Donald Lab Graphic

Donald Lab Alumni

Former Doctoral Students (Ph.D. Advisor)

Anna Lowegard expressing oncoproteins

Nate Guerin predicting cancer resistance

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


Daniela Rus and Karl Böhringer

  1. Nathan Guerin, Ph.D., 2023.
    • Dissertation: "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.
  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.
  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.
  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.
  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).
  7. Stuart Endo-Streeter (2009-2013)
    • Now a Research Associate at UNC, Chapel Hill.
  8. Chittu Tripathy (2012-2013).
  9. Michael Zeng (2011-12).
  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).
  13. Ryan Lilien, (2004-2006).
  14. Rahul Ray (2004-2006).
  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).
  18. Jack Kelley (1999-2001).
  19. Daniela Rus (1992-94).
  20. Jonathan Rees (1991-92).
  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

  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. Caleb Watson, BS Computer Science and Biology
    Senior Thesis: Incorporation of Non-proteinogenic Amino Acids (ncAAs) into OSPREY Protein Framework. High Distinction. (2023).
    • Currently a Research Associate at Duke
  2. Andy Zhang, BS Computer Science and Mathematics
    Continuous Protein Conformational Distributions. (2021).
    • Currently a Ph.D. student in at Princeton
  3. 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.
  4. Donald Lab member 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.
  5. Donald Lab member Tyler Nisonoff, Undergraduate Student (2014)
  6. Donald Lab member David Zhou, Undergraduate Student (2014)
  7. Donald Lab member Nina Sun, HHMI Research Fellow (2014)
    Research
  8. Jonathan (JJ) Jou, 2008
    • Current job: See above.
  9. Nicholas Patrick, 2009
    • Winner of Goldwater Scholarship in science, mathematics and engineering for the 2008-09 academic year.
  10. 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).
  11. Alik Widge, B.S. 1999
  12. Ryan McCullough, 1999
    • Currently a Ph.D. Student in EECS at MIT.
  13. Mona Sridharan
  14. Susanna Leng, 1998
    • Senior Honors thesis: "Data-Directed Conformational Search: Using Global Optimization to Determine Large Protein Structure from Sparse NMR Data."
  15. 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. Henry Childs* Chemistry 2021.
  2. Nathan Wong Chemistry 2021.
  3. Aulane Mpouli* Chemistry 2021.
  4. Niven Singh CBB 2020.
  5. Aaron May Biochemistry 2020.
  6. Justin Martyr Biochemistry 2020.
  7. Rohit Roy Biochemistry 2019
  8. Yuze Hou Biochemistry 2018.
  9. Chia-Chieh Chu Biochemistry 2015.
  10. Ryan Muraglia CBB 2013
  11. Jae Cho Biochemistry 2013
  12. Adriana Hertel-Wulf Biochemistry 2013
  13. Swati Jain** Computational Biology & Bioinformatics (CBB)
  14. Mark Hallen* Biochemistry
  15. Dan Keedy*** Biochemistry. Now at UCSF.
  16. Kyle Roberts* CBB
  17. Cheng-Yu Chen* Biochemistry
  18. Ying Zhao, Biochemistry, 2011
  19. Yu (Tina) Jiang, CMB, 2011
  20. Yazan Alwarawrah, Pharmacology and Cancer Biology, 2011
  21. Lindsay Deis, Biochemistry, 2011
  22. Ka Suen Leung, Biochemistry, 2010-11
  23. Chetan Rupakheti+, CBB, 2010
  24. Robert Gillespie, Biochemistry, 2009
  25. Bradley Hintze, Biochemistry, 2009
  26. Desmond Moore, Biochemistry, 2009
  27. Christopher Williams, Biochemistry, 2007-8
  28. Parawee (Nicky) Lekprasert, CBB 2007

Former Visitors

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