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John H. Reif

Software: Microsoft OfficeSoftware: Microsoft Office

Student and Postdoc Supervision:

- 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)

-   Reem Mokhtar: Ph.D. thesis topic: “DNA Transformers”. Projected Date of Graduation: Spring 2019.

-   Tianqi Song: Ph.D. thesis topic: “DNA-Based Analog Computation”. Projected Date of Graduation: Summer 2018.

-  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.

 

Prior PhD advisees:

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

 Sudhanshu GargPh.D. thesis topic: “Programming Molecular Devices using Nucleic Acid Hairpins”. Date of Graduation: May 2016.

 Harish Chandran: (2007 – Dec 2012) Duke University Ph.D. thesis topic: "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 topic: "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.)

Samuel Slee: (August 30, 2004 – Dec 1, 2010) Duke University Ph.D. thesis topic: "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 topic: “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 Assistant ProfessorDepartment of Systems Biology, Harvard Medical School, Cambridge, MA).

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.)

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)

Master's Advisees:

Ahsan Muhammad: (2010-2012) Duke University Masters thesis topic: “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).

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