Donald Lab Alumni
Former Doctoral Students (Ph.D. Advisor)
Ram Mettu, Bruce Donald, and Ryan Lilien at ISMB '08
Daniela Rus and Karl Böhringer
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.
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.
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.
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)
Faisal Reza, Ph.D., 2010.
- Ivelin Georgiev, Ph.D., 2009.
Yan, Ph.D., 2008.
"Geometric Methods for NMR Structure Determination of Symmetric
- First job: postdoc in the lab of Dr. Pei Zhou, Department of
Biochemistry, Duke University Medical Center.
- Igor Paprotny,
- Dissertation: "Design, Fabrication and Parallel Control of Distributed Systems of Stress-engineered MEMS Microrobots for
- First job: A postdoc at the Berkeley Sensor and Actuator Center (BSAC),
- Dr. Paprotny is an assistant professor at the
University of Illinois starting Sept. 2013.
- Craig McGray, Ph.D., 2005.
- 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.
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.
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.
- Jim Jennings, Ph.D. 1997.
Dissertation: "Distributed Manipulation for Mobile
- First post-Ph.D. job: Assistant Professor
- Currently at IBM.
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
- Amy Briggs, Ph.D.
- Dissertation: "Efficient Geometric Algorithms for Robot Sensing and
- Now full Professor and Chair of Computer
Science at Middlebury.
- 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.
Now at the University of
Illinois at Urbana-Champaign.
Now at Boston University.
- Serkan Apaydin (2004-2008).
- Ryan Lilien, (2004-2006).
- Rahul Ray
- Ram Mettu
Lincong Wang (2001-2005)
- First job: a senior scientist at Boehringer
- 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.
Jack Kelley (1999-2001).
- Daniela Rus (1992-94).
- Jonathan Rees (1991-92).
- 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
- Haoning Fu, 2004.
- Thesis: "An Algorithm For Determining Backbone Structures of
Protein Turns and Loops Using Multiple Residual Dipolar Couplings in
- Haoning is now a senior scientist at
Medical Media Systems, NH.
Former Undergraduate Students
- Jonathan (JJ) Jou, 2008
Currently a Ph.D. Student, Computer Science, Duke University.
- Nicholas Patrick, 2009
Winner of Goldwater Scholarship in science, mathematics and %engineering for the 2008-09 academic year.
- 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).
- Alik Widge, 1999
- Ryan McCullough, 1999
- Currently a Ph.D. Student in EECS at MIT.
- Mona Sridharan
- Susanna Leng, 1998
- Senior Honors thesis: "Data-Directed Conformational Search: Using
Global Optimization to Determine Large Protein Structure from Sparse
- 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.
- Ryan Muraglia CBB 2013
- Jae Cho Biochemistry 2013
- Adriana Hertel-Wulf Biochemistry 2013
- Swati Jain** Computational
Biology & Bioinformatics (CBB)
- Mark Hallen* Biochemistry
- Dan Keedy*** Biochemistry. Now at UCSF.
- Kyle Roberts* CBB
- Cheng-Yu Chen* Biochemistry
- Ying Zhao, Biochemistry, 2011
- Yu (Tina) Jiang, CMB, 2011
- Yazan Alwarawrah, Pharmacology and
Cancer Biology, 2011
- Lindsay Deis, Biochemistry, 2011
- Ka Suen Leung, Biochemistry, 2010-11
- Chetan Rupakheti+, CBB, 2010
- Robert Gillespie, Biochemistry, 2009
- Bradley Hintze, Biochemistry, 2009
- Desmond Moore, Biochemistry, 2009
- Christopher Williams, Biochemistry, 2007-8
- Parawee (Nicky) Lekprasert, CBB 2007