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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.

The Dissertations of the latest 23 of my students (since ~2009), mostly Ph.D. students, can be read here, from Duke library.

1. Nathan Guerin, Ph.D., 2023.
   
   • CS Department Best Dissertation award -
     Thesis title: "New Computational Methods to Predict Cancer Resistance Mutations and Design D-Peptide Therapeutics." Department of Computer Science, Duke University.
   • Dr. Guerin is currently Director of Engineering at Ten63 Therapeutics.
2. Kelly Huynh, Ph.D., 2023.
   
   • Dissertation: "Discovery and Characterization of Novel Thanatin Orthologs Against Escherichia coli LptA and Pseudomonas aeruginosa LptH." Department of Biochemistry, School of Medicine, Duke University Medical Center.
   • Dr. Huynh is currently a senior protein scientist at Generation Bio.
3. Graham Holt, Ph.D., 2022.
   
   • Dissertation: "Ensemble-based Computational Protein Design: Algorithms and Applications." Program in Computational Biology, Duke University.
   • First job: Dr. Holt was a postdoctoral research fellow at Duke.
   • He is currently a senior scientist at VantAI, a subsidiary of Roivant.
4. Siyu Wang, Ph.D., 2021.
   
   • Dissertation: "Computational Protein Design with Non-proteinogenic Amino Acids and Small Molecule Ligands, with Applications to Protein-protein Interaction Inhibitors, Anti-microbial Enzyme Inhibitors, and Antibody Design.'' Program in Computational Biology, Duke University.
   • Dr. Wang is currently at the University of California, Davis.
5. Marcel Frenkel, Ph.D., 2019.
   
   • Dissertation: "Combined computational, experimental, and assay-development studies of protein:protein and protein:small molecule complexes, with applications to the inhibition of enzymes and protein:protein interactions." Department of Biochemistry, School of Medicine, Duke University Medical Center.
   • Dr. Frenkel is currently Co-founder and CEO at Ten63 Therapeutics.
6. Anna Ulrika Lowegard, Ph.D., 2019.
   
   • Dissertation: "Novel Algorithms and Tools for Computational Protein Design with Applications to Drug Resistance Prediction, Antibody Design, Peptide Inhibitor Design, and Protein Stability Prediction." Program in Computational Biology, Duke University.
   • First job: Investigator, Protein Design, at GlaxoSmithKline (GSK), Stevenage, UK.
   • Second job: Research Bio Engineer in BioAI @ InstaDeep.
   • Dr. Lowegard is currently Senior Molecular Data Scientist in Biologics at Novo Nordisk.
7. 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.
   • First job: Dr. Jou was Co-founder and Chief Algorithms Officer at Gavilán Biodesign.
   • He is is currently a scientist and senior developer at Schrodinger.
8. 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.
   • First job: Vertex Fellow (Pre-clinical Modeling and Computational Sciences) at Vertex Pharmaceuticals.
   • Second job: Senior Software Engineer and AI Scientist at Genentech, San Francisco.
   • Dr. Ojewole is currently Global Lead AI/ML Structural Biology, BioPharma AI/ML strategy at NVIDIA.
9. Mark Hallen, Ph.D., 2016.
   
   Research
   Web Page
   • Dissertation: "Protein and drug design algorithms using improved biophysical modeling," Department of Computer Science, Duke University.
   • First job: Assistant Professor at Toyota Technological Institute at the University of Chicago.
   • Dr. Hallen is currently Co-founder and CTO at Ten63 Therapeutics.
10. 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.
    • First job: Dr. Jain was a postdoc in the laboratory of Tamar Schlick, Department of Chemistry, NYU Medical School.
    • She is currently a senior developer and scientist at Ten63 Therapeutics.
11. 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.
    • First job: Dr. Gainza was a research associate (postdoc) in the Laboratory of Protein Design and Immunoengineering, EPFL, Lausanne, Switzerland.
    • He is currently Senior Scientist for Computational Sciences & AI at Monte Rosa Therapeutics, Lausanne, Switzerland.
12. 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.
13. 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.
14. 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.
    • First job: Researcher at Scalable Algorithmics, LLC.
    • Currently CEO and Founder at Cuchaz Interactive, LLC.
15. 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.
    • First job: Dr. Chen was a postdoc in the NMR lab of Prof. Jim Prestegard, University of Georgia.
    • He is now Senior Scientist at Bristol Myers Squibb, Cambridge.
16. 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 Technical Director and Engineering Manager at Intel.
17. 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.
    • He is now Distinguished Data Scientist at Walmart Labs.
18. 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 currently an Associate Professor (with tenure) at Tshingua University (IIIS).
19. 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.
    • First job: Dr. Reza was a postdoc in the laboratory of Peter M. Glazer, Department of Therapeutic Radiology, Yale University School of Medicine.
    • He is currently Team Lead, CDC Vaccine Team, Vaccine Task Force (TF), 2019 Novel Coronavirus Response, and TitleTeam Co-Lead, Tiberius CDC Data Science & Analytics Team, 2019 Novel Coronavirus Response. Canters for Disease Control (CDC).
20. 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 Associate professor (with tenure) at Vanderbilt University Medical Center.
21. 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.
22. 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 currently an Associate professor (with tenure) at the University of Illinois.
23. 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.
24. 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.
      Dr. Lilien is also CSO at Cadre Research Labs.
25. 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.
    • First job: Assistant Professor, then Associate Professor (with tenure) of Computer Science at Carnegie Mellon University.
    • Currently Executive Director of Digital Biologics Discovey, Amgen.
26. 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.
27. Jamie 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.
    • Then Mobile Technical Strategist & Architect, IBM.
    • Currently Professor, Department of Computer Science, North Carolina State University.
28. 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.
    • Now at DiCor Engineering, Wellington, Ontario.
29. 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.
30. Patrick Xavier, Ph.D. 1992.
    • Dissertation: "Provably-Good Approximation Algorithms for Optimal Kinodynamic Robot Plans." Department of Computer Science, Cornell University
    • Dr. Xavier was a Senior Member of the Technical Staff at Sandia National Laboratories (1992-2019).

Former PostDocs

1. Graham Holt (2022-2023).
   See above.
2. Jeffrey Martin (2016-2018, 2020-2022).
   See above.
3. Jonathan Dragon Jou (2018-2020)
   Web page
   See above.
4. Anna Lowegard (2019)
   Web page
   See above.
5. Pablo Gainza (2015)
   Web page
   See above.
6. Kyle Roberts (2014-2015).
   See above.
7. Stuart Endo-Streeter (2009-2013)
   • Now a Research Associate at UNC, Chapel Hill.
8. Chittu Tripathy (2012-2013).
   See above.
9. Michael Zeng (2011-12).
   See above.
10. Anna Yershova (2008-10).
    • Now at the University of Illinois at Urbana-Champaign.
11. Nanjiang Shu (2008-2009).
    • Now at Boston University.
12. Serkan Apaydin (2004-2008).
    • First job: Faculty of Engineering and Sciences at Sabanci University in Istanbul, Turkey.
    • He is now a professor at Izmir Institute of Technology, Turkey.
13. Ryan Lilien, (2004-2006).
    See above.
14. Rahul Ray (2004-2006).
    • First job: Assistant Professor at IIT-Madras.
    • Research in Computational Biology and Chemistry.
15. 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.
16. 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.
17. 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.
18. Jack Kelley (1999-2001).
    • Now at the University of Michigan.
    • Research in Computational Biology and Chemistry.
19. 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
20. 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!
21. 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

Former MS Students

The Dissertations of the latest 23 of my students (since ~2009), including MS students, can be read here, from Duke library.

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

The Dissertations of the latest 23 of my students (since ~2009), including B.S. students, can be read here, from Duke library
1. Yuxi "Jaden" Long, BS Computer Science and Mathematics
   Predicting Affinity Through Homology (PATH): Interpretable Binding Affinity Prediction with Persistent Homology. Graduation with Highest Distinction (2024).
   • (Starting 8/24) a Ph.D. Student at Rockefeller/Cornell/Memorial Sloan Kettering Cancer Center.
   • Webpage
2. Caleb Watson, BS Computer Science and Biology
   Senior Thesis: Incorporation of Non-proteinogenic Amino Acids (ncAAs) into OSPREY Protein Framework. Graduation with High Distinction (2023).
   • Also a Research Associate in the Donald lab, 2024.
   • (Starting 6/24) an MD Student at U.Pitt.
3. Andy Zhang, BS Computer Science and Mathematics
   Continuous Protein Conformational Distributions. (2021).
   • Currently a Ph.D. student in at Princeton
4. 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.
5. 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
   • First job: Computational Drug Designer, D.E. Shaw Research.
   • Currently a Ph.D. student at Berkeley.
6. Tyler Nisonoff, Undergraduate Student (2014)
7. David Zhou, Undergraduate Student (2014)
8. Nina Sun, HHMI Research Fellow (2014)
   Research
9. Jonathan (JJ) Jou, 2008
   • Current job: See above.
10. Nicholas Patrick, 2009
    • Winner of Goldwater Scholarship in science, mathematics and engineering for the 2008-09 academic year.
11. 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).
12. Alik Widge, B.S. 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).
    • M.D.-Ph.D. from Carnegie Mellon University/University of Pittsburgh.
    • Currently Professor at University of Minnesota, Department of Psychiatry.
13. Ryan McCullough, 1999
    • Currently a Ph.D. Student in EECS at MIT.
14. 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.
15. Susanna Leng, 1998
    • Senior Honors thesis: "Data-Directed Conformational Search: Using Global Optimization to Determine Large Protein Structure from Sparse NMR Data."
16. 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, collaborated with D-Lab.

1. Evan Corden CBB 2024.
2. Henry Childs* Chemistry 2021.
3. Nathan Wong Chemistry 2021.
4. Aulane Mpouli* Chemistry 2021.
5. Niven Singh CBB 2020.
6. Aaron May Biochemistry 2020.
7. Justin Martyr Biochemistry 2020.
8. Rohit Roy Biochemistry 2019
9. Yuze Hou Biochemistry 2018.
10. Chia-Chieh Chu Biochemistry 2015.
11. Ryan Muraglia CBB 2013
12. Jae Cho Biochemistry 2013
13. Adriana Hertel-Wulf Biochemistry 2013
14. Swati Jain** Computational Biology & Bioinformatics (CBB)
15. Mark Hallen* Biochemistry
16. Dan Keedy*** Biochemistry. Now at UCSF.
17. Kyle Roberts* CBB
18. Cheng-Yu Chen* Biochemistry
19. Ying Zhao, Biochemistry, 2011
20. Yu (Tina) Jiang, CMB, 2011
21. Yazan Alwarawrah, Pharmacology and Cancer Biology, 2011
22. Lindsay Deis, Biochemistry, 2011
23. Ka Suen Leung, Biochemistry, 2010-11
24. Chetan Rupakheti⁺, CBB, 2010
25. Robert Gillespie, Biochemistry, 2009
26. Bradley Hintze, Biochemistry, 2009
27. Desmond Moore, Biochemistry, 2009
28. Christopher Williams, Biochemistry, 2007-8
29. Parawee (Nicky) Lekprasert, CBB 2007

Former Visitors

1. Ram Mettu, 2019
2. Nikolay Frick, 2014
3. Carlile Lavor, 2013-4
4. Seydou Traore, 2014