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Donald Lab Alumni

Former Doctoral Students (PhD Advisor)

1. Ivelin Georgiev, PhD, 2009.
   • Dissertation: "Novel Algorithms for Computational Protein Design with Applications to Enzyme Redesign and Small-Molecule Inhibitor Design."
   • Now a computational biologist in the Structural Biology Section of the Vaccine Research Center, National Institute for Allergy and Infectious Diseases (NIAID).
2. Tony Yan, PhD, 2008.
   • Dissertation: "Geometric Methods for NMR Structure Determination of Symmetric Homo-oligomers."
   • Now a postdoc in the lab of Dr. Pei Zhou, Department of Biochemistry, Duke University Medical Center.
3. Igor Paprotny, PhD, 2008.
   • Dissertation: "Design, Fabrication and Parallel Control of Distributed Systems of Stress-engineered MEMS Microrobots for Microassembly."
   • Now a postdoc at the Berkeley Sensor and Actuator Center (BSAC), U.C. Berkeley.
4. Craig McGray, PhD, 2005.
   • Dissertation: "Design, Fabrication, Control, and Programming of MEMS Micro-Robots."
   • Now a researcher at the MicroElectroMechanical Systems (MEMS) Project, Semiconductor Electronics Division, Electronics and Electrical Engineering Laboratory, NIST.
5. Ryan Lilien, PhD, 2004, MD 2006.
   • Dissertation: "Novel Algorithms for Structural Molecular Biology and Proteomics."
   • Now an Assistant Professor at the University of Toronto with a joint appointment between Computer Science and the UT Medical School.
6. Chris Langmead, PhD 2003.
   • Dissertation: "Molecular Replacement for Nuclear Magnetic Resonance: Application to NMR Resonance Assignment and Protein Structure Determination."
   • Now an Assistant Professor of Computer Science at Carnegie Mellon University.
7. Karl Böhringer, PhD 1997.
   • Dissertation: "Programmable Force Fields for Distributed Manipulation, and their Implementation Using Micro-fabricated Actuator Arrays."
   • Now a full Professor of Electrical Engineering at the University of Washington, in Seattle, and director of the UW MEMS Lab.
8. Jim Jennings, PhD 1997.
   • Dissertation: "Distributed Manipulation for Mobile Robots."
   • First post-PhD job: Assistant Professor at Tulane.
   • Currently at IBM.
9. Russell Brown, PhD 1995.
   • Dissertation: "Localization, Mapmaking, and Distributed Manipulation with Flexible, Robust Mobile Robots."
   • First post-PhD job: Senior Member of the Technical Staff at Sandia National Laboratories.
10. Amy Briggs, PhD 1994.
    • Dissertation: "Efficient Geometric Algorithms for Robot Sensing and Control."
    • Now full Professor and Chair of Computer Science at Middlebury.
11. Patrick Xavier, PhD 1992.
    • Dissertation: "Provably-Good Approximation Algorithms for Optimal Kinodynamic Robot Plans."
    • Now a Senior Member of the Technical Staff at Sandia National Laboratories.

Former PostDocs

1. Nanjiang Shu (2008-2009).
2. Serkan Apaydin (2004-2008).
   • Now on Faculty of Engineering and Sciences at Sabanci University in Istanbul, Turkey.
3. Ryan Lilien, (2004-2006).
   See above.
4. Rahul Ray (2004-2006).
   • Now an Assistant Professor at IIT-Madras.
   • Research in Computational Biology and Chemistry.
5. Ram Mettu (2002-2005).
   • Now an Assistant Professor at the University of Massachusetts, Amherst.
   • Research in Computational Biology and Chemistry.
6. Lincong Wang (2001-2005)
   • Now a senior scientist at Boehringer Ingelheim Pharmaceuticals
7. Chris Bailey-Kellogg (1999-2001).
   • First job: Assistant Professor of Computer Science at Purdue University.
   • Currently Associate Professor (with tenure) at Dartmouth.
   • Research in Computational Biology and Chemistry.
8. Jack Kelley (1999-2001).
   • Now at the University of Michigan.
   • Research in Computational Biology and Chemistry.
9. Daniela Rus (1992-94).
   • Now Professor of Computer Science at MIT (EECS Department).
   • 2002: Prof. Daniela Rus is named a John D. and Catherine T. MacArthur Fellow
10. Jonathan Rees (1991-92).
    • Currently a Fellow with Science Commons and a Research Affiliate of the Mathematics and Computation group in the MIT Computer Science and Artificial Intelligence Laboratory.
    • Program Mobile Robots in Scheme!
11. Dinesh Pai (1988-91).
    • First job: Assistant Professor of Computer Science at UBC.
    • Now Professor of Computer Science at U.B.C. and Rutgers.
    • Dinesh's research in three areas of computational robotics: architectures for robot locomotion on rough terrain, simulation of physical systems in virtual environments, and assembly systems verification

Selected Former MS Students

1. Haoning Fu, 2004.
   • Thesis: "An Algorithm For Determining Backbone Structures of Protein Turns and Loops Using Multiple Residual Dipolar Couplings in Two Media."
   • Haoning is now a senior scientist at Medical Media Systems, NH.

Former Undergraduate Students

1. Tim Danford, 2001
   • Senior Thesis: "Cleavage-Based Algorithms for Experiment Planning and Data Analysis in Stable Isotope Assisted Structural Mass Spectrometry."
   • Currently a Ph.D. Student in EECS at MIT.
2. Alik Widge, 1999
   • Undergraduate student author of The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J Comput Biol. 2000;7(3-4):537-58. .
   • Senior Honors thesis: "A Method for Automatic Determination of Protein Secondary Structure from Sparse Unassigned NMR Data."
   • Winner, John G. Kemeny Computing Prize (First Prize).
   • Currently an M.D.-Ph.D. Candidate at Carnegie Mellon University/University of Pittsburgh.
3. Ryan McCullough, 1999
   • Currently a Ph.D. Student in EECS at MIT.
4. Mona Sridharan
   • Undergraduate student author of Allosteric Inhibition of the Protein-Protein Interaction between the Leukemia-Associated Proteins Runx1 and CBFbeta. Chem Biol. 2007 Oct;14(10):1186-97.
   • Currently a Ph.D. Student in Molecular Biology and Biophysics at UCSF.
5. Susanna Leng, 1998
   • Senior Honors thesis: "Data-Directed Conformational Search: Using Global Optimization to Determine Large Protein Structure from Sparse NMR Data."
6. Nikolay Stoyanov, Dartmouth, B.S. 1998 (Chemistry)
   • Currently a Ph.D. Student in Chemistry at MIT.

Former Rotation Students

1. Parawee (Nicky) Lekprasert, 2007
2. Christopher Williams, 2007-8