John H. Reif
Student and Postdoc Supervision:
- Current and Prior Graduate Students and Postdocs
- Further Information about my previous graduate students can be found in my vita and at the computer science genealogy.
Current Graduate Students
(Ph.D. candidates)
- Rajiv Nagipogu, Tentative Ph.D. thesis: “Adaptive molecular
computing systems”. Projected Date of Graduation: Fall 2025.
Current Postdoctoral
Assistants:
Xin Song: Research topic: “DNA computation and COVID-19 detection RT-LAMP protocols”, 2021-current.
Daniel (Dan) Fu: Research topics: “DNA Computation on Cell Membranes” and “Casting Metallic Nanoparticles in Multi-layered Encapsulating 3D DNA Nanostructure”. Jan. 2022-current.
Prior Postdoctoral
Assistants:
Xiaoju Guan: (jointly supervised with Hao Yan), (May, 2003 - 2005)
Sang Jung
Ahn: (jointly supervised with Thom
LaBean), (January, 2003 - December, 2004) (jointly supervised with Thom
LaBean), 2003- December, 2004. (Currently Research Scientist, Korea Research
Institute of Standards and Science, Daejeon, South Korea)
Dage Liu: (July 1, 2001 - June, 2004) Postdoc 2001-2004 (Currently Material
Scientist, NY. Previously Research Associate, Department of Chemistry, North
Carolina State University)
Hao Yan: (July 1, 2001 - July 1, 2002) Postdoc 2001-2002 and Research
Assistant Professor, CS Dept, Duke University, 2002-2004 (now Professor,
Chemistry and Biochemistry Department, Arizona State University since August
2004)
Thom
LaBean: (July 1, 1998 - July 1, 2001) (currently
Associate Professor, Materials Science & Engineering, North Carolina State
University)
Sandeep
K. S. Gupta: (1995) Postdoc 1995 (currently Professor,
Department of Computer Science and Engineering, Ira A. Fulton School of
Engineering, Arizona State University, Tempe, AZ 85287-5406).
Steven Tate: (July 1, 1991 - July 1, 1993) (currently Professor and Chairman,
Department of Computer Science, University of North Carolina at Greensboro,
Greensboro, NC)
Hillel Gazit: (1989 - 1991) (currently Software Consultant, San Francisco,
CA)
Prior PhD advisees:
Dan Fu: Ph.D. thesis: “Design
Optimization of Encapsulating 3D DNA Nanostructures with Curvature and
Multi-layers”. Date of Graduation: Dec. 2022.
Xin Song: Ph.D. thesis: “Novel
Techniques and Applications in Molecular Computing, Data Storage, Diagnostics,
and Fabrication”. Date of Graduation:
Fall 2021.
Shalin
Shah: Tentative Ph.D. thesis: “Families of DNA Devices for Super-Resolution Imaging”. Date of
Graduation: Spring 2020.
Abeer Eshra: Ph.D. thesis: “Computing
Machine Implementation using DNA - Reusable DNA Circuits”. Menoufia University Department of
Computer Science and Engineering. Date of Graduation: Spring 2019. (Currently
Postdoc with Damian Woods at at Maynooth University, Ireland)
Tianqi
Song: Ph.D. thesis:
“Theory and Experiments in DNA Analog Computation”. Date of Graduation: Summer
2018. (Currently Postdoc at Cal Tech).
Hieu Bui: Ph.D. thesis: “Localized DNA
Computation”. Date of Graduation: Spring 2017. (Currently National Research
Council Postdoctoral Research Fellowship at the U.S. Naval Research Laboratory
(NRL)).
Sudhanshu
Garg: Ph.D. thesis: “Programming
Molecular Devices using Nucleic Acid Hairpins”. Date of Graduation: May 2016.
(Currently Research Scientist at LinkedIn, Sunnyvale, California).
Harish Chandran: (2007 – Dec 2012) Duke
University Ph.D. thesis: "Molecular Robotic Devices". Date of
Graduation: Fall 2012. (Currently Research
Scientist at Google Corporation, Google Research, Redwood
Shores, California.)
Nikhil
Gopalkrishnan: (2006 - Dec 2012) Duke University Ph.D. thesis: "DNA
Self-Assembly". Date of Graduation: Fall 2012. (Prior Postdoctoral
Assistant, Department of Systems Biology, Harvard Medical
School, Cambridge, MA in the laboratory of Peng Yin. Now Director of Research at 3EO Health, Inc.)
Samuel
Slee: (August 30, 2004 – Dec 1,
2010) Duke University Ph.D. thesis: "Developing Scalable Abilities
for Self-Reconfigurable Robots". (Currently Research Scientist at Google
Research, Redwood Shores, California)
Urmi
Majumder: (August 30, 2004 – March 30, 2009) (also co-advised by Thomas
LaBean), Duke University Ph.D. thesis: “Molecular Computing with DNA Self-Assembly”. Slides: [PPT] [PDF] (Currently Project Leader at Oracle, Washington D.C)
Sudheer Sahu: (January, 2003 - December, 2007) Ph.D. thesis: "DNA
based self-assembly and nanorobotics: Theory and Experiments", December,
2007[PDF] Slides: [PPT] [PDF]. (Currently Research Scientist, Microsoft Live Search, in Redmond, Washington)
Peng Yin: (January, 2002 - May,
2005) 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 Full Professor, Department of Systems Biology, Harvard Medical School, Cambridge, MA. Also Founder, 3EO Health,
Inc.).
Zhung(Robert)
Sun: (2000-2003) 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 94043.)
Deganit
Armon: (1997) Duke University Ph.D. Thesis
"Dynamic Data Structures for Randomized Algorithms that use
Sampling", 1997 [PDF] [abstract]. (Adjunct Professor,
Department of Computer Science & Engineering, University of California,
Riverside and Project Manager at Advatech Pacific, Inc.)
Shenfeng
Chen: (1996) Duke University Ph.D. Thesis
"Algorithmic Applications of Data Compression Techniques",
1996 [PDF] [abstract]. (Currently Technical
Manager of a startup company in China).
Hongyan Wang: (1996) Duke University Ph.D. Thesis "Approximate and
Adaptive Algorithms for Some Optimal Motion-Planning Problems,"
1996 [PDF] [abstract] (Currently Adjunct
Faculty member of University of Maryland University College, Asia. Previously
senior software engineer with Parametric Technology Corporation in
Massachusetts and with Canopus, Ltd. in Kobe, Japan.).
Zhiyong Li: (1996) Duke University
Ph.D. Thesis "Computational Models and Program Synthesis”, [PDF] [abstract] (Currently Research
Scientist, Sun Microsystems, California)
Akitoshi Yoshida: (1994) 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).
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.)
Salman Azhar: (1993) (J. P. Duke Fellow), 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.)
Tassos
Markas: (1993) Duke University Ph.D. Thesis
"Data Compression: Algorithms and Architectures", 1993, Univ.
Microfilms Int. 9405986 [abstract]. (Currently 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.)
Lars Nyland: (1991) 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).
Steve
Tate: (1991) 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)
Sandeep Sen: (1989) 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 and Chairman, Department of Computer Science & Engineering,
Indian Institute of Technology, Delhi, India.)
Sanguthevar
Rajasekaran: (1988) 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
Spirakis: (December 1981) Harvard University Ph.D.
Thesis "Probabilistic Algorithms", Dec. 1981, University Microfilms
International No. 8216206. (Currently Professor, University of Liverpool and
Professor, Department of Computer Engineering & Informatics and
Director Computer Technology Institute, Patris, Greece.)
Prior Master's
Advisees:
Ming Yang: M.S,
thesis: “Social DNA Nanorobots”. Graduation: Fall 2021.
Reem
Mokhtar: M.S,
thesis: “Modeling DNA Nanodevices Using Graph Rewrite Systems”. Date of
Graduation: Spring 2019.
Ahsan
Muhammad: (2010-2012) Duke University Masters thesis:
“Cluster Quantum Computing”. Date of Masters Degree Graduation: Spring 2012.
Guo Bo: (1999-2001) Duke University
Master Thesis "Computing by DNA Self-Assembly". Oct, 2001 (currently
Research Scientist, Mitsubishi Electric, Japan).
Yuan Guangwei: (1998 - 2000) Duke University
Master Thesis "Simulation of DNA Self-Assembly", Fall 2000 (Currently
Research Scientist, China).
Christopher Butler: (1998 - 2000) Duke
University Master Thesis "Simulations of Molectronics architectures".
Xavier Berni: (1998-2000) Duke University
MS Thesis "DNA tagging", May 2000. (Currently Computer Scientist
Consultant, S. Carolina).
Ashish Gehani: (1995 - 1997)
Undergraduate Students Supervised:
Philip Klein:
(1984) Graduated Harvard
University Undergraduate Thesis (awarded Thomas T. Hoopes prize)
"Stacktracking: Parallel Acceptance of Deterministic Context-Free
Languages", 1984 (currently Full Professor, Brown University).
Please let me know if you have any problems with these web pages.