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ORCIDJohn H. Reif
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- affiliation: Duke University, Department of Computer Science
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2020 – today
- 2021
[j102]Xin Song
, Shalin Shah, John H. Reif:
Multidimensional data organization and random access in large-scale DNA storage systems. Theor. Comput. Sci. 894: 190-202 (2021)- 2020
- [j101]Shalin Shah, Abhishek Kumar Dubey, John H. Reif:
ExTemp: A computational and image-processing suite for extracting temporal barcodes. J. Open Source Softw. 5(46): 2026 (2020)
2010 – 2019
- 2019
- [c144]Shalin Shah, Tianqi Song, Xin Song, Ming Yang, John H. Reif:
Implementing Arbitrary CRNs Using Strand Displacing Polymerase. DNA 2019: 21-36 - [p4]Hieu Bui, John H. Reif:
Localized DNA Computation. From Parallel to Emergent Computing 2019: 407-424 - 2018
- [c143]Shalin Shah, John H. Reif:
Temporal DNA Barcodes: A Time-Based Approach for Single-Molecule Imaging. DNA 2018: 71-86 - 2017
- [i1]Abeer Eshra, Shalin Shah, John H. Reif:
DNA Hairpin Gate: A Renewable DNA Seesaw Motif Using Hairpins. CoRR abs/1704.06371 (2017) - 2016
- [j100]Akhilesh Tyagi, John H. Reif:
Energy Complexity of Optical Computations. Int. J. Unconv. Comput. 12(5-6): 393-412 (2016) - [j99]Urmi Majumder, Sudhanshu Garg, Thomas H. LaBean, John H. Reif:
Activatable tiles for compact robust programmable molecular assembly and other applications. Nat. Comput. 15(4): 611-634 (2016) - 2015
- [j98]Wadee Alhalabi, John H. 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. Comput. Hum. Behav. 51: 857-866 (2015) - 2014
- [p3]Hieu Bui, Harish Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan, Reem Mokhtar, John H. Reif, Tianqi Song:
DNA Computing. Computing Handbook, 3rd ed. (1) 2014: 25: 1-42 - 2013
- [j97]Harish Chandran, Nikhil Gopalkrishnan, John H. Reif:
Tile Complexity of Approximate Squares. Algorithmica 66(1): 1-17 (2013) - 2012
- [j96]John H. Reif:
Local Parallel Biomolecular Computation. Int. J. Unconv. Comput. 8(5-6): 459-507 (2012) - [j95]Harish Chandran, Nikhil Gopalkrishnan, John H. Reif:
Tile Complexity of Linear Assemblies. SIAM J. Comput. 41(4): 1051-1073 (2012) - [p2]John H. Reif, Thomas H. LaBean:
Engineering Natural Computation by Autonomous DNA-Based Biomolecular Devices. Handbook of Natural Computing 2012: 1319-1353 - 2011
- [j94]John H. Reif, Sam Slee:
Asymptotically Optimal Kinodynamic Motion Planning for a Class of Modular Self-Reconfigurable Robots. Int. J. Comput. Geom. Appl. 21(2): 131-155 (2011) - [j93]Urmi Majumder, John H. Reif:
Design of a biomolecular device that executes process algebra. Nat. Comput. 10(1): 447-466 (2011) - [j92]John H. Reif, Sudheer Sahu, Peng Yin:
Complexity of graph self-assembly in accretive systems and self-destructible systems. Theor. Comput. Sci. 412(17): 1592-1605 (2011) - [c142]Harish Chandran, Nikhil Gopalkrishnan, Andrew Phillips, John H. Reif:
Localized Hybridization Circuits. DNA 2011: 64-83 - [c141]John H. Reif:
Keynote: DNA-based molecular devices. ICCABS 2011: 3 - 2010
- [j91]Sudheer Sahu, John H. Reif:
Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-Assembly. Algorithmica 56(4): 480-504 (2010) - [j90]John H. Reif, Urmi Majumder:
Isothermal reactivating Whiplash PCR for locally programmable molecular computation. Nat. Comput. 9(1): 183-206 (2010) - [c140]Nikhil Gopalkrishnan, Harish Chandran, John H. Reif:
High-Fidelity DNA Hybridization Using Programmable Molecular DNA Devices. DNA 2010: 59-70 - [c139]Sam Slee, John H. Reif:
Robomotion: Scalable, Physically Stable Locomotion for Self-reconfigurable Robots. WAFR 2010: 121-137
2000 – 2009
- 2009
- [j89]John H. Reif, Sudheer Sahu:
Autonomous programmable DNA nanorobotic devices using DNAzymes. Theor. Comput. Sci. 410(15): 1428-1439 (2009) - [c138]Sudheer Sahu, Peng Yin, John H. Reif:
A Self-assembly Model of Time-Dependent Glue Strength. Algorithmic Bioprocesses 2009: 185-204 - [c137]Urmi Majumder, John H. Reif:
Design of a Biomolecular Device That Executes Process Algebra. DNA 2009: 97-105 - [c136]Harish Chandran, Nikhil Gopalkrishnan, John H. Reif:
The Tile Complexity of Linear Assemblies. ICALP (1) 2009: 235-253 - [r1]John H. Reif:
Mechanical Computing: The Computational Complexity of Physical Devices. Encyclopedia of Complexity and Systems Science 2009: 5466-5482 - 2008
- [j88]John H. Reif, Simon Kasif, Deepak Sherlekar:
Formula dissection: A parallel algorithm for constraint satisfaction. Comput. Math. Appl. 55(6): 1170-1177 (2008) - [c135]John H. Reif, Urmi Majumder:
Isothermal Reactivating Whiplash PCR for Locally Programmable Molecular Computation. DNA 2008: 41-56 - [c134]Urmi Majumder, John H. Reif:
A Framework for Designing Novel Magnetic Tiles Capable of Complex Self-assemblies. UC 2008: 129-145 - 2007
- [j87]John H. Reif, Thomas H. LaBean:
Autonomous programmable biomolecular devices using self-assembled DNA nanostructures. Commun. ACM 50(9): 46-53 (2007) - [j86]John H. Reif, Sukhendu Chakraborty:
Efficient and exact quantum compression. Inf. Comput. 205(7): 967-981 (2007) - [j85]Zheng Sun, John H. Reif:
On Robotic Optimal Path Planning in Polygonal Regions With Pseudo-Euclidean Metrics. IEEE Trans. Syst. Man Cybern. Part B 37(4): 925-936 (2007) - [c133]Urmi Majumder, Thomas H. LaBean, John H. Reif:
Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications. DNA 2007: 15-25 - [c132]John H. Reif, Sudheer Sahu:
Autonomous Programmable Nanorobotic Devices Using DNAzymes. DNA 2007: 66-78 - [c131]Ashish Gehani, John H. Reif:
Super-Resolution Video Analysis for Forensic Investigations. IFIP Int. Conf. Digital Forensics 2007: 281-299 - [c130]John H. Reif, Sam Slee:
Optimal Kinodynamic Motion Planning for 2D Reconfiguration of Self-Reconfigurable Robots. Robotics: Science and Systems 2007 - [c129]John H. Reif, Thomas H. LaBean:
Autonomous Programmable Biomolecular Devices Using Self-assembled DNA Nanostructures. WoLLIC 2007: 297-306 - [e5]Sanguthevar Rajasekaran, John H. Reif:
Handbook of Parallel Computing - Models, Algorithms and Applications. Chapman and Hall/CRC 2007, ISBN 978-1-58488-623-5 [contents] - 2006
- [j84]Zheng Sun, John H. Reif:
On finding approximate optimal paths in weighted regions. J. Algorithms 58(1): 1-32 (2006) - [j83]John H. Reif, Zheng Sun:
On boundaries of highly visible spaces and applications. Theor. Comput. Sci. 354(3): 379-390 (2006) - [c128]Urmi Majumder, Sudheer Sahu, Thomas H. LaBean, John H. Reif:
Design and Simulation of Self-repairing DNA Lattices. DNA 2006: 195-214 - [c127]Sudheer Sahu, John H. Reif:
Capabilities and Limits of Compact Error Resilience Methods for Algorithmic Self-assembly in Two and Three Dimensions. DNA 2006: 223-238 - [c126]Sudheer Sahu, Bei Wang, John H. Reif:
A Framework for Modeling DNA Based Molecular Systems. DNA 2006: 250-265 - [c125]John H. Reif, Sudheer Sahu, Peng Yin:
Compact Error-Resilient Computational DNA Tilings. Nanotechnology: Science and Computation 2006: 79-103 - [c124]John H. Reif, Sam Slee:
Asymptotically Optimal Kinodynamic Motion Planning for Self-reconfigurable Robots. WAFR 2006: 457-472 - 2005
- [j82]John H. Reif:
Efficient parallel factorization and solution of structured and unstructured linear systems. J. Comput. Syst. Sci. 71(1): 86-143 (2005) - [j81]Zheng Sun, John H. Reif:
On finding energy-minimizing paths on terrains. IEEE Trans. Robotics 21(1): 102-114 (2005) - [j80]Zheng Sun, David Hsu, Tingting Jiang, Hanna Kurniawati, John H. Reif:
Narrow passage sampling for probabilistic roadmap planning. IEEE Trans. Robotics 21(6): 1105-1115 (2005) - [c123]John H. Reif, Sudheer Sahu, Peng Yin:
Complexity of Graph Self-assembly in Accretive Systems and Self-destructible Systems. DNA 2005: 257-274 - [c122]Sudheer Sahu, Peng Yin, John H. Reif:
A Self-assembly Model of Time-Dependent Glue Strength. DNA 2005: 290-304 - [c121]Peng Yin, Sudheer Sahu, Andrew J. Turberfield, John H. Reif:
Design of Autonomous DNA Cellular Automata. DNA 2005: 399-416 - 2004
- [j79]John H. Reif, Zheng Sun:
Movement Planning in the Presence of Flows. Algorithmica 39(2): 127-153 (2004) - [c120]Ashish Gehani, Thomas H. LaBean, John H. Reif:
DNA-based Cryptography. Aspects of Molecular Computing 2004: 167-188 - [c119]John H. Reif, Sudheer Sahu, Peng Yin:
Compact Error-Resilient Computational DNA Tiling Assemblies. DNA 2004: 293-307 - [c118]Peng Yin, Andrew J. Turberfield, John H. Reif:
Designs of Autonomous Unidirectional Walking DNA Devices. DNA 2004: 410-425 - [c117]Peng Yin, Andrew J. Turberfield, Sudheer Sahu, John H. Reif:
Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion. DNA 2004: 426-444 - [c116]John H. Reif, Thomas H. LaBean, Sudheer Sahu, Hao Yan, Peng Yin:
Design, Simulation, and Experimental Demonstration of Self-assembled DNA Nanostructures and Motors. UPP 2004: 173-187 - [e4]Junghuei Chen, John H. Reif:
DNA Computing, 9th International Workshop on DNA Based Computers, DNA9, Madison, WI, USA, June 1-3, 2003, revised Papers. Lecture Notes in Computer Science 2943, Springer 2004, ISBN 3-540-20930-1 [contents] - 2003
- [j78]John H. Reif:
Guest Editor's Foreword. J. Comput. Syst. Sci. 67(2): 211 (2003) - [j77]John H. Reif:
The design of autonomous DNA nano-mechanical devices: Walking and rolling DNA. Nat. Comput. 2(4): 439-461 (2003) - [j76]John H. Reif, Zheng Sun:
On Frictional Mechanical Systems and Their Computational Power. SIAM J. Comput. 32(6): 1449-1474 (2003) - [c115]John H. Reif, William L. Scherlis:
Deriving Effcient Graph Algorithms. Verification: Theory and Practice 2003: 645-681 - [c114]Zheng Sun, John H. Reif:
Adaptive and Compact Discretization for Weighted Region Optimal Path Finding. FCT 2003: 258-270 - [c113]John H. Reif, Zheng Sun:
On Boundaries of Highly Visible Spaces and Applications. FCT 2003: 271-283 - [c112]Zheng Sun, John H. Reif:
On energy-minimizing paths on terrains for a mobile robot. ICRA 2003: 3782-3788 - [c111]David Hsu, Tingting Jiang, John H. Reif, Zheng Sun:
The bridge test for sampling narrow passages with probabilistic roadmap planners. ICRA 2003: 4420-4426 - 2002
- [j75]John H. Reif:
DNA lattices: A method for molecular-scale patterning and computation. Comput. Sci. Eng. 4(1): 32-41 (2002) - [j74]John H. Reif:
The Emerging Discipline of Biomolecular Computation in the US. New Gener. Comput. 20(3): 217-236 (2002) - [c110]Dage Liu, John H. Reif, Thomas H. LaBean:
DNA Nanotubes: Construction and Characterization of Filaments Composed of TX-tile Lattice. DNA 2002: 10-21 - [c109]John H. Reif:
The Design of Autonomous DNA Nanomechanical Devices: Walking and Rolling DNA. DNA 2002: 22-37 - [c108]John H. Reif:
Molecular Assembly and Computation: From Theory to Experimental Demonstrations. ICALP 2002: 1-21 - [e3]John H. Reif:
Proceedings on 34th Annual ACM Symposium on Theory of Computing, May 19-21, 2002, Montréal, Québec, Canada. ACM 2002, ISBN 1-58113-495-9 [contents] - 2001
- [j73]John H. Reif:
Efficient Parallel Computation of the Characteristic Polynomial of a Sparse, Separable Matrix. Algorithmica 29(3): 487-510 (2001) - [j72]John H. Reif, James A. Storer:
Optimal encoding of non-stationary sources. Inf. Sci. 135(1-2): 87-105 (2001) - [j71]John H. Reif:
Parallel Output-Sensitive Algorithms for Combinatorial and Linear Algebra Problems. J. Comput. Syst. Sci. 62(3): 398-412 (2001) - [c107]John H. Reif, Thomas H. LaBean, Michael Pirrung, Vipul S. Rana, Bo Guo, Carl Kingsford, Gene S. Wickham:
Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability. DNA 2001: 231-247 - [c106]John H. Reif, Thomas H. LaBean, Nadrian C. Seeman:
Programmable Assembly at the Molecular Scale: Self-Assembly of DNA Lattices (Invited Paper). ICRA 2001: 966-971 - [c105]Zheng Sun, John H. Reif:
BUSHWHACK: An Approximation Algorithm for Minimal Paths through Pseudo-Euclidean Spaces. ISAAC 2001: 160-171 - [c104]John H. Reif, Zheng Sun:
Movement Planning in the Presence of Flows. WADS 2001: 450-461 - 2000
- [j70]John H. Reif:
Fast Spatial Decomposition and Closest Pair Computation for Limited Precision Input. Algorithmica 28(3): 271-287 (2000) - [j69]John H. Reif:
On the Impossibility of Interaction-Free Quantum Sensing for Small I/O Bandwidth. Inf. Comput. 163(1): 103-122 (2000) - [j68]John H. Reif, Hongyan Wang:
Nonuniform Discretization for Kinodynamic Motion Planning and its Applications. SIAM J. Comput. 30(1): 161-190 (2000) - [c103]John H. Reif, Thomas H. LaBean:
Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization. DNA Computing 2000: 145-172 - [c102]John H. Reif, Thomas H. LaBean, Nadrian C. Seeman:
Challenges and Applications for Self-Assembled DNA Nanostructures. DNA Computing 2000: 173-198 - [p1]John H. Reif, Sandeep Sen:
Parallel Computational Geometry: An Approach using Randomization. Handbook of Computational Geometry 2000: 765-828
1990 – 1999
- 1999
- [j67]John H. Reif:
Parallel Biomolecular Computation: Models and Simulations. Algorithmica 25(2-3): 142-175 (1999) - [j66]John H. Reif, Hongyan Wang:
Social potential fields: A distributed behavioral control for autonomous robots. Robotics Auton. Syst. 27(3): 171-194 (1999) - [j65]John H. Reif:
Approximate Complex Polynomial Evaluation in Near Constant Work Per Point. SIAM J. Comput. 28(6): 2059-2089 (1999) - [j64]Zhiyong Li, John H. Reif, Sandeep K. S. Gupta:
Synthesizing Efficient Out-of-Core Programs for Block Recursive Algorithms Using Block-Cyclic Data Distributions. IEEE Trans. Parallel Distributed Syst. 10(3): 297-315 (1999) - [c101]Thomas H. LaBean, Erik Winfree, John H. Reif:
Experimental progress in computation by self-assembly of DNA tilings. DNA Based Computers 1999: 123-140 - [c100]Ashish Gehani, Thomas H. LaBean, John H. Reif:
DNA-based cryptography. DNA Based Computers 1999: 233-249 - 1998
- [j63]Hillel Gazit, John H. Reif:
A Randomized Parallel Algorithm for Planar Graph Isomorphism. J. Algorithms 28(2): 290-314 (1998) - [c99]John H. Reif, James A. Storer:
Optimal Lossless Compression of a Class of Dynamic Sources. Data Compression Conference 1998: 501-510 - [c98]John H. Reif:
Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation. FSTTCS 1998: 102-121 - 1997
- [j62]Yijie Han, Victor Y. Pan, John H. Reif:
Efficient Parallel Algorithms for Computing All Pair Shortest Paths in Directed Graphs. Algorithmica 17(4): 399-415 (1997) - [j61]John H. Reif, Stephen R. Tate:
On Dynamic Algorithms for Algebraic Problems. J. Algorithms 22(2): 347-371 (1997) - [j60]Erol Gelenbe, Nestor A. Schmajuk, John Staddon, John H. Reif:
Autonomous search by robots and animals: A survey. Robotics Auton. Syst. 22(1): 23-34 (1997) - [j59]James A. Storer, John H. Reif:
Error-Resilient Optimal Data Compression. SIAM J. Comput. 26(4): 934-949 (1997) - [c97]James A. Storer, John H. Reif:
Low-Cost Prevention of Error Propagation for Data Compression with Dynamic Dictionaries. Data Compression Conference 1997: 171-180 - [c96]Sefeng Chen, John H. Reif:
Fast and Compact Volume Rendering in the Compressed Transform Domain. Data Compression Conference 1997: 271-280 - [c95]John H. Reif:
Local parallel biomolecular computation. DNA Based Computers 1997: 217-254 - [c94]John H. Reif:
Approximate Complex Polynomial Evaluation in Near Constant Work Per Point. STOC 1997: 30-39 - 1996
- [j58]Ming-Yang Kao, John H. Reif, Stephen R. Tate:
Searching in an Unknown Environment: An Optimal Randomized Algorithm for the Cow-Path Problem. Inf. Comput. 131(1): 63-79 (1996) - [j57]C. Andrew Neff, John H. Reif:
An Efficient Algorithm for the Complex Roots Problem. J. Complex. 12(2): 81-115 (1996) - [j56]Zhiyong Li, Peter Mills, John H. Reif:
Models and Resource Metrics for Parallel and Distributed Computation. Parallel Algorithms Appl. 8(1): 35-59 (1996) - [c93]Shenfeng Chen, John H. Reif:
Efficient Lossless Compression of Trees and Graphs. Data Compression Conference 1996: 428 - [c92]Lars S. Nyland, Jan F. Prins, Allen Goldberg, Peter Mills, John H. Reif, Robert A. Wagner:
A Refinement Methodology for Developing Data-Parallel Applications. Euro-Par, Vol. I 1996: 145-150 - [c91]Zhiyong Li, John H. Reif, Sandeep K. S. Gupta:
Synthesizing Efficient Out-of-Core Programs for Block Recursive Algorithms Using Block-Cyclic Data Distributions. ICPP, Vol. 2 1996: 142-149 - 1995
- [j55]Ramamohan Paturi, Sanguthevar Rajasekaran, John H. Reif:
The Light Bulb Problem. Inf. Comput. 117(2): 187-192 (1995) - [c90]Shenfeng Chen, John H. Reif:
Fast Pattern Matching for Entropy Bounded Text. Data Compression Conference 1995: 282-291 - [c89]John H. Reif:
Efficient Parallel Solution of Sparse Eigenvalue and Eigenvector Problems. FOCS 1995: 123-132 - [c88]Zhiyong Li, Peter Mills, John H. Reif:
Models and resource metrics for parallel and distributed computation. HICSS (2) 1995: 51-60 - [c87]Sotiris E. Nikoletseas, John H. Reif, Paul G. Spirakis, Moti Yung:
Stochastic Graphs Have Short Memory: Fully Dynamic Connectivity in Poly-Log Expected Time. ICALP 1995: 159-170 - [c86]Sandeep K. S. Gupta, Zhiyong Li, John H. Reif:
Generating Efficient Programs for Two-Level Memories from Tensor-products. Parallel and Distributed Computing and Systems 1995: 510-513 - [c85]John H. Reif:
Parallel Molecular Computation. SPAA 1995: 213-223 - [c84]John H. Reif:
Work efficient parallel solution of Toeplitz systems and polynomial GCD. STOC 1995: 751-761 - [c83]Akitoshi Yoshida, Jannick P. Rolland, John H. Reif:
Design and applications of a high-resolution insert head-mounted-display. VRAIS 1995: 84-93 - 1994
- [j54]Joseph Cheriyan, John H. Reif:
Directed s-t Numberings, Rubber Bands, and Testing Digraph k-Vertex Connectivity. Comb. 14(4): 435-451 (1994) - [j53]John H. Reif, J. D. Tygar, Akitoshi Yoshida:
Computability and Complexity of Ray Tracing. Discret. Comput. Geom. 11: 265-287 (1994) - [j52]John H. Reif, Micha Sharir:
Motion Planning in the Presence of Moving Obstacles. J. ACM 41(4): 764-790 (1994) - [j51]James A. Storer, John H. Reif:
Shortest Paths in the Plane with Polygonal Obstacles. J. ACM 41(5): 982-1012 (1994) - [j50]John H. Reif, James A. Storer:
A Single-Exponential Upper Bound for Finding Shortest Paths in Three Dimensions. J. ACM 41(5): 1013-1019 (1994) - [j49]Vijaya Ramachandran, John H. Reif:
Planarity Testing in Parallel. J. Comput. Syst. Sci. 49(3): 517-561 (1994) - [j48]Akitoshi Yoshida, John H. Reif:
Optical computing techniques for image/video compression. Proc. IEEE 82(6): 948-954 (1994) - [j47]