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Donald Lab Alumni

Former Doctoral Students (Ph.D. Advisor)

You can also view a list of Bruce Donald's Completed Ph.D. Students at the Mathematics Genealogy Project

Alumni: If I left you off the list, send me an email! It wasn't intentional.

1. Jonathan Dragon Jou, Ph.D., 2018.
   
   • Dissertation: "Novel Computational Protein Design Algorithms with Sparse Residue Interaction Graphs, Ensembles, and Mathematical Guarantees, and their Application to Antibody Design." Department of Computer Science, Duke University.
   • Dr. Jou is currently a Postdoc at Duke University.
2. Adegoke Ojewole, Ph.D., 2018.
   
   • Dissertation: "Efficient New Computational Protein Design Algorithms, with Applications to Drug Resistance Prediction and HIV Antibody Design." Program in Computational Biology, Duke University Medical Center.
   • Dr. Ojewole is currently a Vertex Fellow at Vertex Pharmaceuticals.
3. Mark Hallen, Ph.D., 2016.
   
   Research
   Web Page
   • Dissertation: "Protein and drug design algorithms using improved biophysical modeling," Department of Computer Science, Duke University.
   • Dr. Hallen is an Assistant Professor at Toyota Technological Institute at the University of Chicago.
4. Swati Jain, Ph.D., 2015.
   
   • Dissertation: "RNA 3D Structure Analysis and Validation, and Design Algorithms for Proteins and RNA," Program in Computational Biology, Duke University Medical Center.
   • Dr. Jain is currently a postdoc in the laboratory of Tamar Schlick, Department of Chemistry, NYU Medical School.
5. Pablo Gainza, Ph.D., 2015.
   Web page
   • Dissertation: "Computational Protein Design with Ensembles, Flexibility and Mathematical Guarantees, and its Application to Drug Resistance Prediction, and Antibody Design," Department of Computer Science, Duke University.
   • Dr. Gainza is now a research associate (postdoc) in the Laboratory of Protein Design and Immunoengineering, EPFL, Lausanne, Switzerland.
6. John MacMaster, Ph.D., 2015.
   
   • Dissertation: "Solution-Phase Nuclear Magnetic Resonance Studies of a Nonribosomal Peptide Synthetase Adenylation Domain, of a Bacterial Glycosyltransferase, and the Rational Design of Inhibitors and Mutants of Glycosyltlransferases," Duke University.
7. Kyle Roberts, Ph.D., 2014.
   Research
   • Dissertation: "Novel Computational Protein Design Algorithms with Applications to Cystic Fibrosis and HIV," Program in Computational Biology, Duke University Medical Center.
   • Dr. Roberts is now a protein design research scientist at Arzeda Corp., Inc.
8. Jeffrey Martin, Ph.D., 2014.
   Research; Webpage
   • Dissertation: "Geometric Algorithms for Protein Structure Determination Using Measurements From NMR Spectroscopy," Department of Computer Science, Duke University.
   • Dr. Martin is now a research scientist in Durham and a postdoc at Duke.
   • First job: was a researcher at Scalable Algorithmics, LLC.
9. 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.
10. 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.
11. 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.
12. 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.
13. 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.
14. Ivelin Georgiev, Ph.D., 2009.
    • Dissertation: "Novel Algorithms for Computational Protein Design with Applications to Enzyme Redesign and Small-Molecule Inhibitor Design." Department of Computer Science, Duke University.
    • First job: computational biologist in the Structural Bioinformatics Section of the Vaccine Research Center, National Institute for Allergy and Infectious Diseases (NIAID).

      Dr. Georgiev was co-head of the Structural Bioinformatics Section at the Vaccine Research Center, NIAID, NIH.

    • Currently a tenure-track assistant professor at Vanderbilt University Medical Center.
15. Tony Yan, Ph.D., 2008.
    • Dissertation: "Geometric Methods for NMR Structure Determination of Symmetric Homo-oligomers." Department of Computer Science.
    • First job: postdoc in the lab of Dr. Pei Zhou, Department of Biochemistry, Duke University Medical Center.
16. Igor Paprotny, Ph.D., 2008.
    • Dissertation: "Design, Fabrication and Parallel Control of Distributed Systems of Stress-engineered MEMS Microrobots for Microassembly."
    Department of Computer Science.
    • 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.
17. Craig McGray, Ph.D., 2005.
    • Dissertation: "Design, Fabrication, Control, and Programming of MEMS Micro-Robots." Department of Computer Science.
    • Now a researcher at the MicroElectroMechanical Systems (MEMS) Project, Semiconductor Electronics Division, Electronics and Electrical Engineering Laboratory, NIST.
18. Ryan Lilien, Ph.D., 2004, MD 2006.
    • Dissertation: "Novel Algorithms for Structural Molecular Biology and Proteomics." Department of Computer Science and Dartmouth Medical School.
    • Now an Assistant Professor at the University of Toronto with a joint appointment between Computer Science and the UT Medical School.
19. Chris Langmead, Ph.D. 2003.
    • Dissertation: "Molecular Replacement for Nuclear Magnetic Resonance: Application to NMR Resonance Assignment and Protein Structure Determination." Department of Computer Science.
    • Now an Associate Professor (with tenure) of Computer Science at Carnegie Mellon University.
20. Karl Böhringer, Ph.D. 1997.
    • Dissertation: "Programmable Force Fields for Distributed Manipulation, and their Implementation Using Micro-fabricated Actuator Arrays." Department of Computer Science, Cornell University.
    • 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.
21. Jim Jennings, Ph.D. 1997.
    • Dissertation: "Distributed Manipulation for Mobile Robots." Department of Computer Science, Cornell University
    • First post-Ph.D. job: Assistant Professor at Tulane.
    • Currently at IBM.
22. Russell Brown, Ph.D. 1995.
    • Dissertation: "Localization, Mapmaking, and Distributed Manipulation with Flexible, Robust Mobile Robots." Department of Computer Science, Cornell University
    • First post-Ph.D. job: Senior Member of the Technical Staff at Sandia National Laboratories.
23. Amy Briggs, Ph.D. 1994.
    • Dissertation: "Efficient Geometric Algorithms for Robot Sensing and Control." Department of Computer Science, Cornell University
    • Now full Professor and Chair of Computer Science at Middlebury.
24. Patrick Xavier, Ph.D. 1992.
    • Dissertation: "Provably-Good Approximation Algorithms for Optimal Kinodynamic Robot Plans." Department of Computer Science, Cornell University
    • Now a Senior Member of the Technical Staff at Sandia National Laboratories.

Former PostDocs

1. Pablo Gainza (2015)
   Web page
   See above.
2. Kyle Roberts (2014-2015).
   See above.
3. Stuart Endo-Streeter (2009-2013)
   • Now a Research Associate at UNC, Chapel Hill.
4. Chittu Tripathy (2012-2013).
   See above.
5. Michael Zeng (2011-12).
   See above.
6. Anna Yershova (2008-10).
   • Now at the University of Illinois at Urbana-Champaign.
7. Nanjiang Shu (2008-2009).
   • Now at Boston University.
8. Serkan Apaydin (2004-2008).
   • Now on Faculty of Engineering and Sciences at Sabanci University in Istanbul, Turkey.
9. Ryan Lilien, (2004-2006).
   See above.
10. Rahul Ray (2004-2006).
    • First job: Assistant Professor at IIT-Madras.
    • Research in Computational Biology and Chemistry.
11. Ram Mettu (2002-2005).
    • First job: Assistant Professor at the University of Massachusetts, Amherst.
    • Now an Associate Professor (with tenure) at Tulane University.
    • Research in Computational Biology and Chemistry.
12. 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.
13. Chris Bailey-Kellogg (1999-2001).
    • First job: Assistant Professor of Computer Science at Purdue University.
    • Currently Full Professor at Dartmouth.
    • Research in Computational Biology and Chemistry.
14. Jack Kelley (1999-2001).
    • Now at the University of Michigan.
    • Research in Computational Biology and Chemistry.
15. Daniela Rus (1992-94).
    • Now Professor of Computer Science at MIT (EECS Department), and Director of the MIT CSAIL (Computer Science and Artificial Intelligence Laboratory).
    • 2002: Prof. Daniela Rus is named a John D. and Catherine T. MacArthur Fellow
16. 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!
17. 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. Yang Qi, M.S. 2016.
   • Thesis: "On Provable Algorithms for Determination of Continuous Protein Interdomain Motions from Residual Dipolar Couplings."
2. Jeff Martin, M.S. 2009.
   • Thesis: "Algorithms for Structure Determination of Symmetric Proteins from Nuclear Magnetic Resonance Data."
3. Haoning Fu, M.S. 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. Francois Thelot, Undergraduate Thesis Student.
   Senior Thesis: A maximum entropy-based approach for the description of the conformational ensemble of calmodulin from paramagnetic NMR , Department of Mathematics, Duke University, B.S. (2016).
   • Currently a Ph.D. student in Biophysics at Havard University.
2. Hunter Nisonoff, Undergraduate Thesis Student.
   Senior Thesis: Efficient Partition Function Estimation in Computational Protein Design: Probabilistic Guarantees and Characterization of a Novel Algorithm, Department of Mathematics, Duke University, B.S. (2015).
   Research
3. Tyler Nisonoff, Undergraduate Student (2014)
4. David Zhou, Undergraduate Student (2014)
5. Nina Sun, HHMI Research Fellow (2014)
   Research
6. Jonathan (JJ) Jou, 2008
   • Currently a Ph.D. Student, Computer Science, Duke University.
7. Nicholas Patrick, 2009
   • Winner of Goldwater Scholarship in science, mathematics and engineering for the 2008-09 academic year.
8. 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).
9. 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.
10. Ryan McCullough, 1999
    • Currently a Ph.D. Student in EECS at MIT.
11. 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.
12. Susanna Leng, 1998
    • Senior Honors thesis: "Data-Directed Conformational Search: Using Global Optimization to Determine Large Protein Structure from Sparse NMR Data."
13. 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. Chia-Chieh Chu Biochemistry 2015.
2. Ryan Muraglia CBB 2013
3. Jae Cho Biochemistry 2013
4. Adriana Hertel-Wulf Biochemistry 2013
5. Swati Jain** Computational Biology & Bioinformatics (CBB)
6. Mark Hallen* Biochemistry
7. Dan Keedy*** Biochemistry. Now at UCSF.
8. Kyle Roberts* CBB
9. Cheng-Yu Chen* Biochemistry
10. Ying Zhao, Biochemistry, 2011
11. Yu (Tina) Jiang, CMB, 2011
12. Yazan Alwarawrah, Pharmacology and Cancer Biology, 2011
13. Lindsay Deis, Biochemistry, 2011
14. Ka Suen Leung, Biochemistry, 2010-11
15. Chetan Rupakheti⁺, CBB, 2010
16. Robert Gillespie, Biochemistry, 2009
17. Bradley Hintze, Biochemistry, 2009
18. Desmond Moore, Biochemistry, 2009
19. Christopher Williams, Biochemistry, 2007-8
20. Parawee (Nicky) Lekprasert, CBB 2007

Former Visitors

1. Nikolay Frick, 2014
2. Carlile Lavor, 2013-4
3. Seydou Traore, 2014