Publications

Functional annotation

  1. M. Moll, P. W. Finn, and L. E. Kavraki, “Structure-Guided Selection of Specificity Determining Positions in the Human Kinome,” BMC Genomics, 2016.
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  2. M. Moll, P. W. Finn, and L. E. Kavraki, “Structure-Guided Selection of Specificity Determining Positions in the Human Kinome,” in IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015, pp. 21–28.
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  3. D. H. Bryant, M. Moll, P. W. Finn, and L. E. Kavraki, “Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome,” PLoS Computational Biology, vol. 9, no. 6, p. e1003087, 2013.
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  4. J. Chyan, M. Moll, and L. E. Kavraki, “Improving the Prediction of Kinase Binding Affinity Using Homology Models,” in Computational Structural Bioinformatics Workshop at the ACM Conf. on Bioinf., Comp. Bio. and Biomedical Informatics, Washington, DC, 2013.
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  5. M. Moll, D. H. Bryant, and L. E. Kavraki, “The LabelHash Server and Tools for Substructure-Based Functional Annotation,” Bioinformatics, vol. 27, no. 15, pp. 2161–2162, 2011.
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  6. D. H. Bryant, M. Moll, B. Y. Chen, V. Y. Fofanov, and L. E. Kavraki, “Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction,” BMC Bioinformatics, vol. 11, no. 242, p. 242, 2010.
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  7. M. Moll, D. H. Bryant, and L. E. Kavraki, “The LabelHash Algorithm for Substructure Matching,” BMC Bioinformatics, vol. 11, p. 555, 2010.
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  8. D. H. Bryant, “Mapping the Structural Landscape of Protein Families with Geometric Feature Vectors,” Master's thesis, Rice University, Department of Computer Science, Houston, TX, 2009.
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  9. M. Moll and L. E. Kavraki, “LabelHash: A Flexible and Extensible Method for Matching Structural Motifs,” in Automated Function Prediction / BioSapiens meeting (AFP-BioSapiens), 2008. Available from Nature Precedings.
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  10. M. Moll and L. E. Kavraki, “Matching of Structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction,” in The Seventh Annual International Conference on Computational Systems Bioinformatics (CSB2008), 2008, pp. 157–168.
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  11. A. Shehu, “Molecules in Motion: Computing Structural Flexibility,” PhD thesis, Rice University, Houston, TX, 2008.
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  12. D. M. Kristensen, M. R. Ward, A. M. Lisewski, S. Edrin, B. Y. Chen, V. Y. Fofanov, M. Kimmel, L. E. Kavraki, and O. Lichtarge, “Prediction of enzyme function based on 3D templates of evolutionarily important amino acids,” BMC Bioinformatics, vol. 9, 2008.
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  13. V. Y. Fofanov, B. Y. Chen, D. H. Bryant, M. Moll, O. Lichtarge, L. E. Kavraki, and M. Kimmel, “A Statistical Model to Correct Systematic Bias Introduced by Algorithmic Thresholds in Protein Structural Comparison Algorithms,” in IEEE Intl. Conf. on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, 2008.
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  14. B. Y. Chen, “Geometry-based methods for protein function prediction,” PhD thesis, Rice University, Department of Computer Science, Houston, Texas, 2008.
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  15. B. Y. Chen, D. H. Bryant, V. Y. Fofanov, D. M. Kristensen, A. E. Cruess, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “Cavity Scaling: Automated Refinement of Cavity-Aware Motifs in Protein Function Prediction,” Journal of Bioinformatics and Computational Biology, vol. 5, no. 2a, pp. 353–382, 2007.
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  16. B. Y. Chen, D. H. Bryant, A. E. Cruess, J. H. Bylund, V. Y. Fofanov, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction,” in Computational Systems Bioinformatics Conference (CSB2007), 2007, pp. 343–355.
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  17. B. Y. Chen, V. Y. Fofanov, D. H. Bryant, B. D. Dodson, D. M. Kristensen, A. M. Lisewski, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs,” Journal of Computational Biology, vol. 14, no. 6, pp. 791–816, 2007.
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  18. B. Y. Chen, D. H. Bryant, V. Y. Fofanov, D. M. Kristensen, A. E. Cruess, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction,” in Systems Bioinformatics Conference (CSB), Stanford, CA, 2006, vol. 4, pp. 311–323.
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  19. B. Y. Chen, V. Y. Fofanov, D. H. Bryant, B. D. Dodson, D. M. Kristensen, A. M. Lisewski, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction,” in Research in Computational Biology: 10th Annual International Conference (RECOMB), Venice, Italy, 2006. Published in Lecture Notes in Computer Science, A. Apostolico, C. Guerra, S. Istrail, P. Pevzner, M. Waterman (Eds), Springer, 3909/2006, 500-515
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  20. A. Shehu, C. Clementi, and L. E. Kavraki, “Modeling Protein Conformational Ensembles: From Missing Loops to Equilibrium Fluctuations,” Proteins: Structure, Function and Bioinformatics, vol. 65, no. 1, pp. 164–179, 2006.
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  21. D. M. Kristensen, B. Y. Chen, V. Y. Fofanov, M. R. Ward, A. M. Lisewski, M. Kimmel, L. E. Kavraki, and O. Lichtarge, “Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity,” Protein Science, vol. 15, no. 6, pp. 1530–1536, 2006.
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  22. B. Y. Chen, V. Y. Fofanov, D. M. Kristensen, M. Kimmel, O. Lichtarge, and L. E. Kavraki, “Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs,” in Pacific Symposium on Biocomputing, Hawaii, USA, 2005.
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  23. M. Zhang, R. A. White, L. Wang, R. Goldman, L. E. Kavraki, and B. Hassett, “Improving Conformational Searches by Geometric Screening,” Bioinformatics, vol. 21, no. 5, pp. 624–630, 2005.
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  24. H. Yao, D. M. Kristensen, I. Mihalek, M. Sowa, C. Shaw, M. Kimmel, L. E. Kavraki, and O. Lichtarge, “An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures,” Journal of Molecular Biology, vol. 326, no. 1, pp. 255–261, 2003.
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Fundamentals of protein modeling

  1. D. Devaurs, D. A. Antunes, M. Papanastasiou, M. Moll, D. Ricklin, J. D. Lambris, and L. E. Kavraki, “Coarse-grained conformational sampling of protein structure improves the fit to experimental hydrogen-exchange data,” Frontiers in Molecular Biosciences, vol. 4, no. 13, 2017.
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  2. A. Novinskaya, D. Devaurs, M. Moll, and L. E. Kavraki, “Defining low-dimensional projections to guide protein conformational sampling,” Journal of Computational Biology, vol. 24, no. 1, pp. 79–89, 2017.
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  3. D. Devaurs, M. Papanastasiou, D. A. Antunes, J. R. Abella, M. Moll, D. Ricklin, J. D. Lambris, and L. E. Kavraki, “Native state of complement protein C3d analysed via hydrogen exchange and conformational sampling,” in International Conference on Intelligent Biology and Medicine (ICIBM), 2016.
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  4. A. Novinskaya, D. Devaurs, M. Moll, and L. E. Kavraki, “Improving protein conformational sampling by using guiding projections,” in IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), 2015, pp. 1272–1279.
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  5. B. Gipson, D. Hsu, L. E. Kavraki, and J.-C. Latombe, “Computational Models of Proteins Kinematics and Dynamics: Beyond Simulation,” Annual Reviews of Analytical Chemistry, vol. 5, pp. 273–291, 2012.
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  6. A. Shehu and L. E. Kavraki, “Modeling Structures and Motions of Loops in Protein Molecules,” Entropy, vol. 14, pp. 252–290, 2012.
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  7. N. Haspel, M. Moll, M. L. Baker, W. Chiu, and L. E. Kavraki, “Tracing conformational changes in proteins,” BMC Structural Biology, vol. 10, no. Suppl. 1, p. S1, 2010.
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  8. A. P. Heath, L. E. Kavraki, and C. Clementi, “From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes,” Proteins: Structure, Function and Bioinformatics, vol. 68, no. 3, pp. 646–661, Aug. 2007.
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  9. H. Stamati, “Analysis of Molecular Motion using Non-Linear Dimensionality Reduction,” Master's thesis, Rice University, Houston, TX, 2007.
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  10. P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi, “Low-dimensional Free-energy Landscapes of Protein-Folding Reactions by Nonlinear Dimensionality Reduction,” Proceedings of the National Academy of Sciences, vol. 103, no. 26, pp. 9885–9890, Jun. 2006.
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  11. M. L. Teodoro, “Modeling Protein Flexibility Using Collective Modes of Motion: Applications to Drug Design,” PhD thesis, Rice University, Houston, TX, 2003.
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  12. M. Zhang and L. E. Kavraki, “Approximating Solutions of Molecular Inverse Kinematics Problems by Subdivision,” in The 24th International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS) and the Annual Meeting of the Biomedical Engineering Society (BMES), 2002, pp. 2182–2183.
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  13. M. Zhang and L. E. Kavraki, “Solving Molecular Inverse Kinematics Problems for Protein Folding and Drug Design,” in Currents in Computational Molecular Biology, 2002, pp. 214–215. Book includes short papers from The Sixth ACM International Conference on Research in Computational Biology (RECOMB 2002), Washington, DC, 2002
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  14. M. Zhang and L. E. Kavraki, “A New Method for Fast and Accurate Derivation of Molecular Conformations,” Journal of Chemical Information and Computer Sciences, vol. 42, no. 1, pp. 64–70, 2002.
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  15. M. L. Teodoro, G. N. P. Jr., and L. E. Kavraki, “Molecular Docking: A Problem with Thousands of Degrees of Freedom,” in Proc. of the 2001 IEEE International Conference on Robotics and Automation (ICRA 2001), Seoul, Korea, 2001, pp. 960–966.
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  16. M. Zhang and L. E. Kavraki, “Efficiently Maintaining Molecular Conformations Using Local Frames,” in Currents in Computational Molecular Biology, Montreal, Canada, 2001, pp. 97–98. Book includes short papers from The Fifth ACM International Conference on Research in Computational Biology (RECOMB), Montreal, Canada, 2001
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  17. M. L. Teodoro, G. N. P. Jr., and L. E. Kavraki, “Singular Value Decomposition of Protein Conformational Motions: Application to HIV-1 Protease,” in Currents in Computational Molecular Biology, Tokyo, Japan, 2000, pp. 198–199. Book includes short papers from The Forth ACM International Conference on Computational Biology (RECOMB), 2000
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Fundamentals of sampling-based motion planning

  1. D. Halperin, L. E. Kavraki, and K. Solovey, “Robotics,” in Handbook of Discrete and Computational Geometry, J. E. Goodman, J. O’Rourke, and C. D. Tóth, Eds. Boca Raton, NY: CRC Press, 2017.
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  2. F. T. Pokorny, D. Kragic, L. E. Kavraki, and K. Goldberg, “High-Dimensional Winding-Augmented Motion Planning with 2D Topological Task Projections and Persistent Homology,” in Proc. IEEE Intl. Conf. on Robotics and Automation, 2016, pp. 24–31.
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  3. D. Devaurs, T. Siméon, and J. Cortés, “Optimal path planning in complex cost spaces with sampling-based algorithms,” IEEE Transactions on Automation Science and Engineering, vol. 13, no. 2, pp. 415–424, 2016.
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  4. L. E. Kavraki and S. M. LaValle, “Motion Planning,” in Handbook of Robotics, 2nd Edition, Springer, 2016.
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  5. M. Moll, I. A. Şucan, and L. E. Kavraki, “Benchmarking Motion Planning Algorithms: An Extensible Infrastructure for Analysis and Visualization,” IEEE Robotics & Automation Magazine (Special Issue on Replicable and Measurable Robotics Research), vol. 22, no. 3, pp. 96–102, 2015.
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  6. R. Luna, I. A. Şucan, M. Moll, and L. E. Kavraki, “Anytime Solution Optimization for Sampling-Based Motion Planning,” in IEEE International Conference on Robotics and Automation, Karlsruhe, Germany, 2013, pp. 5053–5059.
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  7. B. Gipson, M. Moll, and L. E. Kavraki, “Resolution Independent Density Estimation for Motion Planning in High-Dimensional Spaces,” in IEEE International Conference on Robotics and Automation, 2013, pp. 2429–2435.
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  8. I. A. Şucan, M. Moll, and L. E. Kavraki, “The Open Motion Planning Library,” IEEE Robotics & Automation Magazine, vol. 19, pp. 72–82, Dec. 2012. http://ompl.kavrakilab.org
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  9. I. A. Sucan and L. E. Kavraki, “A Sampling-Based Tree Planner for Systems With Complex Dynamics,” IEEE Transactions on Robotics, vol. 28, no. 1, pp. 116–131, 2012.
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  10. I. A. Sucan and L. E. Kavraki, “On the Implementation of Single-Query Sampling-Based Motion Planners,” in IEEE International Conference on Robotics and Automation, Anchorage, Alaska, 2010, pp. 2005–2011.
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  11. I. A. Sucan and L. E. Kavraki, “On the Performance of Random Linear Projections for Sampling-Based Motion Planning,” in IEEE/RSJ International Conference on Intelligent Robots and Systems, St. Louis, 2009, pp. 2434–2439.
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  12. K. I. Tsianos, D. Halperin, L. E. Kavraki, and J.-C. Latombe, “Robot Algorithms,” in Algorithms and Theory of Computation Handbook, Second., vol. 2, Boca Raton, FL: CRC Press, 2008.
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  13. K. I. Tsianos, I. A. Sucan, and L. E. Kavraki, “Sampling-based robot motion planning: Towards realistic applications,” Computer Science Review, vol. 1, pp. 2–11, Aug. 2007.
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  14. E. Plaku and L. E. Kavraki, “Nonlinear Dimensionality Reduction Using Approximate Nearest Neighbors,” in SIAM International Conference on Data Mining (SDM), Minneapolis, Minnesota, 2007, pp. 3711–3716.
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  15. M. Moll and L. E. Kavraki, “Path Planning for Deformable Linear Objects,” IEEE Transactions on Robotics, vol. 22, no. 4, pp. 625–636, Aug. 2006.
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  16. K. E. Bekris, A. A. Argyros, and L. E. Kavraki, “Exploiting Panoramic Vision for Angle-Based Robot Navigation,” in Lecture Notes in Computer Science, Vol. 33, Springer, 2006, pp. 229–251.
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  17. A. M. Ladd, “Motion Planning for Physical Simulation,” PhD thesis, Rice University, Houston, TX, 2006.
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  18. E. Plaku and L. E. Kavraki, “Quantitative Analysis of Nearest Neighbors Search in High-Dimensional Sampling-based Motion Planning,” in Workshop on Algorithmic Foundations of Robotics (WAFR), New York, NY, 2006.
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  19. H. Choset, W. Burgard, S. Hutchinson, G. Kantor, L. E. Kavraki, K. Lynch, and S. Thrun, Principles of Robot Motion: Theory, Algorithms, and Implementation. MIT Press, 2005.
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  20. E. Plaku and L. E. Kavraki, “Distributed Sampling-Based Roadmap of Trees for Large-Scale Motion Planning,” in IEEE International Conference on Robotics and Automation, Barcelona, Spain, 2005, pp. 3879–3884.
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  21. A. M. Ladd and L. E. Kavraki, “Fast Tree-Based Exploration of State Space for Robots with Dynamics,” in Algorithmic Foundations of Robotics VI, Springer, STAR 17, 2005, pp. 297–312.
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  22. M. Akinc, K. E. Bekris, B. Y. Chen, A. M. Ladd, E. Plaku, and L. E. Kavraki, “Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps,” in Robotic Research: The Eleventh International Symposium, Springer, STAR 15, 2005, pp. 80–89.
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  23. E. Plaku, K. E. Bekris, B. Y. Chen, A. M. Ladd, and L. E. Kavraki, “Sampling-Based Roadmap of Trees for Parallel Motion Planning,” IEEE Transactions on Robotics, vol. 21, no. 4, pp. 597–608, 2005.
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  24. A. M. Ladd and L. E. Kavraki, “Measure Theoretic Analysis of Probabilistic Path Planning,” IEEE Transactions on Robotics and Automation, vol. 20, no. 2, pp. 229–242, Apr. 2004.
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  25. D. Halperin, L. E. Kavraki, and J.-C. Latombe, “Robotics,” in Handbook of Discrete and Computational Geometry, Boca Raton, NY: CRC Press, 2004, pp. 1065–1094.
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  26. K. E. Bekris, B. Y. Chen, A. M. Ladd, E. Plaku, and L. E. Kavraki, “Multiple Query Probabilistic Roadmap Planning Using Single Query Planning Primitives,” in 2003 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS), Las Vegas, NV, 2003, pp. 656–661.
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  27. A. M. Ladd and L. E. Kavraki, “Generalizing the Analysis of PRM,” in Proceedings of the 2002 IEEE International Conference on Robotics and Automation (ICRA 2002), Washington, DC, 2002, pp. 2120–2125.
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  28. P. K. Agrawal, L. J. Guibas, H. Edelsbrunner, J. Erickson, M. Isard, S. Har-Peled, J. Hershberger, C. Jensen, L. E. Kavraki, P. Koehl, M. Lin, D. Manocha, D. Metaxas, B. Mirtich, D. Mount, and S. Muthukrishnan, “Algorithmic Issues in Modeling Motion,” ACM Computing Surveys, vol. 34, no. 4, pp. 550–572, 2002.
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  29. O. Brock and L. E. Kavraki, “Decomposition-Based Motion Planning: A Framework for Real-Time Motion Planning in High-Dimensional Configuration Places,” in Proceedings of The 2001 IEEE International Conference on Robotics and Automation (ICRA), 2001, pp. 1469–1475.
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  30. R. Bohlin and L. E. Kavraki, “A Randomized Algorithm for Robot Path Planning Based on Lazy Evaluation,” in Handbook on Randomized Computing, Kluwer Academic Publishers, 2001, pp. 221–249.
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  31. J. Yakey, S. M. LaValle, and L. E. Kavraki, “Randomized Path Planning for Linkages with Closed Kinematics Chains,” IEEE Transactions on Robotics and Automation, vol. 17, no. 6, pp. 951–959, 2001.
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  32. C. Nielsen and L. E. Kavraki, “A Two-Level Fuzzy PRM for Manipulation Planning,” in Proceedings of The IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 2000, vol. 3, pp. 1716–1722.
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  33. R. Bohlin and L. E. Kavraki, “Path Planning Using Lazy PRM,” in Proceedings of the IEEE International Conference on Robotics and Automation, San Fransisco, CA, 2000, vol. 1, pp. 521–528.
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  34. T. Danner and L. E. Kavraki, “Randomized Planning for Short Inspection Paths,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), San Fransisco, CA, 2000, vol. 2, pp. 971–976.
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  35. C. Holleman and L. E. Kavraki, “A Framework for Using the Workspace Medial Axis in PRM Planners,” in Proceedings of the 2000 International Conference on Robotics and Automation (ICRA 2000 ), San Fransisco, CA, 2000, vol. 2, pp. 1408–1413.
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  36. S. M. LaValle, J. Yakey, and L. E. Kavraki, “A Probabilistic Roadmap Approach for Systems with Closed Kinematic Chains,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), Detroit, MI, 1999, vol. 3, pp. 1671–1677.
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  37. L. E. Kavraki, “Algorithms in Robotics: The Motion Planning Perspective,” in Frontiers of Engineering Publication, National Academy of Engineering, 1999, pp. 90–93.
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  38. D. Hsu, L. E. Kavraki, J.-C. Latombe, R. Motwani, and J. Rolim, “Capturing the Connectivity of High-Dimensional Geometric Spaces by Parallelizable Random Sampling Techniques,” in Parallel and Distributed Processing, vol. 1388, Springer Verlag Lecture Notes in Computer Science, 1999, pp. 330–340.
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  39. L. J. Guibas, C. Holleman, and L. E. Kavraki, “A Probabilistic Roadmap Planner for Flexible Objects with a Workspace Medial-Axis Based Sampling Approach,” in Proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), Kyongju, Korea, 1999, vol. 1, pp. 254–260.
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  40. D. Halperin, L. E. Kavraki, J.-C. Latombe, and M. Attalah, “Robot Algorithms,” in Algorithms and Theory of Computation Handbook, Boca Raton, NY: CRC Press, 1999.
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  41. L. E. Kavraki, J.-C. Latombe, R. Motwani, and P. Raghavan, “Randomized Query Processing in Robot Path Planning,” Journal of Computer and System Sciences, vol. 57, no. 1, pp. 50–60, Aug. 1998.
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  42. L. E. Kavraki, M. N. Kolountzakis, and J.-C. Latombe, “Analysis of Probabilistic Roadmaps for Path Planning,” IEEE Transactions on Robotics and Automation, vol. 14, no. 1, pp. 166–171, 1998.
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  43. D. Hsu, L. E. Kavraki, J.-C. Latombe, R. Motwani, and S. Sorkin, “On Finding Narrow Passages with Probabilistic Roadmap Planners,” in Robotics: The algorithmic perspective, Natick, MA: A.K. Peters, 1998, pp. 141–153.
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  44. L. E. Kavraki and J.-C. Latombe, “Probabilistic Roadmaps for Robot Path Planning,” in Practical Motion Planning in Robotics: Current Approaches and Future Directions, John Wiley, 1998, pp. 33–53.
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  45. P. K. Agrawal, L. E. Kavraki, and M. Mason, Robotics: The Algorithmic Perspective. Natick MA: AK Peters, 1998.
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  46. B. Barraquand, L. E. Kavraki, J.-C. Latombe, T.-Y. Li, R. Motwani, and P. Raghavan, “A Random Sampling Scheme for Robot Path Planning,” International Journal of Robotics Research, vol. 16, no. 6, pp. 759–774, 1997.
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  47. L. E. Kavraki, M. N. Kolountzakis, and J.-C. Latombe, “Analysis of Probabilistic Roadmaps for Path Planning,” in Proceeedings of The 1996 International Conference on Robotics and Automation (ICRA 1996), Minneapolis, MN, 1996, pp. 3020–3026.
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  48. L. E. Kavraki, P. Svestka, J.-C. Latombe, and M. Overmars, “Probabilistic Roadmaps for Path Planning in High Dimensional Configuration Spaces,” IEEE Transactions on Robotics and Automation, vol. 12, no. 4, pp. 566–580, 1996.
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  49. B. Barraquand, L. E. Kavraki, J.-C. Latombe, T.-Y. Li, R. Motwani, and P. Raghavan, “A Random Sampling Scheme for Robot Path Planning,” in Robotics Research, North Holland, 1996, pp. 249–264. Book contains selected papers form the 7th International Conference on Robotics Research (ISRR), 1996
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  50. L. E. Kavraki, J.-C. Latombe, R. Motwani, and P. Raghavan, “Randomized Query Processing in Robot Path Planning,” in Proceedings of the 27th Annual ACM Symposium on Theory of Computing (STOC), Las Vegas, NV, 1995, pp. 353–362.
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  51. L. E. Kavraki and J.-C. Latombe, “Randomized Preprocessing of Configuration Space for Fast Path Planning,” in Proceedings of the International Conference on Robotics and Automation (ICRA), San Diego, CA, 1994, pp. 2138–2139.
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  52. L. E. Kavraki and J.-C. Latombe, “Randomized Preprocessing of Configuration Space for Path Planning: Articulated Robots,” in Proceedings of the IEEE/RSJ/GI International Conference on Intelligent Robots and Systems (IROS), Munchen, Germany, 1994, pp. 1764–1771.
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Kinodynamic systems

  1. S. Butler, M. Moll, and L. E. Kavraki, “A General Algorithm for Time-Optimal Trajectory Generation Subject to Minimum and Maximum Constraints,” in Workshop on the Algorithmic Foundations of Robotics, 2016.
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  2. K. E. Bekris, D. K. Grady, M. Moll, and L. E. Kavraki, “Safe Distributed Motion Coordination for Second-Order Systems With Different Planning Cycles,” International Journal of Robotics Research, vol. 31, no. 2, pp. 129–150, 2012.
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  3. D. K. Grady, K. E. Bekris, and L. E. Kavraki, “Asynchronous Distributed Motion Planning with Safety Guarantees under Second-Order Dynamics,” in Algorithmic Foundations of Robotics IX, vol. 68, Singapore, Singapore: Springer Berlin / Heidelberg, 2011, pp. 53–70. 10.1007/978-3-642-17452-0_4
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  4. I. A. Şucan, “Task and Motion Planning for Mobile Manipulators,” PhD thesis, Rice University, Department of Computer Science, Houston, TX, 2011.
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  5. D. K. Grady, “Unsynchronized Distributed Motion Planning with Safety Guarantees under Second-Order Dynamics,” Master's thesis, Rice University, Houston, TX, 2011.
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  6. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Motion Planning with Dynamics by a Synergistic Combination of Layers of Planning,” IEEE Transactions on Robotics, vol. 26, no. 3, pp. 469–482 , 2010.
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  7. I. A. Sucan and L. E. Kavraki, “Kinodynamic Motion Planning by Interior-Exterior Cell Exploration,” in Algorithmic Foundation of Robotics VIII (Proceedings of Workshop on the Algorithmic Foundations of Robotics), Guanajuato, Mexico, 2009, vol. 57, pp. 449–464.
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  8. K. E. Bekris, K. I. Tsianos, and L. E. Kavraki, “Safe and Distributed Kinodynamic Replanning for Vehicular networks,” ACM/Springer Mobile Networks and Applications (MONET), vol. 14, no. 3, pp. 292–308, 2009.
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  9. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Discrete Search Leading Continuous Exploration for Kinodynamic Motion Planning,” in Robotics: Science and Systems, Atlanta, Georgia, 2008, pp. 326–333.
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  10. E. Plaku, “From High-Level Tasks to Low-Level Motions: Motion Planning for High-Dimensional Nonlinear Hybrid Robotic Systems,” PhD thesis, Rice University, Houston, TX, 2008.
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  11. I. A. Şucan, “Kinodynamic Motion Planning for High-dimensional Physical Systems,” Master's thesis, Rice University, Houston, TX, 2008.
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  12. I. A. Sucan, J. F. Kruse, M. Yim, and L. E. Kavraki, “Kinodynamic Motion Planning with Hardware Demonstrations,” in IEEE/RSJ International Conference on Intelligent Robots and Systems, Nice, France, 2008, pp. 1661–1666.
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  13. I. A. Sucan, J. F. Kruse, M. Yim, and L. E. Kavraki, “Reconfiguration for modular robots using kinodynamic motion planning,” in ASME – Dynamic Systems and Control, Ann Arbor, Michigan, USA, 2008.
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  14. K. I. Tsianos and L. E. Kavraki, “Replanning: A powerful planning strategy for hard kinodynamic problems,” in IEEE/RSJ International Conference on Intelligent Robots and Systems, Nice, France, 2008, pp. 1667–1672.
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  15. K. I. Tsianos, “Replanning: A Powerful Planning Strategy for Systems with Differential Constraints,” Master's thesis, Rice University, Houston, TX, 2008.
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  16. K. E. Bekris, K. I. Tsianos, and L. E. Kavraki, “A Distributed Protocol for Safe Real-Time Planning of Communicating Vehicles with Second-Order Dynamics,” in First International Conference on Robot Communication and Coordination (ROBOCOMM 07), Athens, Greece, 2007.
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  17. K. E. Bekris and L. E. Kavraki, “Greedy but Safe Replanning under Kinodynamic Constraints,” in Intl. Conf. on Robotics and Automation, Rome, Italy, 2007, pp. 704–710.
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  18. K. E. Bekris, K. I. Tsianos, and L. E. Kavraki, “A Decentralized Planner that Guarantees the Safety of Communicating Vehicles with Complex Dynamics that Replan Online,” in IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, San Diego, CA, 2007.
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  19. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “A Motion Planner for a Hybrid Robotic System with Kinodynamic Constraints,” in IEEE International Conference on Robotics and Automation (ICRA), Rome, Italy, 2007, pp. 692–697.
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  20. M. Moll, P. Will, M. Krivokon, and W.-M. Shen, “Distributed Control of the Center of Mass of a Modular Robot,” in Proc. 2006 IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, Beijing, China, 2006, pp. 4710–4715.
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  21. A. M. Ladd and L. E. Kavraki, “Motion Planning in the Presence of Drift, Underactuation and Discrete System Changes,” in Robotics: Science and Systems I, Boston, MA, 2005, pp. 233–241.
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  22. J. M. Phillips, N. Bedrosian, and L. E. Kavraki, “Guided Expansive Spaces Trees: A Search Strategy for Motion- and Cost-Constrained State Spaces,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), New Orleans, LA, 2004, pp. 3968–3973.
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  23. J. M. Phillips, L. E. Kavraki, and N. Bedrosian, “Spacecraft Rendezvous and Docking With Real-Time Randomized Optimization,” in AIAA (American Institute of Aeronautics and Astronautics) Guidance, Navigation and Control Conference, Austin, TX, 2003.
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  24. J. M. Phillips, L. E. Kavraki, and N. Bedrosian, “Probabilistic Optimization Applied to Spacecraft Rendezvous and Docking,” in 13th American Astronomical Society/AIAA - Space Flight Mechanics Meeting, Puerto Rico, 2003.
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Localization

  1. K. E. Bekris, M. Glick, and L. E. Kavraki, “Evaluation of Algorithms for Bearing-Only SLAM,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), Orlando, FL, 2006, pp. 1937–1944.
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  2. A. M. Ladd, K. E. Bekris, A. Rudys, G. Marceau, L. E. Kavraki, and D. S. Wallach, “Robotics-Based Location Sensing using Wireless Ethernet (Invited),” Wireless Networks (The Journal of Mobile Communication, Computation and Information), vol. 11, no. 1-2, pp. 189–204, Jan. 2005.
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  3. A. Haeberlen, E. Flannery, A. M. Ladd, A. Rudys, D. S. Wallach, and L. E. Kavraki, “Practical Robust Localization over Large-Scale 802.11 Wireless Networks,” in Proceedings of the Tenth ACM International Conference on Mobile Computing and Networking (MOBICOM 2004), Philadelphia, PA, 2004, pp. 70–84.
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  4. A. M. Ladd, K. E. Bekris, A. Rudys, L. E. Kavraki, and D. S. Wallach, “On the Feasibility of Using Wireless Ethernet for Indoor Localization,” IEEE Transactions on Robotics and Automation, vol. 20, no. 3, pp. 555–559, Jun. 2004.
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  5. A. M. Ladd, K. E. Bekris, A. Rudys, G. Marceau, L. E. Kavraki, and D. S. Wallach, “Robotics-Based Location Sensing using Wireless Ethernet,” in Proceedings of the Eight ACM International Conference on Mobile Computing and Networking (MOBICOM 2002), Atlanta, GE, 2002, pp. 227–238.
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  6. A. M. Ladd, K. E. Bekris, G. Marceau, A. Rudys, L. E. Kavraki, and D. S. Wallach, “Using Wireless Ethernet for Localization,” in Proceedings of the 2002 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS 2002), Lausanne, Switzerland, 2002, vol. 1, pp. 402–408.
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Metabolic networks

  1. S. M. Kim, M. I. Peña, M. Moll, G. Giannakopoulos, G. N. Bennett, and L. E. Kavraki, “An Evaluation of Different Clustering Methods and Distance Measures Used for Grouping Metabolic Pathways,” in Eighth International Conference on Bioinformatics and Computational Biology (BICoB), 2016.
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  2. A. P. Heath, G. N. Bennett, and L. E. Kavraki, “An Algorithm for Efficient Identification of Branched Metabolic Pathways,” Journal of Computational Biology, vol. 18, no. 11, pp. 1575–1597, Nov. 2011.
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  3. A. P. Heath, G. N. Bennett, and L. E. Kavraki, “Identifying Branched Metabolic Pathways by Merging Linear Metabolic Pathways,” 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), vol. 6577/2011, pp. 70–84, 2011.
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  4. A. P. Heath, “Computational Discovery and Analysis of Metabolic Pathways,” PhD thesis, Rice University, Department of Computer Science, Houston, TX, 2010.
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  5. A. P. Heath, G. N. Bennett, and L. E. Kavraki, “Finding Metabolic Pathways Using Atom Tracking,” Bioinformatics, vol. 26, no. 12, pp. 1548–1555, 2010.
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Other biomedical computing

  1. A. P. Heath and L. E. Kavraki, “Computational Challenges in Systems Biology,” Computer Science Review, vol. 3, no. 1, pp. 1–17, 2009.
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  2. A. P. Heath, G. Balázsi, and L. E. Kavraki, “Bipolarity of the saccharomyces cerevisiae genome,” International Conference on Bioinformatics and Biomedical Engineering (iCBBE), pp. 330–333, 2008.
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  3. M. L. Teodoro and L. E. Kavraki, “Pharmacology,” in Handbook of Data Mining and Knowledge Discovery, Oxford University Press, 2002, pp. 808–816.
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  4. A. Schweikard, R. Tombropoulos, L. E. Kavraki, J. Adler, and J.-C. Latombe, “Treatment Planning for a Radiosurgical System with General Kinematics,” in Proceedings of the IEEE/RJS International Conference on Robotics and Automation (ICRA), San Diego, CA, 1994, pp. 1764–1771.
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Other robotics

  1. J. Bohg, M. Ciocarlie, J. Civera, and L. E. Kavraki, “Big Data on Robotics,” Big Data, vol. 4, no. 4, pp. 195–196, Dec. 2016.
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  2. N. T. Dantam, K. Bøndergaard, M. A. Johansson, T. Furuholm, and L. E. Kavraki, “Unix Philosophy and the Real World: Control Software for Humanoid Robots,” Frontiers in Robotics and Artificial Intelligence, vol. 3, Mar. 2016.
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  3. J. D. Hernández, M. Moll, E. Vidal Garcia, M. Carreras, and L. E. Kavraki, “Planning Feasible and Safe Paths Online for Autonomous Underwater Vehicles in Unknown Environments,” in IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, 2016, pp. 1313–1320.
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  4. L. E. Kavraki and M. Moll, “Editorial: Special Issue on the 2014 ‘Robotics: Science & Systems’ Conference,” Intl. J. of Robotics Research, vol. 3–4, no. 1–3, 2016.
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  5. Z. Kingston, N. Dantam, and L. Kavraki, “Kinematically constrained workspace control via linear optimization,” in IEEE-RAS 15th International Conference on Humanoid Robots (Humanoids), 2015, pp. 758–764.
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  6. L. E. Kavraki and M. Likhachev, “Editorial: Special Issue on the 2014 ‘Robotics: Science & Systems’ Conference,” Autonomous Robots, vol. 39, no. 3, 2015.
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  7. D. Coleman, I. A. Şucan, M. Moll, K. Okada, and N. Correll, “Experience-Based Planning with Sparse Roadmap Spanners,” in IEEE Intl. Conf. on Robotics and Automation, Seattle, WA, 2015, pp. 900–905.
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  8. C. Voss, M. Moll, and L. E. Kavraki, “A Heuristic Approach to Finding Diverse Short Paths,” in IEEE Intl. Conf. on Robotics and Automation, Seattle, WA, 2015, pp. 4173–4179.
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  9. M. Moll, J. Bordeaux, and L. E. Kavraki, “Software for Project-Based Learning of Robot Motion Planning,” Computer Science Education, Special Issue on Robotics in CS Education, vol. 23, no. 4, pp. 332–348, 2013.
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  10. D. K. Grady, M. Moll, C. Hegde, A. C. Sankaranarayanan, R. G. Baraniuk, and L. E. Kavraki, “Look Before You Leap: Predictive Sensing and Opportunistic Navigation,” in Workshop on Progress and Open Problems in Motion Planning at the IEEE/RSJ Conf. on Intelligent Robots and Systems, San Francisco, 2011.
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  11. M. Moll, I. A. Sucan, J. Bordeaux, and L. E. Kavraki, “Teaching Motion Planning Concepts to Undergraduate Students,” in IEEE Workshop on Advanced Robotics and its Social Impacts, 2011.
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  12. M. Moll, J. Bordeaux, and L. E. Kavraki, “Teaching Robot Motion Planning,” Computers in Education (Special Issue on Novel Approaches to Robotics Education), vol. 20, no. 3, pp. 50–59, 2010.
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  13. R. B. Rusu, I. A. Sucan, B. P. Gerkey, S. Chitta, M. Beetz, and L. E. Kavraki, “Real-Time Perception-Guided Motion Planning for a Personal Robot,” in IEEE/RSJ International Conference on Intelligent Robots and Systems, St. Louis, 2009, pp. 4245–4252.
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  14. K. E. Bekris, “Informed Planning and Safe Distributed Replanning under Physical Constraints,” PhD thesis, Rice University, Houston, TX, 2008.
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  15. M. Moll and D. Rus, “Special Issue on Self-Reconfiguring Modular Robots (Guest Editorial),” Intl. J. of Robotics Research, vol. 27, pp. 277–278, 2008.
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  16. M. Yim, W.-M. Shen, B. Salemi, D. Rus, M. Moll, H. Lipson, and E. Klavins, “Modular Self-reconfigurable Robot Systems: Challenges and Opportunities for the Future,” IEEE Robotics & Automation Magazine, vol. 14, no. 1, Mar. 2007.
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  17. E. Plaku and L. E. Kavraki, “Distributed Computation of the KNN Graph for Large High-Dimensional Point Sets,” Journal of Parallel and Distributed Computing, vol. 67, no. 3, pp. 346–359, 2007.
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  18. E. Plaku, K. E. Bekris, and L. E. Kavraki, “OOPS for Motion Planning: An Online Open-source Programming System,” in IEEE International Conference on Robotics and Automation (ICRA), Rome, Italy, 2007, pp. 3711–3716.
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  19. B. Salemi, M. Moll, and W.-M. Shen, “SUPERBOT: A Deployable, Multi-Functional, and Modular Self-Reconfigurable Robotic System,” in Proc. 2006 IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, Beijing, China, 2006, pp. 3636–3641.
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  20. M. Moll and L. E. Kavraki, “Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length,” in Proc. 2005 IEEE Intl. Conf. on Robotics and Automation, Barcelona, Spain, 2005, pp. 2143–2147.
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  21. A. A. Argyros, K. E. Bekris, S. C. Orphanoudakis, and L. E. Kavraki, “Robot Homing by Exploiting Panoramic Vision,” Autonomous Robots, vol. 19, no. 1, pp. 7–25, 2005.
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  22. K. E. Bekris, A. A. Argyros, and L. E. Kavraki, “Angle-Based Methods for Mobile Robot Navigation: Reaching the Entire Plane,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), New Orleans, LA, 2004, pp. 2373–2378.
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  23. M. Moll and L. E. Kavraki, “Path Planning for Minimal Energy Curves of Constant Length,” in Proceedings of The IEEE International Conference on, New Orleans, LA, 2004, pp. 2826–2831.
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  24. A. M. Ladd and L. E. Kavraki, “Motion Planning for Knot Untangling,” in Algorithmic Foundations of Robotics V, Springer Tracks in Advanced Robotics, Springer Verlag, STAR 7, 2004, pp. 7–23.
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  25. A. M. Ladd and L. E. Kavraki, “Using Motion Planning for Knot Untangling,” International Journal of Robotics Research, vol. 23, no. 7-8, pp. 797–808, 2004.
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  26. M. Moll and M. A. Erdmann, “Reconstructing the Shape and Motion of Unknown Objects,” in Algorithmic Foundations of Robotics V, Springer, 2003, pp. 293–310.
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  27. J. M. Phillips, A. M. Ladd, and L. E. Kavraki, “Simulated Knot Tying,” in Proceedings of The 2002 IEEE International Conference on Robotics and Automation (ICRA 2002), Washington, DC, 2002, pp. 841–846.
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  28. A. Sudsang and L. E. Kavraki, “Part Orientation with a Force Field: Orienting Multiple Shapes using a Single Field,” in Proceedings of The 2001 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS 2001), 2001, vol. 1, pp. 208–213.
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  29. M. Moll and M. A. Erdmann, “Reconstructing Shape from Motion Using Tactile Sensors,” in Proc. 2001 IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, Maui, HI, 2001, pp. 691–700.
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  30. A. Sudsang and L. E. Kavraki, “A Geometric Approach to Designing a Programmable Force Field with a Unique Stable Equilibrium for Parts in the Plane,” in Proceedings of The 2001 IEEE International Conference on Robotics and Automation (ICRA 2001), Seoul, Korea, 2001, vol. 2, pp. 1079–1085. This paper was a finalist for best conference paper award
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  31. M. Moll and M. A. Erdmann, “Manipulation of Pose Distributions,” in Algorithmic and Computational Robotics: New Directions, A. K. Peters, 2001, pp. 127–141.
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  32. F. Lamiraux and L. E. Kavraki, “Planning Paths for Elastic Objects under Manipulation Constraints,” International Journal of Robotics Research, vol. 20, no. 3, pp. 188–208, 2001.
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  33. F. Lamiraux and L. E. Kavraki, “Positioning of Symmetric and Non-Symmetric Parts Using Radial and Constant Fields: Computation of All Equilibrium Configurations,” International Journal of Robotics Research, vol. 20, no. 8, pp. 635–659, 2001.
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  34. F. Lamiraux and L. E. Kavraki, “Positioning Symmetric and Non-Symmetric Parts using Radial and Constant Force Fields,” in Robotics:New Directions, Natick, MA, 2001, pp. 37–50. Book containts the proceedings of the International Workshop on the Algorithmic Foundations of Robotics (WAFR), Dartmouth, March 2000
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  35. M. Moll and M. A. Erdmann, “Shape Reconstruction in a Planar Dynamic Environment,” no. CMU-CS-01-, 2001.
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  36. J. Luo and L. E. Kavraki, “Part Assembly Using Static and Dynamic Force Fields,” in Proceedings of The IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 2000, vol. 2, pp. 1468–1474.
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  37. O. Brock and L. E. Kavraki, “Towards Real-Time Motion Planning in High Dimensional Spaces,” in Proceedings of The International Symposium on Robotics and Automation (ISRA), Monterey, Mexico, 2000.
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  38. E. Anshelevich, S. Owens, F. Lamiraux, and L. E. Kavraki, “Deformable Volumes in Path Planning Applications,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), San Fransisco, CA, 2000, vol. 3, pp. 2290–2295.
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  39. K.-F. Bohringer, B. R. Donald, L. E. Kavraki, and F. Lamiraux, “A Distributed, Universal Device for Planar Parts Feeding: Unique Part Orientation in Programmable Vector Fields,” in Distributed Manipulation, Kluwer Academic Publishers, 2000, pp. 1–29.
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  40. K.-F. Bohringer, B. R. Donald, L. E. Kavraki, and F. Lamiraux, “Part Orientation with One or Two Stable Equilibria Using Programmable Vector Fields,” IEEE Transactions on Robotics and Automation, vol. 16, no. 2, pp. 157–170, 2000.
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  41. F. Lamiraux and L. E. Kavraki, “Positioning and Orienting a Class of Symmetric Parts Using a Combination of a Unit-Radial and a Constant Force Fields,” in Proceedings of The 2000 IEEE International Conference on Robotics and Automation (ICRA 2000), San Fransisco, CA, 2000, vol. 1, pp. 178–183.
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  42. F. Lamiraux and L. E. Kavraki, “Path Planning for Elastic Plates Under Manipulation,” in Proceedings of The IEEE International Conference on, Detroit, MI, 1999, vol. 1, pp. 151–156.
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  43. K.-F. Bohringer, B. R. Donald, L. E. Kavraki, and F. Lamiraux, “A Single Universal Force Field can Uniquely Orient Non-Symmetric Parts,” in Robotics Research: The 9th International Symposium, Springer, 1999, pp. 395–402.
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  44. C. Holleman, L. E. Kavraki, and J. Warren, “Planning Paths for a Flexible Surface Patch,” in Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), Leuven, Belgium, 1998, vol. 1, pp. 21–26.
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  45. L. E. Kavraki, F. Lamiraux, and C. Holleman, “Towards Planning for Elastic Objects,” in Robotics: The Algorithmic Perspective, Natick, MA, 1998, pp. 313–325. Proceedings of the Third Workshop on the Algorithmic Foundations of Robotics (WAFR), Houston, TX, 1998
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  46. L. E. Kavraki, “Part Orientation with Programmable Vector Fields: Two Stable Equilibria for Most Parts,” in Proceedings of The International Conference on Robotics and Automation (ICRA), Albuquerque, NM, 1997, vol. 3, pp. 2446–2452.
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  47. D. Halperin, L. E. Kavraki, and J.-C. Latombe, “Robotics,” in Handbook of Discrete and Computational Geometry, Boca Raton, NY: CRC Press, 1997, pp. 755–779.
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  48. L. E. Kavraki, “Computation of Configuration Space Obstacles Using the Fast Fourier Transform,” IEEE Transactions on Robotics and Automation, vol. 11, no. 3, pp. 408–413, 1995.
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  49. L. E. Kavraki, “On the Number of Equilibrium Placements of Mass Distributions in Elliptic Potential Fields,” no. 1559, 1995.
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  50. L. E. Kavraki and M. N. Kolountzakis, “Partitioning an Assembly into Connected Parts is NP-hard,” Information Processing Letters, vol. 55, pp. 159–165, 1995.
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  51. R. H. Wilson, L. E. Kavraki, J.-C. Latombe, and T. Lozano-Perez, “Two-Handed Assembly Sequencing,” International Journal of Robotics Research, vol. 14, no. 4, pp. 335–350, 1995.
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  52. L. E. Kavraki, J.-C. Latombe, and R. H. Wilson, “On the Complexity of Assembly Partitioning,” Information Processing Letters, vol. 48, no. 5, pp. 229–235, 1993.
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  53. L. E. Kavraki, “Computation of configuration-space obstacles using the fast Fourier transform,” in IEEE International Conference on Robotics and Automation, 1993, vol. 3, pp. 255–261.
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Planning from high-level specifications

  1. W. Baker, Z. Kingston, M. Moll, J. Badger, and L. Kavraki, “Robonaut 2 and You: Specifying and Executing Complex Operations,” in IEEE Workshop on Advanced Robotics and its Social Impacts (ARSO), Austin, TX, 2017. To appear.
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  2. N. T. Dantam, Z. K. Kingston, S. Chaudhuri, and L. E. Kavraki, “Incremental Task and Motion Planning: A Constraint-Based Approach,” in Robotics: Science and Systems, 2016.
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  3. M. Lahijanian, M. R. Maly, D. Fried, L. E. Kavraki, H. Kress-Gazit, and M. Vardi, “Iterative Temporal Planning in Uncertain Environments with Partial Satisfaction Guarantees,” IEEE Transactions on Robotics, vol. 32, no. 3, pp. 583–599, 2016.
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  4. Y. Wang, N. T. Dantam, S. Chaudhuri, and L. E. Kavraki, “Task and Motion Policy Synthesis as Liveness Games,” in International Conference on Automated Planning and Scheduling, 2016, pp. 536–540.
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  5. K. He, M. Lahijanian, L. E. Kavraki, and M. Y. Vardi, “Towards Manipulation Planning with Temporal Logic Specifications,” in 2015 IEEE Intl. Conf. Robotics and Automation (ICRA), Seattle, WA, 2015, pp. 346–352.
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  6. K. He, “Robot Manipulation Planning Under Linear Temporal Logic Specifications,” Master's thesis, Rice University, Houston, TX, 2015.
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  7. S. Nedunuri, S. Prabhu, M. Moll, S. Chaudhuri, and L. E. Kavraki, “ SMT-Based Synthesis of Integrated Task and Motion Plans for Mobile Manipulation,” in IEEE Intl. Conf. on Robotics and Automation, 2014, pp. 655–662.
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  8. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Falsification of LTL safety properties in hybrid systems,” International Journal on Software Tools for Technology Transfer (STTT), vol. 15, no. 4, pp. 305–320, 2013.
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  9. M. R. Maly, M. Lahijanian, L. E. Kavraki, H. Kress-Gazit, and M. Y. Vardi, “Iterative Temporal Motion Planning for Hybrid Systems in Partially Unknown Environments,” in ACM International Conference on Hybrid Systems: Computation and Control (HSCC), Philadelphia, PA, USA, 2013, pp. 353–362.
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  10. M. R. Maly and L. E. Kavraki, “Low-Dimensional Projections for SyCLoP,” in IEEE/RSJ International Conference on Intelligent Robots and Systems, Vilamoura, Algarve, Portugal, 2012, pp. 420–425.
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  11. I. A. Sucan and L. E. Kavraki, “Accounting for Uncertainty in Simultaneous Task and Motion Planning Using Task Motion Multigraphs,” in IEEE International Conference on Robotics and Automation, St. Paul, 2012, pp. 4822–4828.
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  12. D. K. Grady, M. Moll, C. Hegde, A. C. Sankaranarayanan, R. G. Baraniuk, and L. E. Kavraki, “Multi-Objective Sensor-Based Replanning for a Car-Like Robot,” in IEEE International Symposium on Safety, Security, and Rescue Robotics, College Station, TX, 2012, pp. 1–6.
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  13. D. K. Grady, M. Moll, C. Hegde, A. C. Sankaranarayanan, R. G. Baraniuk, and L. E. Kavraki, “Multi-Robot Target Verification with Reachability Constraints,” in IEEE International Symposium on Safety, Security, and Rescue Robotics, College Station, TX, 2012, pp. 1–6.
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  14. A. Bhatia, M. R. Maly, L. E. Kavraki, and M. Y. Vardi, “Motion Planning with Complex Goals,” Robotics Automation Magazine, IEEE, vol. 18, no. 3, pp. 55–64, Sep. 2011.
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  15. I. A. Sucan and L. E. Kavraki, “On the Advantages of Using Task Motion Multigraphs for Efficient Mobile Manipulation,” in IEEE/RSJ International Conference on Intelligent Robots and Systems, San Francisco, CA, 2011, pp. 4621–4626.
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  16. I. A. Sucan and L. E. Kavraki, “Mobile Manipulation: Encoding Motion Planning Options Using Task Motion Multigraphs,” in IEEE International Conference on Robotics and Automation, Shanghai, China, 2011, pp. 5492–5498.
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  17. A. Bhatia, L. E. Kavraki, and M. Y. Vardi, “Sampling-Based Motion Planning with Temporal Goals,” in IEEE International Conference on Robotics and Automation, Anchorage, Alaska, 2010, pp. 2689–2696.
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  18. A. Bhatia, L. E. Kavraki, and M. Y. Vardi, “Motion Planning with Hybrid Dynamics and Temporal Goals,” in IEEE Conference on Decision and Control, Atlanta, GA, 2010, pp. 1108–1115.
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  19. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Falsification of LTL Safety Properties in Hybrid Systems,” in Proc. of the Conf. on Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2009), York, UK, 2009.
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  20. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Hybrid systems: from verification to falsification by combining motion planning and discrete search,” Formal Methods in System Design, vol. 34, pp. 157–182, 2009.
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  21. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Impact of Workspace Decompositions on Discrete Search Leading Continuous Exploration (DSLX) Motion Planning,” in IEEE International Conference on Robotics and Automation, Pasadena, CA, 2008, pp. 3751–3756.
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  22. E. Plaku, L. E. Kavraki, and M. Y. Vardi, “Hybrid Systems: From Verification to Falsification,” in International Conference on Computer Aided Verification (CAV), vol. 4590, Berlin, Germany: Lecture Notes in Computer Science, Springer-Verlag Heidelberg, 2007, pp. 468–481.
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Proteins and drugs

  1. P. K. Mandal, P. Morlacchi, J. M. Knight, T. M. Link, G. R. Lee, R. Nurieva, D. Singh, A. Dhanik, L. E. Kavraki, D. B. Corry, J. E. Ladbury, and J. S. McMurray, “Targeting the Src homology 2 (SH2) domain of signal transducer and activator of transcription 6 (STAT6) with cell-permeable, phosphatase-stable phosphopeptide mimics potently inhibits Tyr641 phosphorylation and transcriptional activity,” Journal of Medicinal Chemistry, 2015.
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  2. D. A. Antunes, D. Devaurs, and L. E. Kavraki, “Understanding the challenges of protein flexibility in drug design,” Expert Opinion on Drug Discovery, vol. 10, no. 12, pp. 1301–1313, 2015.
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  3. D. Devaurs, K. Molloy, M. Vaisset, A. Shehu, T. Siméon, and J. Cortés, “Characterizing energy landscapes of peptides using a combination of stochastic algorithms,” IEEE Transactions on NanoBioscience, vol. 14, no. 5, pp. 545–552, 2015.
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  4. A. Dhanik, J. McMurray, and L. E. Kavraki, “DINC: A new AutoDock-based protocol for docking large ligands,” BMC Structural Biology, vol. 13, no. Suppl 1, p. S11, 2013.
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  5. B. Gipson, M. Moll, and L. E. Kavraki, “SIMS: A hybrid method for rapid conformational analysis,” PLOS ONE, vol. 8, no. 7, p. e68826, 2013.
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  6. A. Dhanik, J. S. McMurray, and L. E. Kavraki, “AUTODOCK-based Incremental Docking Protocol to Improve Docking of Large Ligands,” in IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), Philadelphia, 2012, pp. 48–55.
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  7. A. Dhanik, J. S. McMurray, and L. E. Kavraki, “Binding Modes of Peptidomimetics Designed to Inhibit STAT3,” PLoS ONE, vol. 7(12), p. e51603, 2012.
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  8. A. Dhanik and L. E. Kavraki, “Protein-ligand interactions: computational docking,” eLS. John Wiley & Sons Ltd, 2012.
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  9. D. H. Bryant, “Redundancy-aware learning of protein structure-function relationships,” PhD thesis, Rice University, Department of Computer Science, Houston, Texas, 2012.
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  10. A. Dhanik, J. S. McMurray, and L. E. Kavraki, “On modeling peptidomimetics in complex with the SH2 domain of Stat3,” in 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC ’11), Boston, Massachusetts, USA, 2011, pp. 3329–3332.
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  11. H. Stamati, C. Clementi, and L. E. Kavraki, “Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides,” Proteins, vol. 78, no. 2, pp. 223–235, Jul. 2010.
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  12. A. Shehu, L. E. Kavraki, and C. Clementi, “Multiscale characterization of protein conformational ensembles,” Proteins, vol. 76, no. 4, pp. 837–851, 2009.
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  13. N. Haspel, B. Geisbrecht, J. D. Lambris, and L. E. Kavraki, “Multi-scale Characterization of the Energy Landscape of Proteins with Application to the C3d/Efb-C Complex,” Proteins: Structure, function and bioinformatics, vol. 78, no. 4, pp. 1004–1014, 2009.
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  14. N. Haspel, M. Moll, M. L. Baker, W. Chiu, and L. E. Kavraki, “Tracing Conformational Changes in Proteins,” in IEEE Intl. Conf. on Bioinformatics and Biomedicine Workshops (BIBMW), Washington, DC, 2009.
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  15. N. Haspel, D. Ricklin, B. Geisbrecht, J. D. Lambris, and L. E. Kavraki, “Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d.,” Protein Science, vol. 17(11), pp. 1894–1906, 2008.
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  16. D. Ricklin, S. K. Ricklin-Lichtsteiner, G. Sfyroera, H. Chen, A. Tzekou, P. Magotti, Y.-Q. Wu, B. L. Garcia, W. J. McWorther, N. Haspel, L. E. Kavraki, B. Geisbrecht, and J. D. Lambris, “Novel insights into target specificities and molecular mechanisms for two potent complement evasion proteins from Staphylococcus aureus.,” in XXII International Complement Workshop, Basel, Switzerland, 2008.
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  17. A. Shehu, L. E. Kavraki, and C. Clementi, “Unfolding the Fold of Cyclic Cysteine-rich Peptides,” Protein Science, vol. 17, pp. 482–493, 2008.
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  18. M. Moll, D. Schwarz, and L. E. Kavraki, “Roadmap Methods for Protein Folding,” in Protein Structure Prediction: Methods and Protocols, Humana Press, 2007.
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  19. A. Shehu, L. E. Kavraki, and C. Clementi, “On the Characterization of Protein Native State Ensembles,” Biophysical Journal, vol. 92, no. 5, pp. 1503–1511, 2007.
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  20. E. Plaku, H. Stamati, C. Clementi, and L. E. Kavraki, “Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction,” Proteins: Structure, Function, and Bioinformatics, vol. 67, no. 4, pp. 897–907, 2007.
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  21. D. Schwarz and L. E. Kavraki, “Protein-Ligand Interactions: Computational Docking,” in Encyclopedia of Life Sciences, Wiley, 2007, pp. Article #A4105.
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  22. A. Shehu, C. Clementi, and L. E. Kavraki, “Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins,” Algorithmica, vol. 48, pp. 303–327, 2007.
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  23. M. Moll, D. Schwarz, A. P. Heath, and L. E. Kavraki, “On Flexible Docking Using Expansive Search,” no. 04-443, 2004.
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  24. M. L. Teodoro and L. E. Kavraki, “Conformational Flexibility Models for the Receptor in Structure Based Drug Design,” Current Pharmaceutical Design, vol. 9, pp. 1419–1431, 2003.
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  25. M. L. Teodoro, G. N. P. Jr., and L. E. Kavraki, “Understanding Protein Flexibility through Dimensionality Reduction,” The Journal of Computational Biology, vol. 10, no. 3-4, pp. 617–634, 2003.
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  26. M. L. Teodoro, G. N. P. Jr., and L. E. Kavraki, “A Dimensionality Reduction Approach to Modeling Protein Flexibility,” in Proceedings of the 2002 ACM International Conference on Research in Computational Biology (RECOMB 2002), 2002, pp. 299–308.
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  27. S. M. LaValle, P. W. Finn, L. E. Kavraki, and J.-C. Latombe, “A Randomized Kinematics-based Approach to Pharmacophore-Constrained Conformational Search and Database Screening,” Journal of Computational Chemistry, vol. 21, no. 9, pp. 731–747, 2000.
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  28. P. W. Finn and L. E. Kavraki, “Computational Approaches to Drug Design,” Algorithmica, vol. 25, pp. 347–371, 1999.
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  29. S. M. LaValle, P. W. Finn, L. E. Kavraki, and J.-C. Latombe, “Efficient Database Screening for Rational Drug Design Using Pharmacophore-Constrained Conformational Search,” in The Third ACM International Conference on Computational Biology (RECOMB), Grenoble, France, 1999, pp. 250–259.