Donald Lab Graphic

Donald Lab Alumni

Former Doctoral Students (Ph.D. Advisor)

Ram Mettu, Bruce Donald, and Ryan Lilien at ISMB '08


Daniela Rus and Karl Böhringer

  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.
    • Dr. Chen is now a postdoc in the NMR lab of Prof. Jim Prestegard, University of Georgia.
  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.
    • Dr. Yoon is now a researcher at Intel.
  3. Chittu Tripathy, Ph.D., 2012.
    • Dissertation: "Novel Algorithms for Protein Structure Determination from Sparse NMR Data," Department of Computer Science, Duke University.
    • First job: Dr. Tripathy was teaching faculty at Duke University 2012-2013.
    • Now a researcher at Amazon.
  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 is 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.
  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."
    • First job: A postdoc at the Berkeley Sensor and Actuator Center (BSAC), U.C. Berkeley.
    • Dr. Paprotny is an assistant professor at the University of Illinois starting Sept. 2013.
  9. Craig McGray, Ph.D., 2005.
  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, and John M. Fluke Distinguished Chair of 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. Stuart Endo-Streeter (2009-2013)
    • Now a Research Associate at UNC, Chapel Hill.
  2. Chittu Tripathy (2012-2013).
  3. Michael Zeng (2011-12).
  4. Anna Yershova (2008-10).
    • Now at the University of Illinois at Urbana-Champaign.
  5. Nanjiang Shu (2008-2009).
    • Now at Boston University.
  6. Serkan Apaydin (2004-2008).
  7. Ryan Lilien, (2004-2006).
  8. Rahul Ray (2004-2006).
  9. Ram Mettu (2002-2005).
    • First job: Assistant Professor at the University of Massachusetts, Amherst.
    • Now an Associate Professor at Tulane University.
    • Research in Computational Biology and Chemistry.
  10. 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.
  11. Chris Bailey-Kellogg (1999-2001).
  12. Jack Kelley (1999-2001).
  13. Daniela Rus (1992-94).
  14. Jonathan Rees (1991-92).
  15. 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
  5. Ryan McCullough, 1999
    • Currently a Ph.D. Student in EECS at MIT.
  6. Mona Sridharan
  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.
+Joined Beratan Lab, collaborates with D-Lab.
  1. Ryan Muraglia CBB 2013
  2. Jae Cho Biochemistry 2013
  3. Adriana Hertel-Wulf Biochemistry 2013
  4. Swati Jain** Computational Biology & Bioinformatics (CBB)
  5. Mark Hallen* Biochemistry
  6. Dan Keedy*** Biochemistry. Now at UCSF.
  7. Kyle Roberts* CBB
  8. Cheng-Yu Chen* Biochemistry
  9. Ying Zhao, Biochemistry, 2011
  10. Yu (Tina) Jiang, CMB, 2011
  11. Yazan Alwarawrah, Pharmacology and Cancer Biology, 2011
  12. Lindsay Deis, Biochemistry, 2011
  13. Ka Suen Leung, Biochemistry, 2010-11
  14. Chetan Rupakheti+, CBB, 2010
  15. Robert Gillespie, Biochemistry, 2009
  16. Bradley Hintze, Biochemistry, 2009
  17. Desmond Moore, Biochemistry, 2009
  18. Christopher Williams, Biochemistry, 2007-8
  19. Parawee (Nicky) Lekprasert, CBB 2007