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
-
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 will be Director of Engineering at Ten63 Therapeutics (starting January 2024).
-
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.
-
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.
-
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.
-
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.
-
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.
- Dr. Lowegard is currently Research Bio Engineer in BioAI @ InstaDeep.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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.
-
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).
-
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).
- Ivelin Georgiev, Ph.D., 2009.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
-
Graham Holt (2022-2023).
See above.
-
Jeffrey Martin (2016-2018, 2020-2022).
See above.
-
Jonathan Dragon Jou (2018-2020)
Web page
See above.
-
Anna Lowegard (2019)
Web page
See above.
-
Pablo Gainza (2015)
Web page
See above.
-
Kyle Roberts
(2014-2015).
- Stuart Endo-Streeter (2009-2013)
- Now a Research Associate at UNC, Chapel Hill.
-
Chittu Tripathy
(2012-2013).
-
Michael Zeng
(2011-12).
-
Anna Yershova
(2008-10).
- Now at the University of Illinois at Urbana-Champaign.
- Nanjiang
Shu (2008-2009).
- Now at Boston University.
- Serkan Apaydin (2004-2008).
- Ryan Lilien, (2004-2006).
- Rahul Ray
(2004-2006).
- 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.
-
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.
- Chris
Bailey-Kellogg (1999-2001).
-
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
Former MS Students
- Yang Qi, M.S. 2016.
- Thesis: "On Provable Algorithms for Determination of Continuous
Protein Interdomain Motions from Residual Dipolar Couplings."
- Jeff Martin, M.S. 2009.
- Thesis: "Algorithms for Structure Determination of
Symmetric Proteins from Nuclear Magnetic Resonance Data."
- 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
-
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
|
-
Andy Zhang,
BS Computer Science and Mathematics
Continuous Protein Conformational Distributions.
(2021).
- Currently a Ph.D. student in at Princeton
|
-
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.
|
-
 |
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.
|
-
 |
Tyler Nisonoff, Undergraduate
Student (2014)
|
-
 |
David Zhou, Undergraduate Student (2014)
|
-
 |
Nina Sun, HHMI
Research Fellow (2014)
Research
|
- Jonathan (JJ) Jou, 2008
- 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, B.S. 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
NMR Data."
- 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.
- Henry Childs* Chemistry 2021.
- Nathan Wong Chemistry 2021.
- Aulane Mpouli* Chemistry 2021.
- Niven Singh CBB 2020.
- Aaron May Biochemistry 2020.
- Justin Martyr Biochemistry 2020.
- Rohit Roy Biochemistry 2019
- Yuze Hou Biochemistry 2018.
- Chia-Chieh Chu Biochemistry 2015.
- 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
- Ram Mettu, 2019
- Nikolay Frick, 2014
- Carlile Lavor, 2013-4
- Seydou Traore, 2014