Bruce Randall Donald -- Selected Publications
Professor of Computer Science and Biochemistry
Duke University

Quick Links: Books - Papers - Cover Articles - Protein Structures - By topic - Categories/Indexes - Movies - Lab YouTube Channel - Papers Before 1994 - Possums

Books

• Algorithms in Structural Molecular Biology. MIT Press (2011).
  464 pages + 52 color plates.
  See the Book Web Page
  
  
  
  
  
  
  
  

• See all 5 books

Selected Recent Papers



• Papers by Topic
  • Structural Molecular Biology and Biochemistry
    • Protein Structure Gallery
      • Search PDB (NCBI) for all our protein structures (NMR, X-ray)
  • Computational Molecular Biology
  • MicroElectroMechanical Systems (MEMS), Nanoscience, and Microrobotics
  • Mobile Robotics
  • Motion Planning and Geometric Algorithms
  • Computer Graphics
  • Computational Geometry
• Cover Articles
• Movies: [Robots, Microrobots and MEMS, MEMS ciliary arrays and distributed manipulation]
  • Our lab has a YouTube channel:
    http://www.youtube.com/user/labdonald/videos,
    with many videos describing our research.
    Most of these videos are on microrobotics and nanoscience. While a lot of our work now is on structural and computational biology, we have not made many videos on those topics yet. However, we have written a textbook and plenty of papers you can read on structural and computational biology and biochemistry.
    Please note that not all of our videos above are on YouTube because some, for example, are hosted in a lecture series at MIT.
• Indexes and Reviews of Our Papers*
  *Indicates indexes and reviews of our papers not written by our group.
  *Please note: Most indexes and collections of our papers are incomplete since the computer science indexes do not list the biomedical journals, and Medline does not list the computer science and robotics papers. As of January 2012, only Google Scholar seems reasonably complete.
  • *Google Scholar Citation Home Page
  • *Our papers listed on [Medline, DBLP, CCSB]
  • *Data analysis (by S. Aerni and E. Eskin) of the impact of our lab on RECOMB.
  • *Review of our papers on protein design (by SM Lippow & B Tidor). Progress in computational protein design. Curr Opin Biotechnol. 2007; Medline, PMID 17644370.
• Indexes of papers listed on
  • Medline
  • Google Scholar
  • DBLP Bibliography Server
  • The Collection of Computer Science Bibliographies
• My C.V. (PDF) (contains a complete list of publications)
• Special Issue of Algorithmica (2000)
• Current Research; Donald Lab; Publications prior to 1994; Publications not listed here

Predicting Resistance Mutations using Protein Design Algorithms. PNAS (2010).
	Computational Structure-Based Redesign of Enzyme Activity. PNAS (2009).
	Cover Article, Chemistry & Biology 2007. [Caption]
	Redesigning the PheA Domain of Gramicidin Synthetase. Biochemistry 2006; 45 (51):15495-15504.
	Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis. (J. Biol. Chem. 2003).
	Cover article, J. Eukaryotic Microbiology (2003).
	Cover article, PROTEINS (2012).
Complete ensemble of NMR structures of the unphosphorylated human cardiac phospholamban pentamer. PDB ID: 2HYN (Proteins, 2006)

List of Selected Papers, Broken into categories

• Cover Articles

  

• Structural Molecular Biology, Biochemistry, & Computational Molecular Biology

  • Structural Molecular Biology and Biochemistry

    • Design of Epitope-Specific Probes for Sera Analysis and Antibody Isolation (with I. Georgiev, P. Acharya, S. Schmidt, Y. Li, D. Wycuff, G. Ofek, N. Doria-Rose, T. Luongo, Y, Yang, T. Zhou, J. Mascola, P. Kwong). Retrovirology 2012; 9(Suppl.2):P50. From AIDS Vaccine. Boston, MA. Sep. 9-12 (2012).
    • Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). PLoS Computational Biology 2012; 8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
      • [Abstract, PDF]
    • Predicting resistance mutations using protein design algorithms (with K. Frey, I. Georgiev, and A. Anderson). Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2010; 107(31):13707-12. PubMed PMID: 20643959.
      • [Abstract, Full text, PDF, PDB Structures: 3GL4, 3F0Q]
    • High-Resolution Protein Structure Determination Starting with a Global Fold Calculated from Exact Solutions to the RDC Equations, (with J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan, and P. Zhou). Journal of Biomolecular NMR 2009; 45(3):265-281. PMID: 19711185
      • [PDF, Supplementary Materials, PDB Structure 2KIQ]
    • Computational Structure-Based Redesign of Enzyme Activity (with C. Chen, I. Georgiev, and A. Anderson). Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2009; 106(10):3764-3769.
      • [PDF, Supporting Information, Open access article, Abstract]
    • Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints (with J. Martin). Progress in NMR Spectroscopy 2009; 55(2):101-127.
      • [PDF, Full text at Jounal Website]
    • "Allosteric Inhibition of the Protein-Protein Interaction Between the Leukemia-Associated Proteins RUNX1 and CBFβ." Chemistry & Biology 2007; 14(10):1186-1197.
      • [Medline, PDF, Supplementary material, PDB structure model, Cover article, Caption, Cover (PDF)]
    • Redesigning the PheA Domain of Gramicidin Synthetase Leads to a New Understanding of the Enzyme's Mechanism and Selectivity (with B. Stevens, R. Lilien, I. Georgiev, and A. Anderson). Biochemistry 2006; 45 (51):15495-15504.
      • [Medline, PDF, Abstract]
    • Structure Determination of Symmetric Homo-oligomers by a Complete Search of Symmetry Configuration Space Using NMR Restraints and van der Waals Packing (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg). Proteins 2006; 65(1):203-219.
      • [Medline, HTML, PDF, Supplementary materials, PDB Structure 2HYN]
    • 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 (with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational Biology 2005; 12(6-7):740-761.
      • [Medline, PDF]
    • Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Biological Chemistry 2003; 278(52):52980-52987.
      • [Medline, PDF, Full text (at JBC), PDB Structure 1QZF]
    • The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis Reveals a Novel Architecture for the Bifunctional Enzyme, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Eukaryotic Microbiology 2003; 50(6):555-556. Cover article.
      • [Medline, PDF, Cover illustration (Jpeg)]

  • Protein Structures Gallery

    
    • Solution structure of the FF Domain 2 of human transcription elongation factor CA150, (with M. Zeng, C. Tripathy, J. Boyles, A. Yan, and P. Zhou), PDB ID: 2KIQ (2009).
    • Complete ensemble of NMR structures of Unphosphorylated Human Phospholamban Pentamer, (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg), PDB ID: 2HYN (2006).
    • Crystal structure of Dihydrofolate Reductase-Thymidylate Synthase (DHFR-TS) from Cryptosporidium hominis, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson), PDB ID: 1QZF (2003).
    • Search PDB (NCBI) for all protein structures reported in our papers (NMR, X-ray)

  • Algorithms in Structural Molecular Biology and Computational Chemistry

    • "OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms" (with P. Gainza, K. Roberts, I. Georgiev, R. Lilien, D. Keedy, C.-Y. Chen, F. Reza, A. Anderson, D. Richardson, and J. S. Richardson). Methods in Enzymology 2013; 523:87-107
      • [Abstract, PDF]
    • "Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure" (with C. Tripathy, A. Yan, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Beijing, China (2013). In Press.
    • "The Role of Local Backrub Motions in Evolved and Designed Mutations" (with D. Keedy, I. Georgiev, E. Triplett, D. Richardson, and J. Richardson). PLoS Computational Biology 2012; 8(8): e1002629. doi:10.1371/journal.pcbi.1002629.
      • [Abstract, Open access at Journal, PDF]
    • "HASH: a Program to Accurately Predict Protein Hα (H-alpha) Shifts from Neighboring Backbone Shifts'' (with J. Zeng, and P. Zhou). Journal of Biomolecular NMR 2012; Dec 16. [Epub ahead of print]
      • [PDF]
    • "Protein Design using Continuous Rotamers" (with P. Gainza and K. Roberts). PLoS Computational Biology (2012) 8(1): e1002335. doi:10.1371/journal.pcbi.1002335.
      • [Open access at the Journal, PDF ]
    • Dead-End Elimination with Perturbations (`DEEPer'): A provable protein design algorithm with continuous sidechain and backbone flexibility (with M. Hallen and D. Keedy). Proteins 2013; 80(1):18-39. DOI: 10.1002/prot.24150
      • [PDF, Abstract]
    • Protein loop closure using orientational restraints from NMR data (with C. Tripathy, J. Zeng, and P. Zhou). Cover Article.
      Proteins: Structure, Function, and Bioinformatics. Volume 80, Issue 2, pages 433-453, 2012. Journal online: DOI: 10.1002/prot.23207
      • [PDF, Abstract, Supplementary Information (SI), Cover (large, PNG)]
    • Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data, (with J. Zeng and P. Zhou). Journal of Biomolecular NMR 2011: 45(3):265-281.
      • [PDF]
    • A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers'' (with J. Martin, A. Yan, C Bailey-Kellogg, and P. Zhou). Protein Science 20(6):970-985 (2011) Mar 16. doi: 10.1002/pro.620. [Epub ahead of print] PMID: 21413097
      • [PDF]
    • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs (with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou). Journal of Computational Biology 2011; 18(11):1507-23.
      • [PDF]
    • NMR Structural Inference of Symmetric Homo-Oligomers (with H. Chandola, A. Yan, S. Potluri, and C. Bailey-Kellogg). Journal of Computational Biology 2011; 18(12):1757-75. PMID: 21718128.
      • [PDF]
    • A Bayesian Approach for Determining Protein Side-chain Rotamer Conformations using Unassigned NOE Data (with J. Zeng, K. Roberts, and P. Zhou). Journal of Computational Biology 2011; 18(11):1661-79.

    • RECOMB 2011 papers

      • Design of protein-protein interactions with a novel ensemble-based scoring algorithm (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 361-376 (2011), DOI: 10.1007/978-3-642-20036-6
        • [PDF, Link to Proceedings]
      • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs (with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 222-237 (2011), DOI: 10.1007/978-3-642-20036-6.
      • Protein loop closure using orientational restraints from NMR data (with C. Tripathy, J. Zeng, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 483-498 (2011), DOI: 10.1007/978-3-642-20036-6
      • A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data (with J. Zeng, K. Roberts, and P. Zhou). In Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer Science, Springer (Berlin), Volume 6577, pp. 563-578 (2011), DOI: 10.1007/978-3-642-20036-6

    • A Markov Random Field Framework for Protein Side-Chain Resonance Assignment (with J. Zeng and P. Zhou). International Conference on Research in Computational Molecular Biology (RECOMB), Lisbon, Portugal. April/August, 2010. In Lecture Notes in Computer Science, Springer (Berlin) Volume LNBI 6044/2010, pp. 550-570. ISBN 978-3-642-12682-6.
    • Algorithms and Analytic Solutions using Sparse Residual Dipolar Couplings for High-Resolution Automated Protein Backbone Structure Determination by NMR (with A. Yershova, C. Tripathy, and P. Zhou), Workshop on the Algorithmic Foundations of Robotics (WAFR), Singapore (2010).
    • OSPREY User Manual (with I. Georgiev). Available online: www.cs.duke.edu/donaldlab/software.php (2009).
    • NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments (with S. Apaydin, B. Catay, and N. Patrick). The Computer Journal 2011; 54:708-716. Appeared Online in (Summer, 2010). doi:10.1093/comjnl/bxp120.
      An earlier conference version of paper in: IEEE 24th International Symposium on Computer and Information Science (ISCIS). Cyprus, 14-16 September 2009.
    • Algorithm for Backrub Motions in Protein Design (with I. Georgiev, D. Keedy, J. Richardson, and D. Richardson). Bioinformatics 2008; 4(13):i196-i204. Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto CA (July, 2008)
      • [PDF, Open access]
    • Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg). In Algorithmic Foundation of Robotics VII. Springer Tracts in Advanced Robotics (vol. 47), Ed. S. Akella et al. Springer-Verlag (Berlin) 2008 pp. 335-340.
    • A Hausdorff-Based NOE Assignment Algorithm Using Protein Backbone Determined from Residual Dipolar Couplings and Rotamer Patterns, (with J. Zeng, C. Tripathy, and P. Zhou). The Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2008) pp. 169-181.
      • [PDF]
    • Structure-Based Protein NMR Assignments using Native Structural Ensembles (with S. Apaydin and V. Conitzer). Journal of Biomolecular NMR 2008; 40(4):263-276. PMID: 18365752.
      • [Medline, PDF]
    • The 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 (with I. Georgiev and R. Lilien). Journal of Computational Chemistry 2008;29(10):1527-42. PMID: 1829329
      • [Medline, PDF]
    • Dead-End Elimination with Backbone Flexibility (with I. Georgiev). Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria: July 21-25, 2007. Appears in in Bioinformatics 2007; 23(13):i185-i195.
      • [Medline, PDF, Open Access]
    • A Complete Algorithm to Resolve Ambiguity for Inter-subunit NOE Assignment in Structure Determination of Symmetric Homo-oligomers (with S. Potluri, A. Yan, and C. Bailey-Kellogg). Protein Science 2007; 16(1):69-81.
      • [Medline, PDF]
    • A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data (with L. Wang and R. Mettu). Journal of Computational Biology 2006; 13(7): 1276-1288.
      • [Medline, PDF]
    • A Data-Driven, Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins (with L. Wang). The Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2006) Pages 67-78. ISBN 1-86094-700-X.
      • Winner of Best Paper Award.
      • [Medline, PDF, Amazon, Imperial College Press]
    • Improved Pruning Algorithms and Divide-and-Conquer Strategies for Dead-End Elimination, with Application to Protein Design (with I. Georgiev and R. Lilien), Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil (2006). Bioinformatics 2006; 22(14):e174-183.
      • [Medline, PDF, Open Access]
    • 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, (with I. Georgiev and R. Lilien). Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Venice, Italy (April 2-5, 2006). In Springer Berlin, Lecture Notes in Computer Science, RECOMB 2006, LNBI 3909, pp. 530-545, 2006.
      • [Medline, PDF]
    • R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics 2005; 21(Suppl. 1):i292-i301.
      • [Medline, PDF, Erratum ]
      • Here is the accepted manuscript, which does not contain the error that Bioinformatics introduced in the abstract. The error is corrected in the published Erratum.
    • L. Wang and B. R. Donald. An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings. The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp. 189-202.
      • [Medline, PDF ]
    • L. Wang, R. Mettu, and B. R. Donald. An Algebraic Geometry Approach to Protein Backbone Structure Determination from NMR Data. The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp. 235-246.
      • [Medline, PDF ]
    • High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data (with R. Mettu and R. Lilien), Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, MI (2005).
    • 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 (with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational Biology 2005; 12(6-7):740-761.
      • [Medline, PDF]
    • Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and Their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure (with L. Wang), Journal of Biomolecular NMR 2004; 29(3):223-242.
      • [Medline, PDF, full text (at JBN)]
    • An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments (with C. Langmead). Journal of Biomolecular NMR 2004; 29(2):111-138.
      • [Medline, PDF, Full text (at JBN) ]
    • 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 (with R. Lilien, B. Stevens, and A. Anderson). Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego (March 27-31, 2004) pp. 46-57.
      • [PDF]
    • A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry (with R. Lilien, C. Bailey-Kellogg, and A. Anderson). Acta Crystallographica D: Biological Crystallography 2004; D60, 1057-1067.
      • [Medline, PDF, Full text (at IUCR)]
    • High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment (with C. Langmead). The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA, (August, 2004) pp. 278-289.
      • [Medline, PDF]
    • Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Couplings (with L. Wang). The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA (August, 2004) pp. 319-330.
      • [Medline, PDF]

      	Nuclear Vector Replacement.

    • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Journal of Computational Biology 2004; 11(2--3):277-298.
      • [Medline, PDF]
    • A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology (with A. Yan and C. Langmead). The International Journal of Robotics Research Special Issue on Robotics Techniques Applied to Computational Biology, 2005; (29)(2-3):165-182.
      • [PDF]
    • "3D Structural Homology Detection via Unassigned Residual Dipolar Couplings," (with C. Langmead) Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 10, 2003) pp. 209-217. ISBN 0-7695-2000-6.
      • [Medline, PDF]
    • "An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings,'' (with L. Wang, R. Mettu, and R.Lilien), Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 10, 2003) pp. 611-612. ISBN 0-7695-2000-6.
      • Winner of Best Poster Award.
    • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Proc. The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (2003) pp. 176-187.
      • [PDF]
    • " Ensembles of active site conformations allow structure-based redesign and drug design," (with A. Anderson, R. Lilien and V. Popov), 225^th American Chemical Society National Meeting, March 23-28, 2003. New Orleans, LA.
    • "Modeling Protein Flexibility for Structure-Based Active Site Redesign", (with R. Lilien and A. Anderson), The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). In Currents in Computational Molecular Biology, 2002 (ed. L. Florea et al.) pp 122-123.
      • [ PDF]
    • "Modeling of Protein Flexibility for Computational Active Site Redesign," (with R. Lilien and A. Anderson) The 16th Annual National MD/PhD Conference, Given Institute, Aspen, Colorado, July 13-15, 2001.
    • "Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data" (with C. Langmead), Proceedings of The Fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Montreal, April 22-25 (2001) pp. 164-175
      • [PDF]
    • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) The Journal of Computational Biology, 8(1):19-36, 2001.
      • [Medline, PDF]
        
      • [The figures look better in this pdfLaTeX reprint]
    • "The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Journal of Computational Biology, 7(3-4) (2000) pp. 537-558.
      • [Medline, PDF]
      • [The figures look better in this pdfLaTeX reprint]
    • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) Proc. the 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA (pp. 13-24).
      • [Medline]
    • "Computational Screening Studies for Core-Binding Factor Beta (CBFβ): Use of Multiple Conformations to Model Receptor Flexibility," (with R. Lilien, M. Sridharan, X. Huang, and J. Bushweller), 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA.
    • "The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB'2000), Tokyo, Japan, April 8-11, 2000, pp. 33-45.
    
    

  • Systems Biology

    • Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin, and D. Madden). PLoS Computational Biology 2012; 8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
      • [Abstract, PDF]
    • R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics 2005; 21(Suppl. 1):i292-i301.
      • [Medline, PDF, Erratum ]
      • Here is the accepted manuscript, which does not contain the error that Bioinformatics introduced in the abstract. The error is corrected in the published Erratum.
    • "Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum," (with R. Lilien and H. Farid), Journal of Computational Biology, 10(6) 2003, pp. 925-946.
      • [Medline, PDF]
      • [The figures may look better in this pdfLaTeX reprint]
    • "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns", (with C. Langmead, A. Yan, and C. R. McClung), Journal of Computational Biology 10(3-4) 2003, pp. 521-536.
      • [Medline, PDF]
      • [The figures may look better in this pdfLaTeX reprint]
    • Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Biological Chemistry 2003; 278(52):52980-52987.
      • [Medline, PDF, Full text (at JBC), Structure (PDB)]
    • "A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns," (with C. Langmead and C. R. McClung) Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 14-16, 2002) pp. 237-245.
      • [Medline, Abstract, PDF]
    • "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns'', (with C. Langmead, T. Yan, and C. R. McClung), The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). pp. 205-215.
      • [Abstract, PDF]
    
    

  • Review/Survey Articles

    • Algorithmic Challenges in Structural Molecular Biology and Proteomics, Plenary lecture at WAFR, Utrecht/Zeist, The Netherlands. July 11-13, 2004. Appears in Springer Tracts in Advanced Robotics (vol. 17), Springer (Berlin) 2005, pp. 1-10.
      • [PDF, HTML]
    • "Physical Geometric Algorithms for Structural Molecular Biology" (with C. Bailey-Kellogg, J. Kelley, and R. Lilien) invited paper at the Special Session on Computational Biology & Chemistry, Proc. International Conference on Robotics and Automation (2001), Seoul, Korea, pp. 940-947.
      • [PostScript, PDF]

• MicroElectroMechanical Systems (MEMS), Nanoscience, and Microrobotics

  Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with many videos describing our MEMS, Microrobotics, and Nanoscience research.

  Scientific papers (with some pointers to videos) are provided for you here, in the list immediately below:

  • Planning and Control for Microassembly of Structures Composed of Stress-Engineered MEMS Microrobots (with C. Levey, C. McGray, I. Paprotny, and D. Rus). International Journal of Robotics Research 2013; 32(2): 218-246.
    • [Abstract, PDF]
  • Turning-rate Selective Control: A New Method for Independent Control of Stress-engineered MEMS Microrobots (with C. Levey and I. Paprotny). Proceedings of Robotics: Science and Systems Conference (RSS), University of Sydney, Sydney, NSW, Australia. July 9-13, 2012 (In press).
    • [Abstract, PDF]
  • The Compass That Steered Robotics. In Logic and Program Semantics, Lecture Notes in Computer Science (LNCS) 7230, Springer-Verlag (Berlin) 2012. pp. 50-65.
    • [PDF]
  • Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording (with I. Borzenets, I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of Applied Physics 2012; 111(7):74703-747036. doi: 10.1063/1.3702802.
    • [Summary, PDF]
  • Simultaneous Control of Multiple MEMS Microrobots (with C. Levey, I. Paprotny, and D. Rus). Proceedings of the Eighth International Workshop on the Algorithmic Foundations of Robotics (WAFR), Guanajuato, Mexico, December 7-9, 2008.
    Book chapter version (final) appears in: Springer Tracts on Advanced Robotics, 57, Springer-Verlag (Berlin), (2010), pp. 69-84.
    • [PDF, Supplementary Material]
  • Planar Microassembly by Parallel Actuation of MEMS Microrobots (with C. Levey and I. Paprotny). Journal of Microelectromechanical Systems 2008; 17(4): 789-808.
    • [PDF, Video, Supporting Material, Ballet video, Youtube videos, Movies ]
  • Assembly of Planar Structures by Parallel Actuation of MEMS Microrobots (with C. Levey and I. Paprotny). Hilton Head Workshop: A Solid-State Sensors, Actuators and Microsystems Workshop pp. 202-207. June 1-2, 2008, Hilton Head, SC.
    • [PDF, Video, Supporting Material, Ballet video, Youtube videos]
  • A Steerable, Untethered MEMS Mobile Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). In Robotics Research, Springer Tracks in Advanced Robotics 28, ed. S. Thrun, et al., Springer-Verlag (Berlin) 2007, pp. 337-356.
  • An Untethered, Electrostatic, Globally-Controllable MEMS Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). Journal of Microelectromechanical Systems, 2006; 15(1):1-15.
    • [PDF, Full text at IEEE, Supplementary Material (Videos)]
  • A Steerable, Untethered, 250 x 60 µm MEMS Mobile Micro-Robot (with C. Levey, C.McGray, I. Paprotny, and D. Rus). 12th International Symposium of Robotics Research (ISRR), October 12-15, 2005, San Francisco, CA.
  • Power Delivery and Locomotion of Untethered Micro-Actuators (with C. Levey, C. McGray, D. Rus, and M. Sinclair). Journal of Microelectromechanical Systems 2003; 10(6):947-959.
    • [PDF, Movies]
  • Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and M. Sinclair). in Robotics Research eds. P. Dario and R. Chatila. Springer-Verlag (London) 2005, pp.502--516.
  • Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design, Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and M. Sinclair) 11^th International Symposium of Robotics Research (ISRR), October 19-22, 2003, Siena, Italy.
  • Power Delivery and Locomotion of Untethered Micro-Actuators, (with C. Levey, C. McGray, D. Rus, and M. Sinclair) IEEE MEMS (Proc. IEEE International Conference on Micro Electro Mechanical Systems), Kyoto, Japan, January 19-23, 2003. pp.124-129.
    • [PDF, Movies]
  • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE Transactions on Robotics and Automation, 16(2), April 2000, pp. 157-170.
    • [Abstract, PDF]

  • Fully Programmable MEMS Ciliary Actuator Arrays for Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G.Kovacs), the IEEE International Conference on Robotics and Automation (ICRA) San Francisco (April, 2000) pp. 1101-1108.
  • Sensorless Manipulation Algorithms Using a Vibrating Surface, (with K.-F. Böhringer, V. Bhatt, and K. Goldberg) Algorithmica 26(3/4), March/April (2000) pp. 389-429.

  • CMOS Integrated Organic Ciliary Actuator Arrays for General-Purpose Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs) Journal of Microelectromechanical Systems, vol. 8, No. 4 (Dec. 1999), pp. 483-496.
    • [PDF] B&W version of published paper
  • "A Single Universal Force Field Can Uniquely Pose Any Part Up To Symmetry," (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki) 9th International Symposium of Robotics Research (ISRR) Snowbird, Utah October 9-12 (1999).
    • [PDF]
  • We have three chapters in Distributed Manipulation, ed. K. Böhringer et al., Kluwer Academic Publishing, Boston (2000):
    1. CMOS Integrated Organic Ciliary Actuator Arrays for General-Purpose Micromanipulation Tasks, (with J. Suh, R. B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs).
    2. A Distributed, Universal Device for Planar Parts Feeding: Unique Part Orientation in Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki).
    3. Constrained Prehensile Manipulation: Distributed Manipulation with Ropes (with L. Gariepy and D. Rus).
  • CMOS Integrated Organic Ciliary Actuator Array as a General-Purpose Micromanipulation Tool (with J. Suh, B. Darling, K.-F. Böhringer, H. Baltes, and G. Kovacs) IEEE International Conference on Robotics and Automation, Workshop on Distributed Manipulation, (Detroit) May 11, 1999.
  • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE International Conference on Robotics and Automation, Workshop on Distributed Manipulation (Detroit) May 11, 1999.
  • Algorithmic MEMS, (with K.-F. Böhringer), Invited lecture at the Third International Workshop on the Algorithmic Foundations of Robotics (WAFR), Houston, TX (March, 1998). Book version: In Robotics: The Algorithmic Perspective, ed. P. Agarwal et al., A. K. Peters, Natick, MA (1998). pp. 1-20.
  • Computational Methods for the Design and Control of MEMS Micromanipulator Arrays (with K.-F. Böhringer, G. Kovacs, N. MacDonald, and J. Suh) IEEE Computational Science and Engineering, Vol. 4, No. 1. Special Issue on Computational MEMS (Jan-March 1997). pp. 17-29.
    • [PDF]
  • On The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Discrete and Computational Geometry, vol. 22 (1999), pp. 269-285.
  • Programmable Vector Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders, [TR FTP] (with K.-F. Böhringer, and N. C. MacDonald), (International Journal of Robotics Research). vol. 18(2), pp. 168-200 (1999).
    • Galleys from IJRR: [PDF]
  • Micro Contacts and Micro Manipulation with MEMS Actuator Arrays, (with K.-F. Böhringer IEEE International Conference on Robotics and Automation, Workshop on Modeling, Contact Analysis, and Simulation of Mechanical Systems in Robotics and Manufacturing, (Belgium, 1998).
  • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
  • Vector Fields for Task-Level Distributed Manipulation: Experiments with Organic Micro Actuator Arrays [TR FTP], (with K.-F. Böhringer, J. Suh, and G. Kovacs) in Proc. IEEE International Conference on Robotics and Automation, Albuquerque, NM (1997). pp 1779-1786.
  • The Area Bisectors of a Polygon and Force Equilibria in Programmable Vector Fields [TR FTP], (with K.-F. Böhringer, and D. Halperin) 13th Proc. ACM Symposium on Computational Geometry, Nice, France (1997) pp. 457-459.
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Single-Crystal Silicon Actuator Arrays for Micro Manipulation Tasks [TR FTP], IEEE Workshop on Micro Electro Mechanical Systems (MEMS), San Diego, California (February 1996).
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Classification and Lower Bounds for MEMS Arrays and Vibratory Parts Feeders: What Programmable Vector Fields Can (and Cannot) Do, IEEE International Conference on Robotics and Automation (ICRA), Minneapolis, Minnesota (April 1996).
  • Distributed Robotic Manipulation: Experiments in Minimalism [TR FTP], in International Symposium on Experimental Robotics, (ISER) Stanford, CA (1995). Appears in: in Experimental Robotics IV, Lecture Notes in Control and Information Sciences 223, ed. O. Khatib et al., Springer Verlag (Berlin) 1997 pp. 11-25.
  • Sensorless Manipulation Using Massively Parallel Micro-fabricated Actuator Arrays [TR FTP] (with K.-F. Böhringer, R. Mihailovich, and Noel C. MacDonald), Proc. IEEE International Conference on Robotics and Automation, San Diego, CA (May, 1994).
    A demo and more detailed explanation.
  • K.-F. Böhringer, B. R. Donald, R. Mihailovich, and N. C. MacDonald, A Theory of Manipulation and Control for Microfabricated Actuator Arrays, Proceedings of the IEEE Workshop on Micro Electro Mechanical Systems (MEMS), Oiso, Japan (January 1994).
    • [PDF]
  • Planning Multi-Step Error Detection and Recovery Strategies. International Journal of Robotics Research, 9(1), 1990. pp. 3-60.

• Mobile Robotics

  Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with many videos describing our mobile robotics research.

  Scientific papers (with some pointers to videos) are provided for you here, in the list immediately below:

  • The Compass That Steered Robotics. In Logic and Program Semantics, Lecture Notes in Computer Science (LNCS) 7230, Springer-Verlag (Berlin) 2012. pp. 50-65.
    • [PDF]
  • Distributed Manipulation of Multiple Objects Using Ropes, (with L. Gariepy and D. Rus), Proc. IEEE International Conference on Robotics and Automation (ICRA), San Francisco (April, 2000) pp. 450-457.
  • Practical Mobile Robot Self-Localization (with J. Howell) Proceedings, International Conference on Robotics and Automation, San Francisco, CA, April 24-28, 2000. pp. 3485-3492.

    Movie, 4:30, Quicktime w/Sorenson codec, max 250 kb/s (42MB)	mapmaking-movie-5.250kbit.mov
    Movie, 4:30, Quicktime w/Sorenson codec, max 100 kb/s (26MB)	mapmaking-movie-5.100kbit.mov
    The paper (Gzipped PostScript) (0.8 MB)	ICRA'2000 paper

  • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.
  • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.
  • We have three chapters in Distributed Manipulation, ed. K. Böhringer et al., Kluwer Academic Publishing, Boston (2000).
  • Experiments in Constrained Prehensile Manipulation: Distributed Manipulation with Ropes, with Larry Gariepy and Daniela Rus, In Experimental Robotics VI, Lecture Notes in Control and Information Sciences, Vol. 250, eds. P. Corke, Springer-Verlag, (2000).

  • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
  • Information Invariants for Distributed Manipulation (with J. Jennings and D. Rus) in International Journal of Robotics Research, Vol. 16, No. 5 (1997). pp. 673-702.
    • Here are the galleys from MIT Press (7/14/97).
    • Technical Report (1994) [TR FTP]
    • [Movie]

  • B. R. Donald, J. Jennings, and D. Rus, Minimalism + Distribution = Supermodularity [TR FTP], Journal of Experimental and Theoretical Artificial Intelligence (JETAI), Special issue on Software Architectures for Hardware Agents; Vol. 9 No. 2-3 (1997) pp. 293-321.

  • . On Information Invariants in Robotics. Artificial Intelligence 72 (Jan, 1995) pp. 217-304.
    • [ Abstract, PDF, Accepted Manuscript ]

  • Cost-effective, Capable, and Configurable Multiple Robots: A Report to the ARPA ISAT Study Group, Summer, 1996 (with J. Jennings and D. Rus).
  • R.G. Brown and J.S. Jennings. A pusher/steerer model for strongly cooperative mobile robot cooperation. In IEEE/RSJ IROS, pages 562-568, 1995.
  • Moving Furniture with Teams of Automonous Mobile Robots [TR FTP], (with J. Jennings and D. Rus) in

    Proc. IEEE/Robotics Society of Japan International Workshop on Intelligent Robots and Systems, (IROS) Pittsburgh, PA (1995).

  • .
    Program Mobile Robots in Scheme (with J. Rees) Proc. IEEE International Conference on Robotics and Automation Nice, France (May, 1992), pp. 2681-2688.
    
    [PDF]
    Many people do not realize that the title of this paper is in the imperative mode. It should be read as:
    Program Mobile Robots in Scheme! Note the exclamation point.

  • Information Invariants for Distributed Manipulation [TR FTP] (with J. Jennings and D. Rus) in The First Workshop on the Algorithmic Foundations of Robotics, A. K. Peters, Boston, MA. ed. R. Wilson and J.-C.Latombe (1994).
    • [Movie]
  • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
  • ``Towards a Theory of Information Invariants for Cooperating Autonomous Mobile Robots,'' (with J. Jennings and D. Rus) International Symposium of Robotics Research (ISRR). Hidden Valley, PA (October 2, 1993).

• Motion Planning and Geometric Algorithms

  • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.

  • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.

  • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
  • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
    • [PDF]
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
    • [PDF]
  • . Kinodynamic Motion Planning [TR FTP] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
    • [PDF]
  • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
  • ``The Motion of Planar Compliantly-Connected Rigid Bodies in Contact, with Applications to Automatic Fastening,'' B. R. Donald and D. Pai. International Journal of Robotics Research 12(4), August 1993, pp. 307-338.
    • [PDF]
  • ``Symbolic Methods for the Simulation of Planar Mechanical Systems in Design,'' B. R. Donald and D. Pai. in Symbolic and Numerical Computation for Artificial Intelligence, (ed. B. Donald et al.) Academic Press, Harcourt Jovanovich, (London: 1992), pp. 245-258.
  • A Geometric Approach to Error Detection and Recovery for Robot Motion Planning with Uncertainty, Artificial Intelligence, 1988: 37(1-3), pp. 223-271.
    • [PDF]
  • A Search Algorithm for Motion Planning with Six Degrees of Freedom, Artificial Intelligence 31(3), 1987. pp. 295-353.
    • [PDF]

• Graphics, Haptics, Computer-Aided Architecture, and Animation

  Our lab has a YouTube channel: http://www.youtube.com/user/labdonald/videos, with some videos describing our graphics and animation research.

  Scientific papers (with some pointers to videos) are provided for you here, in the list immediately below:

  • "Accessible Animation and Customizable Graphics via Simplicial Configuration Modeling'' (with T. Ngo, D. Cutrell, J. Dana, L. Loeb, and S. Zhu), in Proc. ACM SIGGRAPH (New Orleans) July, 2000, pp. 403-410.
    • [PDF]
  • Using Haptic Vector Fields for Animation Motion Control (with F. Henle) Proc. IEEE Int. Conf. on Robotics and Automation (ICRA), San Francisco (April, 2000) pp. 3435-3442.
    • Animations and Figures.
    • PDF.
  • Prototyping Animation Motion Control with Haptic Programmable Force Fields, Workshop on "Motion Support in Virtual Prototyping," (with Fred Henle) Stanford, May 5-7, 1999.
  • System for Image Manipulation and Animation Using Embedded Constraint Graphics (with J. T. Ngo), U.S. Patent #5,933,150, issued August 3, 1999.
    • [PDF]

    

  • Real-Time Robot Motion Planning Using Rasterizing Computer Graphics Hardware, (with J. Lengyel, M. Reichert, and D. Greenberg), Proc. SIGGRAPH '90, Dallas, TX (Aug 1990), pp. 327-336.
    • [PostScript , PDF, Movie]

  
  
  
  
  
  

  • Selected Manuals, Software Documentation, Technical Reports, and Design Exhibitions

    • The EIGHT Manual: An Introduction to Geometric Modelling and Three-Dimensional Graphics on the Lisp Machine. Working Paper 262, MIT Artificial Intelligence Laboratory, Cambridge, MA (1984); and Cornell Computer Science Department Technical Report TR 91-1186, Cornell University, Ithaca NY (1991).
      • [PDF]
      
    •  BUILDER: A Database and Display Program for Computer-aided Architectural Design. A system for representation and display of design problems in architecture and urban design. Laboratory for Computer Graphics and Spatial Analysis, Graduate School of Design, Harvard University. Cambridge, MA (1981).
      NB: The manual is mostly text with a few black-and-white images. Some nice color images from BUILDER can be found here.
      • [PDF, Color images from BUILDER, BUILDER Exhibitions]
    • BUILDER: A Database and Display Program for Computer-aided Architectural Design. Harvard Computer Graphics Conference, (Session 17, Architectural Practice) July 27, 1982. Cambridge, MA.
      • [Scanned 35 mm slides]
      
    • A Familiar Space in Two Dimensions: Piper Auditorium Computer-aided Design (CAD) Study (with Paul Stevenson Oles). Design Exhibition. Graduate School of Design, Harvard University (1982).
      • [Scanned renderings and images from exhibition]
    •  Alternative Methods of Language Creation. Documentation of the GLIB language maker for the LINGUIST language system. Laboratory for Computer Graphics and Spatial Analysis, Graduate School of Design, Harvard University. Cambridge, MA (1979).
      • [PDF]

• Computational Geometry

  • Protein loop closure using orientational restraints from NMR data (with C. Tripathy, J. Zeng, and P. Zhou). Cover Article.
    Proteins: Structure, Function, and Bioinformatics. Volume 80, Issue 2, pages 433-453, 2012. Journal online: DOI: 10.1002/prot.23207
    • [PDF, Abstract, Supplementary Information (SI), Cover (large, PNG)]
  • A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs (with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou). Journal of Computational Biology 2011; 18(11):1507-23.
    • [PDF]
  • A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers'' (with J. Martin, A. Yan, C Bailey-Kellogg, and P. Zhou). Protein Science 20(6):970-985 (2011) Mar 16. doi: 10.1002/pro.620. [Epub ahead of print] PMID: 21413097
    • [PDF]
  • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Proc. The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (2003) pp. 176-187.
    • [PDF]

  • Mobile Robot Self-Localization without Explicit Landmarks, (with R. G. Brown), Algorithmica 26(3/4), March/April (2000) pp. 515-559.

  • Visibility-Based Planning of Sensor Control Strategies, (with Amy Briggs), Algorithmica 26(3/4), March/April (2000) pp. 364-388.

  • Part Orientation with One or Two Stable Equilibria Using Programmable Force Fields, (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), IEEE Transactions on Robotics and Automation, 16(2), April 2000, pp. 157-170.
  • "A Single Universal Force Field Can Uniquely Pose Any Part Up To Symmetry," (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki) 9th International Symposium of Robotics Research (ISRR) Snowbird, Utah October 9-12 (1999).
  • On The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Discrete and Computational Geometry, vol. 22 (1999), pp. 269-285.
  • Part Orientation with One or Two Stable Equilibria , (with K.-F. Böhringer, F. Lamiraux, and L. Kavraki), International Conference on Robotics and Automation, Workshop on Distributed Manipulation (Detroit) May 11, 1999.
  • The Area Bisectors of a Polygon, (with K.-F. Böhringer, and D. Halperin) Second CGC Workshop on Computational Geometry, (October 18-19, 1997) Duke University, Durham, NC.
  • The Area Bisectors of a Polygon and Force Equilibria in Programmable Vector Fields [TR FTP], (with K.-F. Böhringer, and D. Halperin) 13th Proc. ACM Symposium on Computational Geometry, Nice, France (1997) pp. 457-459.

  • Programmable Vector Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders, [TR FTP] (with K.-F. Böhringer, and N. C. MacDonald), (International Journal of Robotics Research, 1999) vol. 18(2) pp. 168-200.
    • Galleys from IJRR: [PDF]
  • K.-F. Böhringer, B. R. Donald, and N. C. MacDonald, Upper and Lower Bounds for Programmable Vector Fields with Applications to MEMS and Vibratory Parts Feeders, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996). in Algorithms for Robotic Motion and Manipulation,, ed. J. P. Laumond and M. Overmars, A. K. Peters, Wellesley, MA (1997). pp. 255-276.
  • Amy Briggs and B. R. Donald, Robust Geometric Algorithms for Sensor Planning, [TR FTP] International Workshop on the Algorithmic Foundations of Robotics, Toulouse, France (1996).
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning: Robots with Decoupled Dynamics Bounds [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 443-479.
  • Provably Good Approximation Algorithms for Optimal Kinodynamic Planning for Cartesian Robots and Open Chain Manipulators [TR FTP] (with P. Xavier) Algorithmica (Vol 14, no 6) (1995). pp. 480-530.
  • . Kinodynamic Motion Planning [TR FTP] (with P. Xavier, J. Canny, and J. Reif) Journal of the ACM, Vol. 40, No. 5, Nov., 1993. pp. 1048-1066.
    • [PDF reprint]
  • Automatic Sensor Configuration for Task-Directed Planning (with Amy Briggs), Proceedings 1994 IEEE International Conference on Robotics and Automation, San Diego, CA (May 1994).
  • A Rational Rotation Method for Robust Geometric Algorithms, (with J. Canny and E. Ressler). Annual Symposium on Computational Geometry, Proceedings of the Eighth Annual Symposium on Computational Geometry, (1992) Berlin, Germany pp. 251-260.