison , and Univ. of Penn.)
Hao Yan, Postdoc 2001-2002 and Research Assistant Professor, CS Dept, Duke University, 2002-2004 (Currently Distinguished Professor, Chemistry and Biochemistry Department, Arizona State University, August 2004-current.)

Thom LaBean, Postdoc 1998-2001 (Associate Professor, Materials Science & Engineering, North Carolina State University. Previously Research Associate Professor, CS Dept, Duke University)

Sandeep K. S. Gupta, Postdoc 1995 (currently Professor, Department of Computer Science and Engineering, Ira A. Fulton School of Engineering, Arizona State University, Tempe, AZ 85287-5406).

Lars Nyland, Postdoc 1991-1991 (Currently Senior Architect, NVIDIA, Durham, NC and Adjunct Associate Professor, Department of Computer Science, University of North Carolina, Chapel Hill, NC.)

Steven Tate, Postdoc 1991-1993 (Currently Professor and Chairman, Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC)

Hillel Gazit, Postdoc 1989-1991 (Currently Software Consultant, San Francisco, CA)

Paul G. Spirakis, Postdoc 1982-1982 (Currently Full Professor and Chairman, Department of Computer Science, University of Liverpool, UK and Professor, Department of Computer Engineering & Informatics, University of Patras, School of Engineering, Patras, Greece and Director Computer Technology Institute, Patris, Greece.)

Current Graduate Students (Ph.D. candidates)

Reem Mokhtar, Ph.D. thesis topic: “DNA Origami Transformers”. Projected Date of Graduation: Spring 2017.

Tianqi Song Ph.D. thesis topic: “Theory and Experiments in DNA Analog Computation”. Projected Date of Graduation: Summer 208.

Xin Song, Tentative Ph.D. thesis topic: “Reusable DNA Circuits”. Projected Date of Graduation: Spring 2019.

Shalin Shah, Tentative Ph.D. thesis topic: “Families of DNA Devices for Super-Resolution Imaging”. Projected Date of Graduation: Spring 2019.

Dan Fu, Tentative Ph.D. thesis topic: 3D DNA Shapes for Nanocasting. Projected Date of Graduation: Spring 2020.

Ming Yang: 1st year PhD candidate. Projected Date of Graduation: Spring 2021.

Graduate Student Supervision (Completed Degrees):

Hieu BuiPh.D. thesis topic: “Localized DNA Computation”. Date of Graduation: Spring 2017. 

Sudhanshu Garg, Ph.D. thesis topic: “Programming Molecular Devices using Nucleic Acid Hairpins
”. Date of Graduation: May 2016. (Currently Research Scientist at LinkedIn, Sunnyvale, California).

Nikhil Gopalkrishnan, Duke University Ph.D. thesis topic: “Computational and Experimental DNA Self-Assembly”. Date of Graduation: Fall 2012. (Currently Postdoctoral Assistant, Department of Systems Biology, Harvard Medical School, Cambridge, MA in the laboratory of Peng Yin.)

Harish Chandran, Duke University Ph.D. thesis topic: “A Theoretical and Experimental Study of DNA Self-assembly”. Date of Graduation: Fall 2012. Currently Research Scientist, DeepMind, Mountain View, California 94043 (Previously 2012-2017, Research Scientist and Tech Lead Manager at Google Research, Google Corporation, Redwood Shores, California.)

Tianqi Song, Duke University Masters thesis topic: “Stochastic DNA Tiling Assembly”. Date of Masters Graduation: Spring 2012. 

Ahsan Muhammad, Duke University Masters thesis topic: “Cluster Quantum Computing”. Date of Masters Degree Graduation: Spring 2012.

Samuel Slee, Duke University Ph.D. thesis: “Developing Scalable Abilities for Self-Reconfigurable Robots”. Dec. 1, 2010. (Currently Research Scientist at Google Research, Google Corporation, Redwood Shores, California.)

Urmi Majumder (also co-advised by Thomas LaBean), Duke University Ph.D. thesis: “Molecular Computing with DNA Self-Assembly”. March 30, 2009. [PPT] [PDF] (Currently Senior Software Developer/Architect at Oracle Corporation, Washington D.C)).

Sudheer Sahu, Duke University Ph.D. thesis: “DNA based self-assembly and nanorobotics: Theory and Experiments”, December, 2007 [PDF] Slides: [PPT] [PDF]. (Previously Research Scientist, Microsoft Live Search, in Redmond, Washington. Currently Executive Director of Engineering: Data, Search, and Application Services, Microsoft, Los Angeles Area, Microsoft.)

Peng Yin, Duke University Ph.d thesis: Theoretical and Practical Study in DNA Based Self-Assembly, Nanorobotics, and Nanocomputation. May, 2005 [PDF] [abstract] Slides: [PPT] [PDF]. (2005-2009, CPI Postdoctoral Researcher, Caltech, Pasadena, CA). (Currently Associate Professor, Department of Systems Biology, Harvard Medical School, Cambridge, MA.)

Sung Ha Park, Duke University Ph.D. thesis: “Self-assembled DNA Nanostructures and DNA-templated Silver Nanowires” Thesis: [PDF] Slides: [PPT] [PDF] (Reif was secondary adviser only; primary supervisors are Thom LaBean and Gleb Finkelstein (Dept of Physics), Department of Physics, May, 2005 (2005-2007, CPI Postdoctoral Researcher, Caltech, Pasadena, CA), (Currently Associate Professor, Sungkyunkwan University, South Korea).

Zhung (Robert) Sun, Duke University Duke University Ph.D. thesis: Complexity of Robotic Movement Problems. Date of Graduation: April 2003 [PDF] [abstract] Slides: [PPT] [PDF]. Masters Thesis "The Computational Power of Frictional Mechanical Systems, May, 1999. (Currently Research Scientist, Google Inc., Mountain View, CA)

Guo Bo, Duke University Master Thesis "Computing by DNA Self-Assembly". Oct, 2001 (currently Research Scientist, Mitsubishi Electric, Japan).

Yuan Guangwei, Duke University Master Thesis "Simulation of DNA Self-Assembly", Fall 2000 (Currently Research Scientist, China).

Christopher Butler, Duke University Master Thesis "Simulations of Molectronics architectures", 2000.

Xavier Berni: Duke University MS Thesis "DNA tagging", May 2000. (Currently Computer Scientist Consultant, S. Carolina)

Deganit Armon, Duke University Ph.D. Thesis "Dynamic Data Structures for Randomized Algorithms that use Sampling", 1997. Thesis: [PDF] [abstract] Lecturer at Afeka Tel Aviv Academic College of Engineering.

Ashish Gehani, Duke University Masters Thesis "Image Resolution Enhancement via Data Compression Techniques", 1997 (Currently Senior Computer Sciencist, SRI International, Menlo Park, CA. Previously Research Assistant Professor, Department of Computer Science and Engineering, University of Notre Dame.)

Shenfeng Chen, Duke University Ph.D. Thesis "Algorithmic Applications of Data Compression Techniques", 1996. Thesis: [PDF] [abstract]. Currently Technical Manager of a startup company in China.

Hongyan Wang, Duke University Ph.D. Thesis “Approximate and Adaptive Algorithms for Some Optimal Motion-Planning Problems,” 1996 Thesis: [PDF] [abstract] (Currently Adjunct Faculty member of University of Maryland University College. Previously senior software engineer with Parametric Technology Corporation in Massachusetts and with Canopus, Ltd. in Kobe, Japan.).

Zhiyong Li, Duke University Ph.D. Thesis "Computational Models and Program Synthesis for Parallel Out-of-Core Computation", May, 1996 [PDF] [abstract]. (Currently Research Scientist, Sun Microsystems, California)

Akitoshi Yoshida, Duke University Ph.D. Thesis "Applications of Optical Techniques in Interconnections, Image/Video Compression, and Computational Geometry", 1994, Univ. Microfilms Int. 9424616 [abstract] (Currently Research Scientist, Computing Center of the University of Mannheim, Germany).

Salman Azhar (J.P. Duke Fellow as Graduate Student), Duke University Ph.D. Thesis "Computational Aspects of Multiagent Systems: Modeling Efficiency and Computing Sequential Equilibrium", 1993, Univ. Microfilms Int. 9420402 [abstract]. Masters Thesis "Efficient Learning of Permutation Groups by Examples", 1990 (Currently Visiting Professor of the Practice, Dept of Computer Science, Duke University. Previously Executive Consultant at Eike Consulting, LLC and Advisor (2008-2014) & VP Engineering (2006-08) at DecisionStreet, Inc. Previously Associate Professor at University of San Francisco.)

Peter Su, Dartmouth University Ph.D. Thesis (Ph.D. completed at Duke but Scott Drysdale was official Supervisor) "Efficient Parallel Algorithms for Closest Point Problems", 1994 Univ. Microfilms Int. 9524419 (Previously Research Assistant Professor, Software Institute, Carnegie Mellon University.)

Tassos Markas, Duke University Ph.D. Thesis "Data Compression: Algorithms and Architectures", 1993, Univ. Microfilms Int. 9405986 [abstract]. (Currently President & CEO, 3DMedia, RTP, NC. Previously Director of Multimedia, Atmel Corporation, San Jose, CA. Previously Research Scientist, VLSI Design and Test Department, Center for Digital Systems Engineering, Research Triangle Institute, RTP, NC.)

Steven Tate, Duke University Ph.D. Thesis "Arithmetic Circuit Complexity and Motion Planning", 1991, Univ. Microfilms Int. 9127527 [abstract]. (Currently Professor and Chairman, Department of Computer Science, University of North Carolina at Greensboro, Greensboro, NC.)

Lars Nyland, Duke University Ph.D. Thesis "The Design of a Prototyping Programming Language for Parallel and Sequential Algorithms", 1991, Univ. Microfilms Int. 9127499 [abstract]. (Currently Senior Architect, NVIDIA, Durham, NC and Adjunct Associate Professor, Department of Computer Science, University of North Carolina, Chapel Hill, NC.)

Sandeep Sen, Duke University Ph.D. Thesis "Random Sampling Techniques for Efficient Parallel Algorithms in Computational Geometry", 1989, Univ. Microfilms Int. 9025050 [PDF] [abstract] (Currently Full Professor, Department of Computer Science & Engineering, Indian Institute of Technology, Delhi, India).

Sanguthevar Rajasekaran, Harvard University Ph.D. Thesis "Randomized Parallel Computation", 1988, Univ. Microfilms Int. 8909005. (Currently UTC Chair Professor of CSE and Director of the Booth Engineering Center for Advanced Technologies (BECAT), Computer Science and Engineering Department, University of Connecticut.)

Paul G. Spirakis, Harvard University Ph.D. Thesis "Probabilistic Algorithms", Dec. 1981, University Microfilms International No. 8216206. (Currently Professor and Chairman, University of Liverpool, UK and Professor, Department of Computer Engineering & Informatics, University of Patras, School of Engineering, Patras, Greece and Director Computer Technology Institute, Patris, Greece.)

Undergraduate Thesis Supervision

Philip Klein; Harvard University Undergraduate Thesis(awarded Thomas T. Hoopes priz) "Stacktracking: Parallel Acceptance of Deterministic Context-Free Languages", 1984 (Currently Full Professor, Brown University).

Research Support: Principal Investigator or Co-Investigator

NSF CCF1617791, SHF: Small: DNA Circuits for Analog Computations, 6/30/2016 - 6/30/2019, $308,001.

NSF CCF-1320360, SHF: Small: Localized DNA Hybridization Computation (PI John H. Reif), 8/6/2013 – 7/30/2016, $400,000.

NSF CCF- 1217457, SHF: Small: Error Correction for Biomolecular Computations (PI John H. Reif), 7/1/2012 – 6/30/2015, $449,998.

NSF CCF-1141847, EAGER: Exploratory Software Development & Experiments of Dynamic DNA Nanosystems (PI John H. Reif), 9/1/2011 – 8/31/2013, $199,997.

NSF EMT Grant CCF-0829797: EMT/NANO: Autonomous Programmable DNA Devices Using DNAzymes (PI John H. Reif), 09/4/2008-08/31/2011, $200,000.00.

NSF EMT Grant CCF-0829798: EMT/NANO: Polymerase-Based Self-Activating and Reactivating DNA Systems, (PI John H. Reif with coPI Thomas H. LaBean), 09/01/2008-08/31/2009, $200,000, with expected continued support for 2009 and 2010 for $150,000/year.   

AFSOR Contract FA9550-08-1-0188, Bio-X-AFSOR: Encapsulated DNA-Based Molecular Autonomous Sensing Devices With Photonic Output (PI John H. Reif), April, 2008-Dec 2008, $200,000

NSF EMT Grant CCF-0551965: EMT: NSF Workshop: Emerging Opportunities of Nanoscience to Energy Conversion and Storage (PI John H. Reif), September 1, 2005- September 1, 2006, $49,900. http://www.cs.duke.edu/~reif/NSF.NanoEnergy/

NSF EMT Grant CCF-0523555: EMT: A DNA-Based Autonomous Programmable Molecular Transport Network (PI John H. Reif with coPI Thomas H. LaBean), July 15, 2005- August 31, 2007, $300,000

NSF EMT Grant CCF-0523558: EMT: NSF Workshop of Programmed Self-Assembly (PI John H. Reif), May. 1, 2005-October 31, 2005, $30,000.

NSF EMT Grant CCF-0432038: Nano: Error-Resilient DNA Tiling Assemblies (PI John H. Reif with coPI Thomas H. LaBean), Sept. 1, 2004-Aug. 30, 2007, $295,000.

NSF EMT Grant CCF-0432047: NANO: Combinatorial Self-assembly of Nanocircuits on Addressable DNA Nanoscaffolds (PI Hao Yan with coPIs: Chris L. Dwyer, Gleb Finkelstein, John H. Reif, Thomas LaBean), Sept. 1, 2004-Aug. 30, 2007, $300,000

Taiko Denki Inc. Industrial Grant: Applications of DNA Self-Assembly Nanofabrication Technology to Molecular Scale Electrical Contacts (PI John H. Reif with coPI Thomas H. LaBean), Taiko Denki Inc., Tokyo, Japan, Jan. 1, 2004-Dec. 30, 2005, $110,000.

NSF ITR 0326157: Nanoarchitecture: Balancing Regularity, Complexity and Defect Tolerance using DNA for Nanoelectronic Integration(PI: Alvin LeBeck CoPIs: Dan Sorin, Jie Liu, John H. Reif, Thom LaBean, Hao Yan, Sean Washburn, Dorothy Erie, Paul Franzon), Sept 1, 2003- Aug 31, 2006. $1,200,000.

NSF QuBIC EIA-0218376: Novel DNA Nanostructures for Targeted Molecular Scale to Micro Scale Interconnects. (PI: Thomas H. LaBean, CoPI: John H. Reif) NSF EIA-0218376, Sept 1, 2002- Aug 31, 2005. $349,999.

NSF EIA-0218359: Molecular Robotics for DNA Nanostructures. (PI: Hao Yan, CoPI: John H. Reif), Sept 1, 2002- Aug 31, 2005. $349,995.

Taiko Denki Inc. Industrial Grant: DNA Self-Assembly Nanofabrication Technology to Molecular Scale Electrical Contacts (PI John H. Reif with coPI Thomas H. LaBean), Taiko Denki Inc., Tokyo, Japan, Sept. 1, 2002- Sept. 30, 2003, $60,000.

Programmable DNA Lattices: Design, Synthesis and Applications (PI John H. Reif), BioComp Program, DARPA/AFSOR Contract, F30602-01-2-0561 July 1, 2000-Dec 30, 2004, $2,550,000.

Supplemental Augmentation to: Programmable DNA Lattices: Design, Synthesis and Applications (PI John H. Reif), BioComp Program, DARPA/AFSOR Contract, F30602-01-2-0561 Jan 1, 2002-Dec 30, 2002, $112,662 for FY2002.

Micro and Nano-Robotics Motion Control Algorithms (PI John H. Reif), NSF SEGR Award NSF-11S-01-94604, Sept 1, 2000-Sept 30, 2001, $80,772.

NSF ITR Grant EIA-0086015: Supplemental Augmentation to: Self-Assembly of DNA Nano-Scale Structures for Computation (PI John H. Reif), additional $413,000 awarded in FY 2004.

NSF ITR Grant EIA-0086015: Self-Assembly of DNA Nano-Scale Structures for Computation, (PI John H. Reif), Sept 1, 2000-Sept 30, 2005, $2,019,999. (awarded $1,184,999 September 1, 2000-August 31, 2003.

Prototyping Biomolecular Computations, (PI John H. Reif), jointly funded by Defense Advanced Research Projects Agency and National Science Foundation, NSF CCR-9725021, July 1997-Sept 2001, $2,748,017.

Moleware and the Molecular Computer, Subcontract PI (overall PI: James M. Tour), DARPA/ONR N00014-99-1-0406, 01 Mar 99 through 28 Feb. 2001, Subcontract $50,000.

Robust, Adaptive and Dynamic Robotic Motion Planning, (PI John H. Reif), NSF Grant NSF-IRI-9619647, 5/97-06/2000, $295,000.

SEGR: Design of a Biomolecular Distributed Operating System, (PI John H. Reif), NSF Grant CCR-9810000, Aug 1998-1999, $50,000.

CURIOUS: (C)enter for (U)ndergraduate Education and (R)esearch: (I)ntegration Thr(OU)gh Vi(S)ualization, (Co-principal investigator). NSF CDA-96-34475 09/96 - 08/99 $ 405,200

Acquisition of a Workstation Cluster Testbed for Next-Generation Collaborative Computing (Co-principal investigator). National Science Foundation Grant contract CDA-95-12356, 09/95 - 08/98, $489,600

Multidisciplinary Research for Demining, (Co-principal investigator of subcontract with E. Gelenbe, N Schmajuk and J. Staddon,) Army Research Office(ARO) contract DAAH-04-96-1-0448, 11/96 - 10/99, total contract: $3,000,600, Subcontract $431,000./year.

An Exploratory Study of Parallel Molecular Computation, (PI John H. Reif) National Science Foundation Grant number CCR-96-33567, 08/96 - 07/97 $50,000

Toward Autonomous Robots: Robust, Adaptive and Dynamic Motion Planning, (PI John H. Reif), National Science Foundation Grant NSF-IRI-91-00681,02/92 - 01/97, $365,755,

SIMD/MIMD Parallel Computing: Computational Theory, Scientific Applications, and Systems Research, (Co-principal investigator with C.S. Ellis, C. Gardner, H.S. Greenside, D.W. Loveland, and D.J. Rose) National Science Foundation Grant number CDA-91-23483, CISE Institutional Infrastructure Program, 09/92 - 08/98, $1,420,001 plus institutional support of $421,209.

A Refinement-Based Methodology for the Architecture-Independent Design and Development of Parallel Software, (Co-principal investigator with Andrew Goldberg and Jan Prins). Rome Laboratory contract F30602-94-C-0037, Subcontract to Kestrel Development Corporation, $314,495.

Common Prototyping Language (CPL) based on SETL, REFINE, and UNITY, DARPA/ISTO contract N00014-92-C-0182 under subcontract KI-92-01-0182 from Kestrel Institute, Additional $665,147, September 1, 1992 through August 31, 1995

Common Prototyping Language (CPL) based on SETL, REFINE, and UNITY, DARPA/ISTO, Subcontracted from Kestrel Institute, Additional $240,000, May 1, 1991-March 30, 1992.

Derivation and Analysis Tools for the Synthesis and Implementation of Parallel Algorithms, (PI John H. Reif), DARPA/ISTO contract N00014-91-J-1985, $1,560,000, July 1, 1991-June 30, 1994.

Parallel Compression of Space and Earth Data, (PI John H. Reif), NASA, Prime Contract Number: NAS5-30428, Subcontract 550-63, $491,699, October 1, 1991-September 30, 1993.

Randomized Methods in Distributed and Parallel Computation, (with B. Chor), Binational Science Foundation, $36,000, September 1, 1989-August 31, 1992.

Common Prototyping Language (CPL) based on SETL, REFINE, and UNITY, DARPA/ISTO, Subcontracted from Kestrel Institute, $162,240, October 1, 1989-September 30, 1990.

Very High Speed Holographic Message Routing for Parallel Machines, (PI John H. Reif), DARPA/ARMY, $290,673, September 1, 1988-August 31, 1990.

Parallel Compression of Space and Earth Data, (PI John H. Reif), NASA, $435,000, October 1, 1988-September 30, 1991.

Parallel Algorithm Derivation, (PI John H. Reif), DARPA/ISTO, $696,899, July 1, 1987-June 30, 1991.

Computational Complexity and Efficiency in Electro-optical Computing Systems, (PI John H. Reif), Air Force Office of Scientific Research, $442,772, September 1, 1987-August 31,1990.

Randomized Parallel Algorithms in Learning, (PI John H. Reif), Office of Naval Research, $228,707, January 1, 1987-February 28, 1989.

Randomized Techniques for Highly Parallel Computing, (PI John H. Reif), Office for Naval Research, $93,475, July 1, 1984-June 30, 1986.

Parallel and Probabilistic Computations, (Co-Investigator with H. R. Lewis) National Science Foundation, $113,455, July 1, 1982-December 31, 1984.

Distributed Multi-processing, (PI John H. Reif), Office for Naval Research, $132,000, July 1, 1980 -June 30,1984.

Graph Algorithms in Program Analysis and Topological Imbeddings, (PI John H. Reif), National Science Foundation, $25,000, October 1, 1979-July 31, 1982.

Experimental Projects: Hardware, Software and Biochemistry

1. (Current) President of Eagle Eye, Inc., a small business based in the Research Triangle, NC. It was originally engaged in reconnaissance multi-spectral image target recognition. EagleEye, Inc. now specializes in contract research in the areas of defense applications of DNA biotechnology. Eagle Eye, Inc. has executed a number of federal research contracts over the last three years. In 2000, Eagle Eye developed (in collaboration with M. Pirrung, Dept of Chemistry, Duke Univ.) a biomolecular system for associative search in pedabit size DNA libraries.

2. DNA Tagging Project(with C. X. Berni, C. Kingsford) We made improvements to SAGE tagging to allow the technology to be applied to universal DNA hybridization arrays. Also, developed simulation software for the improved tagging process with a highly interactive graphic interface.

3. (Previous) Chief scientist of Rtware, 1995-1999, which produces real-time control software which is currently used for both commercial and military applications; military customers include the Airforce and Navy. RTware has received a Phase I SBIR from ONR, It was bought out by Datacode (a large hardware corporation) in 1999.

4.   (Previous) President of RSIC Associates, which received a Phase I and Phase II NASA Small Business Innovation Research Grant to build very high rate (.20 gigabit/second) lossless data compression hardware system that was successfully demonstrated. The multiprocessor chip (1.2 micron CMOS with approx. 330,000 transistors and with 128 specialized systolic processor cells per chip) was been fabricated and tested. A number of compression boards, each containing 16 of these chips, have been running since spring, 1992 and can be used by remote login to MCNC. In collaboration with Professor Jim Storer of Brandeis University. VLSI design by Research Triangle Institute, Research Triangle Park, NC in 1989. Board Level Design by MCNC, NC. Also funded by DARPA/ISTO for MOSES fabrication by HP. RSIC Associates has received contracts totaling $1,200,000 from various defense agencies, for the development of this hardware.

5.   Co-architect of BLITZEN (with Ed Davis), a 16,000 processor Massively Parallel Machine under NASA contract at Microelectronics Center of North Carolina (MCNC). The main component of the system was a BLITZEN chip, consisting of 128 bit serial processors (.25 gigabits/second). This chip is 1.2 micron CMOS and has 1,100,000 transistors, making it the largest (nonmemory) chip manufactured in the world during early 1989. The chip is tested and functional. A prototype BLITZEN system has been running since spring, 1989. See Publications (references #73,76).

6.   Inventor of Holographic Based Message Routing Systems for Massively Parallel Machines. The prototype was constructed under DARPA Contract by Kristina Johnson at the Center for Electro-Optical Computing Systems, Boulder, CO, April 2, 1989. See Publications (reference #80).

7.   Implementation (in collaboration with Charles Leiserson, Jill Mesirov, Lena Nekluvova, Steven Omohandro, and Washington Tayler) of Parallel Nested Dissection Algorithms for Solution of Large Sparse Linear Systems on the 64,000 process Connection Machine. Thinking Machines, Inc., Cambridge, MA, 1985-1986. See Publications (reference #62).

8.   Implementation (in collaboration with John Dorband and Torstein Opsahl) of Parallel Nested Dissection on 16,000 Processor Massively Parallel Processing Machine (MPP), NASA Goddard Space Center, Greenbelt, MD, 1985-1986. See Publications (reference #63). 

Patents

1. John H Reif, Peng Yin, Thomas H. LaBean, Geetha Shetty, Erik A. Schultes, Analyte Detection Using Autocatalytic Chain Reactions, US Non-Provisional Patent Application 11/775,740, filed July 10, 2007, publication Date: April 2, 2009. [PDF]. Approved, issued Oct 25, 2011 as US Patent 8,043,810 B2 [GooglePatent][USPO]. Assignee: Eagle Eye Research, Inc.

2. John H Reif, Thomas H. LaBean, Erik A. Schultes, Autonomous in Vitro Evolution, US Non-Provisional Patent Application 12/042,276, filed July 10, 2007, publication: September 10, 2009 [GooglePatent][USPO]. Assignee: Eagle Eye Research, Inc.

3. John H Reif and Katie L. Reif (joint inventors), "Solar Concentrator System for Solar Energy Plants", US Non-Provisional Patent Application 12/889,313, filed Sept 23, 2010 [GooglePatent][USPO]. Also, Australian Patent number 61/245,250, filed Sept 23, 2009, granted July 24, 2014. Assignee: Eagle Eye Research, Inc.

4. John H Reif and Karl F. Bohringer, Microelectronic Devices for Harvesting Vibrational Energy and Associated Systems and Methods, US Provisional Patent Application 61/417,362, filed Nov 29, 2010, published June 7, 2012, US Non-Provisional Patent Application US 12/0139389. Assignee: Ruamoko MEMS, Inc.

5. John H Reif, Levitation with switchable inductive element and associated systems, devices, and methods, Provisional Patent Application 61561918, Filed Nov 20, 2011, US Non-Provisional Patent Application No. 13/682,712 filed Nov 20, 2012. Approved Dec 24, 2014. Issued as U.S. Patent No. 9,024,487 on May 5, 2015. Assignee: Eagle Eye Research, Inc. [GooglePatent][USPO].

6. John H Reif and Karl F. Bohringer, Microelectronic Devices for Harvesting Vibrational Energy and Associated Systems and Methods, US Provisional Patent Application 61/656,425, filed June 6, 2012. US Non-Provisional Patent Application 13/910,9795, Filed June 5, 2013 [GooglePatent][USPO]. Assignee: Ruamoko MEMS, Inc.

 

Consulting Positions

1.   NASA Johnson Space Flight Center, consultant on Consolidated Space Operations Contract, Houston, Texas, July, 1997.

2. NASA ICASE Space Flight Center, Norfolk, Virginia, July, 1996.

3. NEC research center, Princeton New Jersey, July, 1995.

4.   RTware, NC, real time software and algorithms, 1993.

5.   Department of Mathematical Sciences, IBM Watson Research Institute. Yorktown Heights, NY, Summers of 1983 and 1984.

6.   GTE Laboratories, VLSI Design Project. Waltham, MA, Spring and Summer 1985.

7.   Thinking Machines, Inc. Connection Machine Project. Cambridge, MA, 1985-1988.

8.   Barakat Associates, Air Force contract: Optical Devices and Optical Computing. Lexington, MA, Fall 1985.

9.   MRJ, Park and Elmer, Design of Parallel Algorithms for the Connection Machine. Fairfax, VA, 1985-1988

10.NASA Goddard Space Flight Center, Space Data and Computing Division, Massive Parallel Processing (MPP) Project. Greenbelt, MD, 1985-1988.

11.Microelectronic Center for North Carolina (MCNC), 2nd Generation Massively Parallel Processor Project, (PI of $300,000 NASA contract supporting this work), initiator of and co-architect (with Ed Davis) of BLITZEN 128 processor chip, 1986-1988. (see System Projects #2)

Journals and Book Series Advisory Boards

1. Editor, Special Issue on STOC2003, (devoted to selected papers from the 34th Annual ACM Symposium on Theory of Computing (STOC2002), Journal of Computer and System Sciences (JCSS), Volume 67. No. 2, Sept. 2003, pp. 211-471. [PDF]

2. Member of Editorial Board of the Journal of Computational and Theoretical Nanoscience (CTN), American Scientific Publishers, USA, 2004-2006.

3. Member of Advisory Board, Theory and Practice of Object Systems, Wiley, New York, 2000-2007.

4. Member of Editorial Board of the Journal of Experimental Nanoscience, Taylor and Francis, USA, 2006 - current.

  1. Member of Advisory Board, Series on Natural Computing, Springer-Verlag, 2006 - current.
  2. Member of Advisory Board, Springer Series in Computer Science and Computer Security for Higher Education Press of Ministry of Education of China, 2009 - current.
  3. Member of Editorial Advisory Board / DNA and RNA Nanotechnology, 2014 - current

 

Conference Organizations

1.   Member of Program Committee, Aegean Workshop on Computing, Corfu, Greece, June 1986.

2.   Member of Program Committee, 20th Symposium on Theory of Computer Science, May 1988.

3.   Member of Program Committee, 3rd International Conference on Supercomputing, Boston, Massachusetts, May 1988.

4.   Chairman of Program Committee, Aegean Workshop on Computing, Corfu, Greece, June 1988.

5.   Member of Program Committee, 2nd Symposium on Frontiers of Massively Parallel Computing, Fairfax, Virginia, October 1988.

6.   Member of Program Committee, 22nd Symposium on Theory of Computer Science, May 1990.

7.   Member of Program Committee, 4th Symposium on Frontiers of Massively Parallel Computing, Fairfax, Virginia, October 1990.

8.   Program co-Chairman, First IEEE Conference on Data Compression, Snowbird, Utah, April 1991. (Sponsored by IEEE Computer Society)

9.   Member of Program Committee, 32nd IEEE Symposium on Foundations of Computer Science, October 1991. (Sponsored by IEEE Computer Society)

10.  Member of Program Committee, Sixth International Parallel Processing Symposium, Beverly Hills, California, March 23-26, 1992. (Sponsored by IEEE Computer Society)

11.  Member of Program Committee, Second IEEE Conference on Data Compression, Snowbird, Utah, March 1992. (Sponsored by IEEE Computer Society)

13.  Member of Program Committee, Third IEEE Conference on Data Compression, Snowbird, Utah, March 1993. (Sponsored by IEEE Computer Society)

14.  Member of Program Committee, Fourth IEEE Conference on Data Compression, Snowbird, Utah, March 1994. (Sponsored by IEEE Computer Society)

15.  Member of Advisory Committee, Workshop of Parallel Algorithms (WOPA),1994.

16.  Member of Program Committee, Second International Conference on Massively Parallel Processing Using Optical Interconnects (MPPOI1995)

19.  Member of Program Committee, IEEE Data Compression Conference(DCC95)

20.  Member of Program Committee, 1st Annual Meeting on DNA Based Computers(1995)

21.  Member of Program Committee, Workshop On Randomized Parallel Computing, 10th International Parallel Processing Symposium (IPPS '96).

22.  Member of Program Committee, 8th Annual ACM Symposium on Parallel Algorithms and Architectures(SPAA96)

23.  Member of Program Committee, IEEE Data Compression Conference(DCC96)

24.  Member of Program Committee, 2nd Annual Meeting on DNA Based Computers(1996)

25.  Member of Program Committee, 3rd annual IEEE Conference on Massively Parallel Processing Architectures using Optical Interconnections (MPPOI'96)

26.  Member of Program Committee, IEEE Data Compression Conference(DCC97).

27.  Member of Program Committee, 3rd Annual Meeting on DNA Based Computers(1997).

28.  Member of Program Committee, Workshop On Randomized Parallel Computing, 11th International Parallel Processing Symposium (IPPS '97).

29.  Member of Program Committee, DIMACS Workshop on "Randomization Methods in Algorithm Design", Dec. 12-14, 1997, Princeton University. Probability.

30.  Member of Program Committee, 4th International Symposium on Solving Irregularly Structured Problems in Parallel (IRREGULAR'97) University of Paderborn, Germany, 11-13 June 1997.

31. Member of Program Committee for the Algorithms and Applications track of 26th International Conference on Parallel Processing (ICPP97) August 11-15, Indian Lakes Resort in Bloomingdale, IL.

32. Member of Program Committee for the IEEE International Conference On Robotics And Automation, 1997.

33. Member of Organizing Committee, 4rth Annual Meeting on DNA Based Computing (1998).

34. Member of Program Committee, vIEEE Data Compression Conference(DCC98), Snowbird, Utah, 1998.

35. Member of Advisory Committee, Workshop on Parallel Algorithms (WOPA), 1998.

36. Member of Advisory Committee, 1999 Workshop on Algorithms and Data Structures (WADS'99) August 12-14, 1999 Vancouver, British Columbia, Canada.

37. Program Chair, Workshop in Biomolecular Computation: Its Potential and Applications, NSF, Arlington VI, Oct 1, 1999.

38. Member of Program Committee, IEEE Data Compression Conference(DCC99), Snowbird, Utah, 1999.

39. Member of Program Committee, Workshop on Algorithms and Data Structures (WADS1999).

40. Co-Organizer of East Coast Computer Algebra Day(ECCAD'99), NC State, Raleigh, NC, April 24, 1999.

41. Member of Program Committee, Workshop on Algorithmic Foundations of Robotics (WAFR2000).

42. Member of Executive Committee, DNA Based Computers, 2000.

43. Team Leader (with M. Morf) for DNA/Biological SRC meeting ADT Novel Technologies for Information Processing:, San Jose CA, (March 26, 2000).

43. Member of Program Committee, Seventh DNA Based Computers, June 2001.

43. Panel Moderator: Critical Assessment of Techniques for Microarray Data Analysis (CAMDA2000 Conference), Duke University, Durham, NC, 2001

44. Member of Organizing Committee, Special session on Molecular Evolutionary Computing, 2001 Congress on Evolutionary Computation (CEC2001) Seoul, Korea during May 27-30, 2001. at CEC2001.

45. Member of Program Committee, Seventh International Meeting on DNA Based Computers (DNA7), Tampa, FL, June 11-13, 2001.

46. Chairman of Program Committee, Symposium on Theory of Computing (STOC2002), May, 2002.

47. Member of Program Committee, track on Biomolecular Computing and Quantum Computing at Genetic & Evolutionary Computation Conference Conference (GECCO 03), Chicago, IL, July 2002.

48. co-Chairman of Program Committee, Ninth International Symposium on DNA Based Computers (DNA9), Madison, Wisconsin, June, 2003.

49. Program Chairman of the First Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO04), Snowbird, Utah, (April 21-23, 2004).

50. Member of the Godel Prize Committee, ACM SIGACT, 2004-2005.

51. Member of Program Committee, Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005).

52. Program Chairman of the Second Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO05), Snowbird, Utah, (April 24-28, 2005).

53. Program coChairman of the NSF Workshop: Emerging Opportunities of Nanoscience to Energy Conversion and Storage, Arlington VI, November 21-22, 2005.

54. Member of the Godel Prize Committee, ACM SIGACT, 2005-2008.

55. Member of Program Committee, 18th ACM Symposium on Parallelism in Algorithms and Architectures(SPAA06), Cambridge, MA, July 30 - August 2, 2006.

56. Program Chairman of the Third Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO06), Snowbird, Utah, (April 23-27, 2006).

57.  Member of the Program Committee (for Programmable self assembly) of 2006 Robotics Science and Systems Conference (RSS 2006), University of Pennsylvania, Philadelphia, PA, August 16th-19th, 2006.

58. Chair of the Godel Prize Committee, ACM SIGACT, 2006-2007.

59.  Program Chairman of the Fourth Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO07), Snowbird, Utah, (April 18-21, 2007).

60. General Chairman of the Fifth Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO08), Snowbird, Utah, (April 25-28, 2008).

61. Member of Committee for NSF Bio-inspired Molecular Computing and Self-Assembly Thrust, Princeton, BC 2008.

62. Member of Steering committee of International Conference on Bioinformatics and Computational Biology (BICoB09), New Orleans, Louisiana USA (March 25-27, 2009).

63. General Chairman of the Sixth Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO09), Snowbird, Utah, (April 20-24, 2009).

64. Member of Program Committee of Sixteenth Annual International Symposium on DNA Based Computers (DNA16) Hong Kong, China (June 2010).

65. Member of Advisory Board of Series on Computer Science and Computer Security for Higher Education Press of Ministry of Education of China and Springer (2009-present).

66. Member of Program Committee of International International Colloquium on Automata, Languages, and Programming(ICALP), 2010 Track A

67. General Chairman of the Seventh Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO10), Snowbird, Utah, (April 27-30, 2010).

68. General Chairman of the Eighth Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO11), Snowbird, Utah, (April 11-15, 2011).

69. Member of Program Committee of Seventeenth Annual International Symposium on DNA Based Computers (DNA17), Pasadena, CA (June 2011).

70. General Chairman of the Ninth Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO12), Snowbird, Utah, (April 16-19, 2012).

71. Member of Program Committee of Eighteenth Annual International Symposium on DNA Based Computers (DNA18), Aarhus, Denmark (June 2012).

72. General Chairman of the Tenth Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices(FNANO13), Snowbird, Utah, (April 15-18, 2013).

73. Member of Program Committee of Nineteenth Annual International Symposium on DNA Based Computers (DNA19), Tempe, AZ (Aug 2013).

74. General Chairman of the Eleventh Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO14), Snowbird, Utah, (April 14-17, 2014).

75. Member of Program Committee of 20th Annual International Symposium on DNA Based Computers (DNA20), Kyoto, Japan (Aug 2014).

76. General Chairman of the 12th Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO15), Snowbird, Utah, (April 13-16, 2015).

77. Member of Program Committee of 21th Annual International Symposium on DNA Based Computers (DNA21), Cambridge, MA (Aug 2015).

78. Member of Steering Committee of IEEE International Conference on Computations and Biomedical Systems (IEEE CBS), since 2010.

79. Member of Advisory Board of Wiley Book Series on Nature Inspired Computing, 2009-present

80. Member of the Advisory Board of your Journal of King Abdulaziz University Computing and Information Technology, 2013-2014.

81. Member of the DNA Computing Steering Committee, 2001-current.

82. Member of the ISNSCE Council, 2006-current.

83. Chair of ISNSCE Scientific Advisory Council, 2006-current.

84. Member of Faculty 1000 (member 2007-current)

 

Courses Taught

Fall, 2017, Algorithm Paradigms, COMPSCI 530, Duke University.

Spring, 2017, Computational Complexity, CPS 531, Duke University.

Fall, 2016, Algorithm Paradigms, COMPSCI 530, Duke University

Spring, 2016, Molecular Assembly and Computation, COMPSCI 590.01, Duke University.

Fall, 2015, Algorithm Paradigms, COMPSCI 530, Duke University.

Spring, 2015, Computational Complexity, CPS 531, Duke University.

Fall, 2014, Algorithm Paradigms, COMPSCI 530, Duke University.

Fall, 2013, Algorithm Paradigms, COMPSCI 530, Duke University.

Spring, 2012, Molecular Assembly and Computation, COMPSCI 590.02, Duke University.

Fall, 2011, Analysis of Algorithms, CPS 130, Duke University.

Spring, 2011, Computational Complexity, CPS 240, Duke University.

Fall, 2010, Analysis of Algorithms, CPS 130, Duke University.

Spring, 2010. Alternative Computational Models, Spring 2010.

Fall, 2009, Analysis of Algorithms, CPS 130, Duke University.

Spring, 2009, Computational Complexity, CPS 240, Duke University.

Fall, 2008, Analysis of Algorithms, CPS 130, Duke University.

Spring, 2008, Randomized Algorithms, CPS 237, Duke University.

Fall, 2007, Analysis of Algorithms, CPS 130, Duke University.

Spring, 2007, Computational Complexity, CPS 240, Duke University.

Fall, 2006, Analysis of Algorithms, CPS 130, Duke University.

Spring, 2006, Randomized Algorithms, CPS 237, Duke University.

Fall, 2005, Analysis of Algorithms, CPS 130, Duke University.

Summer, 2005, Analysis of Algorithms(NCSC 6021). Taught this masters-level remote instructional course for National Technical University(Walden University), produced at MGM Studios, Orlando, FL, June, 2005.

Spring, 2005, Analysis of Algorithms, CPS 130, Duke University.

Fall, 2004, Efficient Algorithms, CPS 230, Duke University.

Spring, 2003, Analysis of Algorithms, CPS 130, Duke University.

Fall, 2002, Efficient Algorithms, CPS 230, Duke University.

Spring, 2002, Randomized Algorithms, CPS 237, Duke University.

Fall 2001, Analysis of Algorithms, CPS 130, Duke University.

Spring 2001, Mathematical Foundations of Computer Science, CPS 140, Duke University.

Fall 2000, Computational Biology, CPS 296.2, Duke University.

Spring 2000, Computational Biology and Biomolecular Computation, CPS 296.2, Duke University.

Fall 1999, Analysis of Algorithms, CPS 130, Duke University.

Spring 1999, Analysis of Algorithms, CPS 130, Duke University.

Fall 1998, Parallel Algorithms, CPS 236, Duke University.

Spring 1998, Analysis of Algorithms, CPS 130, Duke University.

Fall 1997, Design and Analysis of Algorithms, CPS 230, Duke University.

Spring 1997, Analysis of Algorithms, CPS 130, Duke University.

Fall 1996, Design and Analysis of Algorithms, CPS 230, Duke University.

Spring 1996, Parallel Algorithms, CPS 236, Duke University.

Fall 1995, Analysis of Algorithms, CPS 130, Duke University.

Spring 1995, Parallel Algorithms, CPS 236, Duke University.

Fall 1994, Analysis of Algorithms, CPS 230, Duke University.

Fall 1993, Analysis of Algorithms, CPS 174, Duke University.

Spring 1993, Parallel Algorithms, CPS 230, Duke University.

Fall 1992, Analysis of Algorithms, CPS 174, Duke University.

Spring 1992, Numerical and Algebraic Algorithms, CPS 206, Duke University.

Fall 1991, Parallel Algorithm Implementation, CPS 265, Duke University.

Spring 1991, Computational Robotics, CPS 265, Duke University.

Fall 1990, Analysis of Algorithms, CPS 174, Duke University.

Spring 1990, Advanced Topics in Theory, CPS 265, Duke University.

Fall 1989, Analysis of Algorithms, CPS 224, Duke University.

Spring 1989, Advanced Topics in Massively Parallel Processing, CPS 265, Duke University.

Spring 1989, Advanced Topics in Algorithms, CPS 265, Duke University.

Fall 1988, Analysis of Algorithms, CPS 174, Duke University.

Spring 1988, Parallel Algorithms, CPS 265, Duke University.

Fall 1987, Analysis of Algorithms, CPS 224, Duke University.

Spring 1987, Parallel Algorithms, CPS 265, Duke University.

Fall 1986, Analysis of Algorithms, CPS 224, Duke University.

Spring 1994, Algorithms for Scientific Computation CS 15-850, Carnegie-Mellon University.

Fall 1985, Introduction to the Theory of Computing, CS 207, Harvard University.

Spring 1985, The Complexity of Computations: Parallel Computation, CS 224, Harvard University.

Spring 1984, The Complexity of Computations: Parallel Computation, CS 224, Harvard University.

Fall 1983, Efficient Algorithms, CS 226, Harvard University.

Spring 1983, The Complexity of Computations: Parallel Computation, AM 224, Harvard University.

Fall 1982, Efficient Algorithms, AM 226, Harvard University.

Spring 1982, The Complexity of Computations: Parallel Computation, AM 224, Harvard University.

Fall 1981, Introduction to the Theory of Computing, AM 207, Harvard University.

Spring 1981, Data Structures, AM 119, Harvard University.

Fall 1980, Introduction to the Theory of Computing, AM 207, Harvard University.

Spring 1980, Introduction to the Theory of Computing, AM 207, Harvard University.

Fall 1979, Efficient Algorithms, AM 226, Harvard University.

Spring 1979, Seminar in Research Topics, CSC 589, University of Rochester.

Fall 1978, Introduction to Theory of Computation, CSC 281/481, University of Rochester.

Fall 1978, Programming Problems Seminar, CSC 400, University of Rochester.

Spring 1978, Seminar on Optimization of Computer Programs, CSC 589, University of Rochester.

Fall 1977, Programming Problems Seminar, CSC 400, University of Rochester.

Recent Invited Talks

Biomolecular Computation by Local Assembly, University of Delaware, Mathematics Dept, April 19, 1997

Biomolecular Computation by Local Assembly, U Pennsylvania, April 18, 1997

Biomolecular Computation, Ultrascale Meeting, DARPA, Estes Park, CO, Oct 14, 1997.

Biomolecular Computation (Distinguished Lecture Series), Department of Computer Science, Rice University, April 30, 1997

Approximate Complex Polynomial Evaluation, Department of Computer Science, U. of Houston, May 1, 1997

Randomized parallel algorithms in computational geometry, October 10, 1997, School and Workshop on Randomized Algorithms in Sequential, Parallel, and Distributed Computing(RALCOM 97),Santorini Island, Greece.

Randomized parallel algorithms for routing and sorting October 11, 1997, Workshop on Randomized Algorithms in Sequential, Parallel, and Distributed Computing(RALCOM 97), Santorini Island, Greece.

Biomolecular Computation, CS Dept, Brandeis University, Nov 22, 1997.

Toward Autonomous Robots: Robust, Adaptive and Dynamic Motion, 19 NSF Design and Manufactoring Grantees Conference, Monterrey, Mexico, Jan 1998.

Paradigms for Biomolecular Computation, First International Conference on Unconventional Models of Computation, Auckland, New Zealand, January 1998. in Unconventional Models of Computation, edited by C.S. Calude, J. Casti, and M.J. Dinneen, Springer Publishers, January 1998, pp. 72-93.

Microflow Bio-Molecular Computation, 4th DIMACS Workshop on DNA Based Computers, University of Pennsylvania, June, 1998.

Nano-Robotics Motion Planning and Its Applications in Nanotechnology and Biomolecular Computing, NSF Design and Manufacturing Grantees Conference, Longbeach, CA, Jan 5-8, 1999.

Quantum Information Processing: Compression, Coding, and Related Computations, Plenary Talk, IEEE Data Compression Conference (DCC'99) Snowbird, Utah, March 29 - 31, 1999.

Experimental Progress in Computation by Self-Assembly of DNA Tilings, 5th DIMACS Workshop on DNA Based Computers, MIT, June 14, 1999.

DNA-based Cryptography, 5th DIMACS Workshop on DNA Based Computers, MIT, June 15, 1999.

Molectronics Software Architecture, DARPA Molelectronics Meeting, Ashburn, VI, July8-9, 1999.

DNA Cryptosystems, Workshop in Biomolecular Computation: Its Potential and Applications, NSF, Arlington VI, Oct 1, 1999, (abstract).

Collaborative Biomolecular Computation Projects in Europe, Japan, & the US, Workshop in Biomolecular Computation: Its Potential and Applications, NSF, Arlington VI, Oct 1, 1999, (abstract).

Nonparametric Multiscale Multimodal Model for Detection/Recognition, Multi-Modality Image Fusion Conference, Rochester, NY, Oct 7, 1999.

Software Architecture for a Molecular Computer, DARPA, Arlington VI, Nov 30, 1999.

Molectronics Software Architecture, Center Nanoscale Science and Technology, Rice University, Dec 3, 1999.

DNA Cryptosystems, Invited Talk, National Security Agency(NSA), Fort Meade, Maryland, Dec 13, 1999.

Associative Search in DNA Databases, Invited Talk, National Reconnaissance Office(NRO), Chantilly, VA, Dec 14, 1999.

Software Design for Molectronics, DARPA Molectronics Meeting, Arlington, VI, (Feb 26,2000).

An Efficient Approximation Algorithm for Weighted Region Optimal Path Problem, Workshop on Foundations of Robotics (WFR2000), Dartmouth, NH, (March 17, 2000).

Self-Assembled DNA Nanostructures, ADT Novel Technologies for Information: DNA/Biological SRC meeting, San Jose CA, (March 26, 2000).

Self-Assembled DNA Nanostructures, NSF workshop on nano-scale molecular based electronics, Arlington, VI, (May 18, 2000).

Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization, Invited Talk, Sixth International Meeting on DNA Based Computers (DNA6), Leiden, The Netherlands, (June 14, 2000)

Challenges and Applications for Self-Assembled DNA Nanostructures, Plenary Talk, Sixth International Meeting on DNA Based Computers (DNA6), Leiden, The Netherlands, (June 16, 2000)

Algorithmic self-assembly of DNA Tilings, City University of Hong Kong, Kowloon, Hong Kong, Oct 2, 2000.

Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization, City University of Hong Kong, Kowloon, Hong Kong, Oct 3, 2000.

On the Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth, City University of Hong Kong, Kowloon, Hong Kong, Oct 4, 2000.

A Biomolecular System for Ultra-Scale Associative Search, Invited Talk, National Reconnaissance Office(NRO), Chantilly, VA, November, 2000.

A Biomolecular System for Ultra-Scale Associative Search, Theory Seminar, CS Dept, Duke University, Durham, NC, November 16, 2000.

Experimental Demonstrations of Ultra-Scale Molecular Data Storage & Retrieval, Computation and Assembly, Information Science and Technology Colloquium Series Invited Talk, NASA Goddard, Maryland, Jan 17, 2001.

Programmable Assembly at the Molecular Scale: Self-Assembly of DNA Lattices, Plenary Talk, 2001 IEEE International Conference on Robotics and Automation (ICRA2001), Seoul, Korea, May 26, 2001

Molecular Computing via Programmed Self-Assembly of Patterned Molecules, Plenary Talk, 2001 Congress on Evolutionary Computation (CEC2001), Seoul, Korea, May 28, 2001

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.

Molecular Database Systems for Storage, Processing & Retrieval of Genetic Information & Material, Invited Talk, MiniSymposium "On Interfaces among Information Technology, sensing sciences, and Biological Systems", organized by Jagdish Chandra and Srikanta Kumar, SIAM Annual Meeting, San Diego, California, July 9-13, 2001

Movement Planning in the Presence of Flows, Workshop on Algorithms and Data Structures (WADS2001), Brown University, Providence, RI, August 8-10, (2001).

Computations & patterned structures via DNA self-assembly, Invited talk, Max Planck Institute for the Physics of Complex Systems, Dresden, Germany, August 20-24,2001.

DNA in NanoScience, Invited talk, Department of Computer Science Seminar Series, Duke University, Durham, NC, October 22, 2001

DNA Computation by Self-Assembly of DNA Nano-Scale Structures, Symposium on New Approaches toward Computing, Plenary Talk, National Academy of Arts and Sciences, Brussels, Belguim, November 9, 2001

Programmable DNA Lattices: Design, Synthesis and Applications, Invited Talk, Joint DARPA/NSF BioComp PI Meeting, Monterey Bay, CA. November, 27 - 30, 2001.

Self-Assembly of DNA Nano-Scale Structures for Computation, Invited Talk, Joint DARPA/NSF BioComp PI Meeting, Monterey Bay, CA. November, 27 - 30, 2001.

Self-Assembly of DNA Nano-Scale Structures, Invited Talk, DARPA ITO BioComp PI Meeting, Washington, DC, May 22-24, 2002.

DARPA Supplemental Project Overview, Invited Talk, Central Intelligence Agency(CIA), McLean, VI, Feb 12, 2002.

DNA Database Project Final Report Talk, National Reconnaissance Office(NRO), Chantilly, VA, Feb 12, 2002.

The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA, The 8th International Meeting on DNA Based Computers (DNA 8), Sapporo, Japan, June 10-13, 2002.

Molecular Assembly and Computation: From Theory to Experimental Demonstrations, Plenary Talk, 29th International Colloquium on Automata, Languages, and Programming(ICALP), Málaga, Spain (July 8, 2002).

Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations, invited talk, Alternative Computing Workshop, Mathematics in Nanoscale Science and Engineering, UCLA, September 30, 2002.

Programmable Molecular Self-Assembly: Theory and Experimental Demonstrations, distinguished lecture, Computer Science Department, John Hopkins University, Baltimore, Maryland, October 3, 2002.

DARPA Supplemental Project Overview Talk & Demonstration, MITRE Corporation, McLean, VI, October 4, 2002

Programmable DNA Lattices: Design, Synthesis and Applications, Invited Talk, Department of Computer Science, Boston University, Boston, MA, December 2, 2002.

Patterned Molecular Self-Assembly, Invited Talk, Joint DARPA/NSF BioComp PI Meeting, San Deigo, CA. December 7, 2002.

DARPA Supplemental Project Overview Talk & Demonstration, MITRE Corporation, McLean, VI, April 14, 2003

DNA Nanostructures: Patterning and Computation, Duke Nanostructure Workshop, Duke University, Durham, NC, May 5, 2003

Achieving Patterned Molecular Self-Assembly, Invited Talk, DARPA BioComp PI Meeting, Fort Lauderdale, Florida, May 15, 2003.

Directed Nucleation Assembly of Barcode Patterned DNA Lattices, DNA9 Conference, Madison, Wisconsin, June 2, 2003

Programmable DNA Lattices: Design, Synthesis and Applications, Keynote Talk, 5th Conference on Computational Biology and Genome Informatics (CBGI), 7th Joint Conference on Information Sciences (JCIS 2003), September 26-30,2003. Cary, NC, USA.

Compact Error-Resilient Computational DNA Tiling Assemblies, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.

Designs for Autonomous Unidirectional Walking DNA Devices, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.

Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion, Poster Presentation, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.

TileSoft: Sequence Optimization Software For Designing DNA Secondary Structures, Poster Presentation, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.

DNA-Based Nano-Engineering: DNA and its Enzymes as the Engines of Creation at the Molecular Scale, Plenary Invited Talk, Tenth International Meeting on DNA Based Computers (DNA10), Milano, Italy, June 7-10, 2004.

Design, Simulation, and Experimental Demonstration of Self-Assembled DNA Nanostructures and DNA Motors, Invited Talk, Computational Modeling and Simulation of Materials (CIMTEC) Conference, Acireale, Sicily, Italy, May 29-June 4, 2004.

Molecular Computations Using Self-Assembled DNA Nanostructures and Autonomous Motors, Invited Talk, Bio-inspired Computing Track, Unconventional Programming Paradigms (UPP), Mont Saint-Michel, France, September 15–17, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Korean Society for Bioinformatics Conference, Seoul, South Korea, November 5, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Nano System Institute (NSI_NCRC), Seoul National University, Seoul, South Korea, November 8, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Biomedical MEMS Laboratory, Korea Institute of Science and Technology (KIST), Seoul, South Korea, November 8, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Division of Nano Science, Ewha Woman’s University, Seoul, South Korea, November 9, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Department of BioSystems, Korean Advanced Institute of Science and Technology (KAIST), Taejon, South Korea, November 9, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, December 6, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Department of Chemistry, Tufts University, Medford, MA, December 7, 2004.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Workshop on Engineering a DNA World, Center for Biological Circuit Design, California Institute of Technology (Caltech), Pasadena, CA, January 6-8, 2005.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Departments of EE and Material Science, Seattle, WA, February 15, 2005.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Motors, Invited Talk, Frontiers 2005, Duke University, Durham, NC, May 4, 2005.

Complexity of Graph Self-Assembly in Accretive Systems and Self-Destructible Systems, Eleventh International Meeting on DNA Based Computers (DNA11), London, Ontario, June, 2005.

Design of Autonomous DNA Cellular Automata, Eleventh International Meeting on DNA Based Computers (DNA11), London, Ontario, June, 2005.

A Self-Assembly Model of Time-Dependent Glue Strength, Eleventh International Meeting on DNA Based Computers (DNA11), London, Ontario, June, 2005.

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Transport, Invited Talk, New York Academy of Science, New York, NY, Oct 11, 2005.

Design and Simulation of Self-Repairing DNA Lattices, 12th International Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006.

On Constructing Tile-less DNA Ribbons and Tubes, 12th International Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006.

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.

DNA Modeller: Modeling DNA based Molecular Systems, Poster Abstract, 12th International Meeting on DNA Computing (DNA 12), Seoul, Korea, June 5-9, 2006. (Poster Abstract).

Self-Assembled DNA Nanostructures for Molecular Scale Patterning, Computation and Transport, Invited Talk, 14th Workshop on Logic, Language, Information and Computation (WoLLIC'2007), Rio de Janeiro, Brazil, July 2-5, 2007.

DNA Self-assembly and Autonoumous R Molecular Robots. Invited Talk, presented at the Conference on Morphological Computation, Venice, Italy, March 26-28, 2007.

Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited talk, Fourteenth Workshop on Logic, Language, Information and Computation (WoLLIC'2007), Rio de Janeiro, Brazil, July 2-5, 2007.

Autonomous Programmable DNA Nanorobotic Devices Using DNAzymes, 13th International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8, 2007.

Activatable Tiles for Compact Error-Resilient Directional Assembly. 13th International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8, 2007.

Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited talk, Workshop on Algorithmic Bioprocesses, Lorentz Center, Leiden University, Leiden, Netherlands, Dec 3-7, 2007.

Autonomous Programmable Biomolecular Devices Using Self-Assembled DNA Nanostructures, invited talk, joint talk, University of Vancouver & Simon-Fraser University, Vancouver, BC, Jan 30, 2008.

Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation, Fourteenth International Meeting on DNA Based Computers (DNA14), Prague, Czech Republic (June, 2008).

Programmable DNA Nanodevices, NSF EMT 2008 Workshop, Princeton, NJ, July 24-25, 2008.

DNA Nanoassembly and DNA Nanodevices: Challenges, Applications and Research Progress, DNA-based nanotechnology: Construction, mechanics, and electronics, International Workshop, Dresden, Germany, (May 11 - 15, 2009).

DNA nanoassembly and DNA Nanodevices: Challenges, Applications and Research Progress, Future and Emerging Technologies (FET) seminar, European Commission, Brussels, Belgium, (May 20, 2009).

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).

The Tile Complexity of Linear Assemblies, 36th International Colloquium on Automata, Languages and Programming (ICALP 2009), Rhodes, Greece (July 5 - 12, 2009).

DNA Nanoassembly and DNA Nanodevices: Challenges, Applications and Research Progress, Computer Technology Institute, University of Patras, Patras, Greece (July 19, 2009).

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Wuhan University. Hubei, China, May 17, 2010.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Hefei University of Technology, Hefei, China, May 18, 2010.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Anhui University, Hefei, China, May 18, 2010.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, North China University of Technology, Beijing, China, May, 2010.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, College of Computer Science and Information Technology, Kunming Normal University, Kunming, China, June 1 2010.

The Theory of Self-Assembly, Tuitorial, International Conference on DNA Computing and Molecular Programming, (DNA16), Hong Kong University of Science and Technology. Hong Kong, China, June 14, 2010.

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.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Bioengineering Seminar Series, Hong Kong University of Science and Technology (HKUST), Department of Chemical and Biomolecular Engineering, Hong Kong, China, June 18. 2010.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Chinese University of Hong Kong, Hong Kong, China, June 18. 2010.

DNA-Based Assembly of Molecular-Scale Autonomous Devices for Sensing, Transport and Computation, Distinguished Lecture, North Eastern University, College of Computer Science, Boston, MA, November 18, 2010.

DNA-Based Molecular Devices, Keynote talk ICCABS, Orlando, FL, Feb. 3‐5, 2011.

DNA Self-Assembled Autonomous Devices for Programmed Molecular Computation, Transport, and Amplified Sensing, van Leeuwenhoek Lecture on BioScience, Leiden University, Leiden, Netherlands, May 26 2011.

Programmable Self-Assembled DNA-Based Autonomous Molecular Devices, Microsoft Research, Cambridge, June 2, 2011.

Programmable Self-Assembled DNA-Based Autonomous Molecular Devices, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford University, UK, June 7, 2011.

Localized Hybridization Circuits, International Conference on DNA Computing and Molecular Programming, (DNA17), California Institute of Technology, Pasadena, California, Sept 19-23, 2011.

Programmable Self-Assembled DNA-Based Autonomous Molecular Devices, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University (KAU), Jeddah, Saudi Arabia, December 4, 2011.

Development and Demonstration of an Energy-Efficient Cost-Effective Durable Solar Concentrator, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University (KAU), Jeddah, Saudi Arabia, December 11, 2011.

Development and Demonstration of an Energy-Efficient Cost-Effective Durable Solar Concentrator, King Abdullah City for Atomic and Renewable Energy (KACARE), Riyadh, Saudi Arabia, December 13, 2011

Programmable Self-Assembled DNA-Based Autonomous Molecular Devices, Effat University, Jeddah, Saudi Arabia, May 13, 2012.

Development and Demonstration of an Energy-Efficient Cost-Effective Durable Solar Concentrator for Powering Desalination, King Abdullah City for Atomic and Renewable Energy (KACARE), Riyadh, Saudi Arabia, Sept 16, 2012.

Development and Demonstration of an Energy-Efficient Cost-Effective Durable Solar Concentrator for Powering Desalination, Saudi Arabian Ministry of Water and Electricity, Riyadh, Saudi Arabia, Sept 16, 2012.

Keynote Talk, Future Challenges for DNA-Based Nano-Architectures and Nano-Devices, Workshop on Molecular Programming and Computing, Copenhagen, Denmark, May 2-4, 2013.

Keynote talk, 4th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami Beach Resort and Spa, Miami Beach, FL, June 2-4, 2014.

DNA Computing: Theory, Experiments & Software, Computability in Europe: Evolving Computability (CiE 2015), Bucharest, Romania, July 2, 2015.

Self-Assembled DNA Nanostructures, Computability in Europe: Evolving Computability (CiE 2015), Bucharest, Romania, July 3, 2015.

DNA-Based Programmable Autonomous Molecular Robotic Devices, Computability in Europe: Evolving Computability (CiE 2015), Bucharest, Romania, July 4, 2015.

DNA-Based Molecular Assembly and Computation, Dagstuhl Seminar 15402 Self-assembly and Self-organization in Computer Science and Biology, Sept 27-October 02, Dagstuhl Saarbrücken, Germany, July 2, 2015.

DNA-Based Programmable Autonomous Molecular Devices, MSE Department, Boise State University, Boise, ID, October 30, 2015.

DNA-Based Programmable Autonomous Molecular Devices, Chemistry Department, UNC Charlotte, NC, October 20, 2016.

DNA-Based Programmable Autonomous Molecular Devices, Chemistry Department, University of New Mexico, Albuquerque, May 3, 2017.

 

Books

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]

  1. 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]
  2. 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]
  3. John H. Reif, Logics for Probabilistic Programming. 12th Annual ACM Symposium on Theory of Computing, Los Angeles, CA, April 1980, pp. 8-13. [PDF]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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])
  12. John H. Reif and Paul G. Spirakis, Strong k-connectivity in Digraphs and Random Digraphs, Harvard University TR-25-81. [PDF]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. John H. Reif, Depth-First Search is Inherently Sequential. Information Processing Letters, Vol. 20, No. 5, June 12, 1985, pp. 229-234. [PDF]
  25. John H. Reif, A Topological Approach to Dynamic Graph Connectivity. Information Processing Letters, Vol. 25, No. 1, April 20, 1987, pp. 65-70. [PDF]
  26. Gautam Kar, Christos N. Nikolaou, and John H. Reif, Assigning Processes to Processors: A Fault-Tolerant Approach, 14th International Conference on Fault-Tolerant Computing, Kissimmee, FL, June 1984, pp. 306-309. [PDF]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. John H. Reif, Efficient VLSI Fault Simulation. Computers and Mathematics with Applications, Vol 25, No. 2, Jan. 1993, pp. 15-32. [PDF]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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])
  37. 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] [PDF] 
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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].
  44. 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]
  45. 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]
  46. 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]
  47. 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.
  48. 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]
  49. 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]
  50. 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]
  51. John H. Reif and Steve R. Tate, Approximate Kinodynamic Planning Using L2-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]
  52. 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]
  53. Micheal Karr, S. Krishnan, John H. Reif, Derivation of the Ellipsoid Algorithm, Duke University Technical Report CS-1991-17, (1990). [PDF]
  54. 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]
  55. Selman Azhar and John H. Reif, Crypto-Complexity Based Models of Efficiency in Capital Markets, 1994. [PDF]
  56. 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]
  57. 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]
  58. 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]
  59. 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]
  60. 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]
  61. S. Krishnan and John H. Reif, Towards Randomized Strongly Polynomial Algorithms for Linear Programming, Duke University Technical Report CS-1991-18. [PDF]
  62. 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]
  63. Tassos Markas and John H. Reif, Fast Computations of Vector Quantization Algorithms. NASA Technical Report TR-91-58, 1991.
  64. 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]
  65. 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]
  66. 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]
  67. 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]
  68. 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]
  69. 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]
  70. 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]
  71. Tassos Markas and John H. Reif, Memory-Shared Parallel Architectures for Vector Quantization Algorithms, 1992. Picture Coding Symposium, Lusanne Switzerland, March, 1993.
  72. 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]
  73. 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]
  74. 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]
  75. 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]
  76. 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]
  77. 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]
  78. 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]
  79. 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]
  80. 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]
  81. 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]
  82. 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]
  83. 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]
  84. 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]
  85. 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]
  86. 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]
  87. 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]
  88. Richard Barakat and John H. Reif, Diffraction Realization of an Optical Expander, (1993). [PDF]
  89. 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]
  90. 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]
  91. 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]
  92. 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]
  93. 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]
  94. 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]
  95. Victor Y. Pan and John H. Reif, Generalized Compact Multi-grid, Computers Math Applications, Volume 25, Number 9, pp. 3-5, May 1993. [PDF]

138.       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]

  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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. Proceedings 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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])
  15. 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]
  16. 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]
  17. John H. Reif and Doreen Yen, Derivation of Parallel Graph Connectivity Algorithms via Stream Contraction, Duke University Technical Report, 1989. [PDF]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. John H. Reif and Sukhendu Chakraborty, Efficient and Exact Quantum Compression, Journal of Information and Computation, Vol. 205, pp. 967-981 (2007). [PDF] [PDF]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. 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]
  46. 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]
  47. Dage Liu, John H. Reif, Thomas H. LaBean, DNA Nanotubes, Construction and Characterization of Filaments Composed of TX-tile Lattice. 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. 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]
  48. John H. Reif, DNA Computation - Perspectives: Successes and Challenges, Science, 296: 478-479, April 19, 2002. PubMed PMID: 11964464. [PostScript][PDF]
  49. 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]
  50. 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]
  51. 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]
  52. 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]
  53. 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]
  54. 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]
  55. 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]
  56. 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].
  57. Tinging Jiang and John H. Reif, Efficient Methods for Stochastic Simulations of Biomolecular Motions, submitted for publication, July, 2003. [PDF]
  58. 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]
  59. 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]
  60. 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]
  61. 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]
  62. 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]
  63. 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]
  64. 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]
  65. 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]
  66. 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 BanČtre, Pascal Fradet, Jean-Louis Giavitto, Olivier Michel, Lecture Notes for Computer Science (LNCS) 3566, pp. 173-187, (2005). [PDF] Talk: [PDF] [PPT]
  67. 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]
  68. 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]
  69. 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]
  70. 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]
  71. 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].
  72. 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].
  73. 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]
  74. 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]
  75. 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].
  76. 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]
  77. 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]
  78. 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-Reconřgurable Robots, International Journal of Computational Geometry & Applications (IJCGA), Vol. 21, No. 2, pp. 131-155 (2011). DOI: 10.1142/S0218195911003585 [PDF]
  79. 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]
  80. 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]
  81. 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. Published in 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 (2010). Full Paper: [PDF]
  82. 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]
  83. 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]
  84. John H. Reif and Sam Slee, Optimal Kinodynamic Motion Planning for Self-Reconřgurable Robots Between Arbitrary 2D Conřgurations, Robotics: Science and Systems Conference, Georgia Institute of Technology, Atlanta, GA, June 27-30, 2007. [PDF]
  85. 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].
  86. 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]
  87. 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].
  88. 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.
  89. 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]
  90. 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]
  91. 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)
  92. 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).
  93. 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]
  94. 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]
  95. 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].
  96. John Reif, Harish Chandran, Nikhil Gopalkrishnan, and Thomas LaBean, Self-assembled DNA Nanostructures and DNA Devices. Invited Chapter 14, pages 299-328, Nanofabrication Handbook (Edited by Stefano Cabrini and Satoshi Kawata), Taylor and Francis Group, New York, NY, ISBN13:9781420090529, ISBN10: 1420090526 (2012). [PDF] [PDF]
  97. 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]
  98. 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]
  99. Sam Slee and John H. Reif, Robomotion: 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]
  100. 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]
  101. 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]
  102. John H. Reif, Perspectives: Biochemistry: Scaling Up DNA Computation, Science, Vol. 332, pp. 1156-1157 (June 3, 2011). DOI: 10.1126/science.1208068 [PDF]
  103. 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]
  104. 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]
  105. 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]
  106. 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
  107. 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]
  108. Sudhanshu Garg, Nikhil Gopalkrishnan, Harish Chandran, and John Reif, Self-Replicating DNA Nanostructures: Autocatalytic Nanodevices derived from Catalytic Nanodevices, Poster Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013. Published as Sudhanshu Garg, Nikhil Gopalkrishnan, Harish Chandran, Tianqi Song, Hieu Bui, Reem Mokhtar, and John Reif, An Enzyme-free Autocatalytic Self-Replicating DNA Nanodevice, invited chapter in Soft Nanomaterials (Edited by Ye Zhang), Published by World Scientific Co., to appear (2018).

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

248. Hieu Bui, Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, and John Reif, Local Hybridization Chain-Reactions on the Surface of DNA Origami, Poster Abstract, FNANO 2013, Snowbird, Utah, April 15-18, 2013. Also Design DNA Hairpin Systems for Localized DNA Hybridization Reactions, poster abstract, FNANO2015, p169, April 2015. Expanded paper rewritten for journal publication as: Hieu Bui, Sudhanshu Garg, Reem Mokhtar, Harish Chandran, Vincent Miao and John Reif, Design and Analysis of Localized DNA Hybridization Chain Reactions, Small (2017), 1602983. DOI: 10.1002/smll.201602983 [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, (2012). [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, (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 Garg, Tianqi Song, Reem Mokhtar, Hieu Bui, and John Reif, Asynchronous Time-Responsive DNA Circuits for Universal Computation, Submitted for publication (2017).

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

259. Daniel Fu, Shalin Shah, Tianqi Song and John H Reif, DNA-based Analog Computing, Chapter in book: “Synthetic Biology”, (Edited by ‪Jeff Braman), published by Springer, to appear (2018). [PDF[PDF

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

261. Xin Song, Abeer Eshra, Chris Dwyer1, and John Reif, Renewable DNA Seesaw Logic Circuits Enabled by Photoregulation of Toehold-Mediated Strand Displacement, RSC Advances, Volume 7, Issue 45, pp. 28130-28144 (March, 2017). DOI: 10.1039/C7RA02607B [PDF] (supplementary: [PDF])

262. Sudhanshu Garg, Hieu Bui, Abeer Eshra, Shalin Shah and John H Reif, Nucleic Acid Hairpins: A Robust and Powerful Motif for Molecular Devices, Chapter in book: “Soft Nanomaterials” (Edited by Ye Zhang), World Scientific, to appear (June 2017).

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

264. Hieu Bui, Tianqi Song, and John H Reif, Localized DNA Computation, Chapter in book: “From Parallel to Emergent Computing” (Edited by Andrew Adamatzky), CRC Press, to appear (2018).