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Donald Lab Alumni

Former Doctoral Students (Ph.D. Advisor)

1. Cheng-Yu Chen, Ph.D., 2013.
   • Dissertation: "Studies on Redesign and Solution Structure Determination of Nonribosomal Peptide Synthetases and Redox Regulation of Phosphatases," Department of Biochemistry, School of Medicine, Duke University Medical Center.
2. Inho Yoon, Ph.D., 2013.
   • Dissertation: "Developing In Vivo Intra-cellular Neuronal Recording System for Freely Behaving Small Animals," Department of Electrical and Computer Engineering, Pratt School of Engineering, Duke University.
3. Chittu Tripathy, Ph.D., 2012.
   • Dissertation: "Novel Algorithms for Protein Structure Determination from Sparse NMR Data," Department of Computer Science, Duke University.

   Dr. Tripathy will be a teaching faculty at Duke University starting 6/2012.

4. Michael Zeng, Ph.D., 2011.
   • Dissertation: "Novel Algorithms for Automated NMR Assignment and Protein Structure Determination," Department of Computer Science, Duke University.

   Dr. Zeng will be an Assistant Professor at Tshingua University (IIIS) starting 9/2012.

5. Faisal Reza, Ph.D., 2010.
   • Dissertation: "Computational Molecular Engineering of Nucleic Acid Binding Proteins and Enzymes." Department of Biomedical Engineering and Program in Computational Biology and Bioinformatics, Duke University.

     Dr. Reza is currently a postdoc in the laboratory of Peter M. Glazer, Department of Therapeutic Radiology, Yale University School of Medicine.

6. Ivelin Georgiev, Ph.D., 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 Bioinformatics Section of the Vaccine Research Center, National Institute for Allergy and Infectious Diseases (NIAID).
7. Tony Yan, Ph.D., 2008.
   • Dissertation: "Geometric Methods for NMR Structure Determination of Symmetric Homo-oligomers."
   • First job: postdoc in the lab of Dr. Pei Zhou, Department of Biochemistry, Duke University Medical Center.
8. Igor Paprotny, Ph.D., 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.
9. Craig McGray, Ph.D., 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.
10. Ryan Lilien, Ph.D., 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.
11. Chris Langmead, Ph.D. 2003.
    • Dissertation: "Molecular Replacement for Nuclear Magnetic Resonance: Application to NMR Resonance Assignment and Protein Structure Determination."
    • Now an Associate Professor of Computer Science at Carnegie Mellon University.
12. Karl Böhringer, Ph.D. 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.
13. Jim Jennings, Ph.D. 1997.
    • Dissertation: "Distributed Manipulation for Mobile Robots."
    • First post-Ph.D. job: Assistant Professor at Tulane.
    • Currently at IBM.
14. Russell Brown, Ph.D. 1995.
    • Dissertation: "Localization, Mapmaking, and Distributed Manipulation with Flexible, Robust Mobile Robots."
    • First post-Ph.D. job: Senior Member of the Technical Staff at Sandia National Laboratories.
15. Amy Briggs, Ph.D. 1994.
    • Dissertation: "Efficient Geometric Algorithms for Robot Sensing and Control."
    • Now full Professor and Chair of Computer Science at Middlebury.
16. Patrick Xavier, Ph.D. 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. Anna Yershova (2008-10).
   Now at the University of Illinois at Urbana-Champaign.
2. Nanjiang Shu (2008-2009).
   Now at Boston University.
3. Serkan Apaydin (2004-2008).
   • Now on Faculty of Engineering and Sciences at Sabanci University in Istanbul, Turkey.
4. Ryan Lilien, (2004-2006).
   See above.
5. Rahul Ray (2004-2006).
   • First job: Assistant Professor at IIT-Madras.
   • Research in Computational Biology and Chemistry.
6. Ram Mettu (2002-2005).
   • Now an Assistant Professor at the University of Massachusetts, Amherst.
   • Research in Computational Biology and Chemistry.
7. Lincong Wang (2001-2005)
   • First job: a senior scientist at Boehringer Ingelheim Pharmaceuticals
   • Now a full Professor at the Joint Center for Systems Biology of Jilin University and the University of Georgia, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, P. R. China.
8. 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.
9. Jack Kelley (1999-2001).
   • Now at the University of Michigan.
   • Research in Computational Biology and Chemistry.
10. 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
11. 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!
12. 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. Jonathan (JJ) Jou, 2008

Currently a Ph.D. Student, Computer Science, Duke University.
2. Nicholas Patrick, 2009

Winner of Goldwater Scholarship in science, mathematics and %engineering for the 2008-09 academic year.
3. Tim Danford, 2001
   • Senior Thesis: "Cleavage-Based Algorithms for Experiment Planning and Data Analysis in Stable Isotope Assisted Structural Mass Spectrometry."
   • Ph.D. in EECS (MIT, 2009).
4. 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.
5. Ryan McCullough, 1999
   • Currently a Ph.D. Student in EECS at MIT.
6. 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.
7. Susanna Leng, 1998
   • Senior Honors thesis: "Data-Directed Conformational Search: Using Global Optimization to Determine Large Protein Structure from Sparse NMR Data."
8. Nikolay Stoyanov, Dartmouth, B.S. 1998 (Chemistry)
   • Currently a Ph.D. Student in Chemistry at MIT.

Former Rotation Students

*Joined D-lab as Ph.D. Student
**Joined as joint R-Lab/D-Lab Ph.D. student.
***Joined R-Lab, collaborates with D-Lab.

1. Swati Jain** Computational Biology & Bioinformatics (CBB)
2. Mark Hallen* Biochemistry
3. Dan Keedy*** Biochemistry
4. Kyle Roberts* CBB
5. Cheng-Yu Chen* Biochemistry
6. Ying Zhao, Biochemistry, 2011
7. Yu (Tina) Jiang, CMB, 2011
8. Yazan Alwarawrah, Pharmacology and Cancer Biology, 2011
9. Lindsay Deis, Biochemistry, 2011
10. Ka Suen Leung, Biochemistry, 2010-11
11. Chetan Rupakheti, CBB, 2010
12. Robert Gillespie, Biochemistry, 2009
13. Bradley Hintze, Biochemistry, 2009
14. Desmond Moore, Biochemistry, 2009
15. Christopher Williams, Biochemistry, 2007-8
16. Parawee (Nicky) Lekprasert, CBB 2007