| 2024 | RECOMB | DexDesign: A New OSPREY-Based Algorithm for Designing de novo D-peptide Inhibitors. | Nathan Guerin, Henry Childs, Pei Zhou, Bruce Randall Donald |
| 2022 | RECOMB | Resistor: An Algorithm for Predicting Resistance Mutations Using Pareto Optimization over Multistate Protein Design and Mutational Signatures. | Nathan Guerin, Teresa Kaserer, Bruce Randall Donald |
| 2019 | RECOMB | Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. | Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald |
| 2017 | RECOMB | BBK | Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce Randall Donald |
| 2016 | RECOMB | LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid-rotamer-like Efficiency. | Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald |
| 2015 | RECOMB | Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence. | Mark Hallen, Bruce Randall Donald |
| 2015 | RECOMB | BWM*: A Novel, Provable, Ensemble-Based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. | Jonathan D. Jou, Swati Jain, Ivelin Georgiev, Bruce Randall Donald |
| 2013 | ICRA | MicroStressBots: Species Differentiation in Surface Micromachined Microrobots. | Christopher G. Levey, Igor Paprotny, Bruce Randall Donald |
| 2013 | RECOMB | Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure. | Chittaranjan Tripathy, Anthony K. Yan, Pei Zhou, Bruce Randall Donald |
| 2011 | RECOMB | A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-oligomers from NOEs and RDCs. | Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, Bruce Randall Donald |
| 2011 | RECOMB | Design of Protein-Protein Interactions with a Novel Ensemble-Based Scoring Algorithm. | Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce Randall Donald |
| 2011 | RECOMB | Protein Loop Closure Using Orientational Restraints from NMR Data. | Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2011 | RECOMB | A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data. | Jianyang Zeng, Kyle E. Roberts, Pei Zhou, Bruce Randall Donald |
| 2010 | RECOMB | A Markov Random Field Framework for Protein Side-Chain Resonance Assignment. | Jianyang Zeng, Pei Zhou, Bruce Randall Donald |
| 2010 | WAFR | Algorithms and Analytic Solutions Using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR. | Anna Yershova, Chittaranjan Tripathy, Pei Zhou, Bruce Randall Donald |
| 2008 | ISMB | Algorithm for backrub motions in protein design. | Ivelin Georgiev, Daniel A. Keedy, Jane S. Richardson, David C. Richardson, Bruce Randall Donald |
| 2008 | WAFR | Simultaneous Control of Multiple MEMS Microrobots. | Bruce Randall Donald, Christopher G. Levey, Igor Paprotny, Daniela Rus |
| 2007 | ISMB | Dead-End Elimination with Backbone Flexibility. | Ivelin Georgiev, Bruce Randall Donald |
| 2006 | ISMB | Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. | Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2006 | RECOMB | A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles. | Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald |
| 2006 | WAFR | Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints. | Shobha Potluri, Anthony K. Yan, James J. Chou, Bruce Randall Donald, Chris Bailey-Kellogg |
| 2005 | ISMB | High-throughput inference of protein-protein interfaces from unassigned NMR data. | Ramgopal R. Mettu, Ryan H. Lilien, Bruce Randall Donald |
| 2005 | ISRR | A Steerable, Untethered, 250 60m MEMS Mobile Micro-Robot. | Bruce Randall Donald, Christopher G. Levey, Craig D. McGray, Igor Paprotny, Daniela Rus |
| 2004 | RECOMB | A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. | Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald |
| 2004 | WAFR | Algorithmic Challenges in Structural Molecular Biology and Proteomics. | Bruce Randall Donald |
| 2003 | ISRR | UntetheredMicro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance. | Bruce Randall Donald, Christopher G. Levey, Craig D. McGray, Daniela Rus, Mike Sinclair |
| 2003 | RECOMB | Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. | Christopher James Langmead, Anthony K. Yan, Ryan H. Lilien, Lincong Wang, Bruce Randall Donald |
| 2002 | RECOMB | Phase-independent rhythmic analysis of genome-wide expression patterns. | Christopher James Langmead, Anthony K. Yan, C. Robertson McClung, Bruce Randall Donald |
| 2001 | ICRA | Physical Geometric Algorithms for Structural Molecular Biology. | Bruce Randall Donald, Christopher Bailey-Kellogg, Jack Kelley, Ryan H. Lilien |
| 2001 | RECOMB | Extracting structural information using time-frequency analysis of protein NMR data. | Christopher James Langmead, Bruce Randall Donald |
| 2000 | ICRA | Distributed Manipulation of Multiple Objects using Ropes. | Bruce Randall Donald, Larry Gariepy, Daniela Rus |
| 2000 | ICRA | Using Haptic Vector Fields for Animation Motion Control. | Bruce Randall Donald, Frederick Henle |
| 2000 | ICRA | Practical Mobile Robot Self-Localization. | Jon Howell, Bruce Randall Donald |
| 2000 | ICRA | Fully Programmable MEMS Ciliary Actuator Arrays for Micromanipulation Tasks. | John W. Suh, R. Bruce Darling, Karl-Friedrich Bhringer, Bruce Randall Donald, Henry Baltes, Gregory T. A. Kovacs |
| 2000 | ISMB | Reducing Mass Degeneracy in SAR by MS by Stable Isotopic Labeling. | Christopher Bailey-Kellogg, John J. Kelley, Clifford Stein, Bruce Randall Donald |
| 2000 | RECOMB | The NOESY jigsaw: automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. | Christopher Bailey-Kellogg, Alik Widge, John J. Kelley, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald |
| 2000 | SIGGRAPH | Accessible animation and customizable graphics via simplicial configuration modeling. | Tom Ngo, Doug Cutrell, Jenny Dana, Bruce Randall Donald, Lorie Loeb, Shunhui Zhu |
| 1997 | ICRA | Vector fields for task-level distributed manipulation: experiments with organic micro actuator arrays. | Karl-Friedrich Bhringer, John W. Suh, Bruce Randall Donald, Gregory T. A. Kovacs |
| 1996 | ICRA | What programmable vector fields can (and cannot) do: force field algorithms for MEMS and vibratory plate parts feeders. | Karl-Friedrich Bhringer, Bruce Randall Donald, Noel C. MacDonald |
| 1995 | IROS | Moving furniture with teams of autonomous robots. | Daniela Rus, Bruce Randall Donald, Jim Jennings |
| 1994 | ICRA | Sensorless Manipulation Using Massively Parallel Microfabricated Actuator Arrays. | Karl-Friedrich Bhringer, Bruce Randall Donald, Robert Mihailovich, Noel C. MacDonald |
| 1994 | ICRA | Automatic Sensor Configuration for Task-Directed Planning. | Amy J. Briggs, Bruce Randall Donald |
| 1994 | ICRA | Analyzing Teams of Cooperating Mobile Robots. | Bruce Randall Donald, James S. Jennings, Daniela Rus |
| 1993 | ICRA | Information Invariants in Robotics: Part I - State, Communication, and Side-Effects. | Bruce Randall Donald |
| 1993 | ICRA | Information Invariants in Robotics: Part II - Sensors and Computation. | Bruce Randall Donald |
| 1992 | ICRA | Constructive recognizability for task-directed robot programming. | Bruce Randall Donald, James S. Jennings |
| 1992 | ICRA | Program mobile robots in Scheme. | Jonathan Rees, Bruce Randall Donald |
| 1991 | FOCS | On the Complexity of Computing the Homology Type of a Triangulation | Bruce Randall Donald, Davied Renpan Chang |
| 1991 | ICRA | Sensor interpretation and task-directed planning using perceptual equivalence classes. | Bruce Randall Donald, Jim Jennings |
| 1991 | ICRA | Time-safety trade-offs and a bang-bang algorithm for kinodynamic planning. | Bruce Randall Donald, Patrick G. Xavier |
| 1991 | IROS | Perceptual limits, perceptual equivalence classes, and a robot's sensori-computational capabilities (extended abstract). | Bruce Randall Donald, James S. Jennings |
| 1990 | ICRA | On the motion of compliantly-connected rigid bodies in contact. II. A system for analyzing designs for assembly. | Bruce Randall Donald, Dinesh K. Pai |
| 1990 | SIGGRAPH | Real-time robot motion planning using rasterizing computer graphics hardware. | Jed Lengyel, Mark Reichert, Bruce Randall Donald, Donald P. Greenberg |
| 1989 | ICRA | A provably good approximation algorithm for optimal-time trajectory planning. | Bruce Randall Donald, Patrick G. Xavier |
| 1989 | ICRA | Towards experimental verification of an automated compliant motion planner based on a geometric theory of error detection and recovery. | James S. Jennings, Bruce Randall Donald, Doug Campbell |
| 1988 | FOCS | On the Complexity of Kinodynamic Planning | John F. Canny, Bruce Randall Donald, John H. Reif, Patrick G. Xavier |
| 1988 | ICRA | Planning multistep error detection and recovery strategies. | Bruce Randall Donald |
| 1986 | ICRA | Robot motion planning with uncertainty in the geometric models of the robot and environment: A formal framework for error detection and recovery. | Bruce Randall Donald |
| 1985 | ICRA | On motion planning with six degrees of freedom: Solving the intersection problems in configuration space. | Bruce Randall Donald |