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Scholarly Interest Report
         
Lydia Kavraki
Professor
Noah Harding Professor of Computer Science and Bioengineering
 
e-mail:kavraki@rice.edu
 
  • B.S. (1989) University of Crete, Greece
  • M.S. (1992) Stanford University
  • Ph.D. (1995) Stanford University
 
Primary Department
   Department of Computer Science
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Department Affiliations
 
  • Department of Bioengineering
  • Institute of Biosciences and Bioengineering
  • Keck Center for Quantitative Biomedical Sciences
  • Ken Kennedy Institute for Information Technology
  •  
    Other Affiliations
     
  • Baylor College of Medicine
  •  
    Websites
     Kavraki Lab Page
     Kavraki Personal Page
     
    Research Areas
     Robotics, Bioinformatics, Algorithms
     

    Research Interests

     

    The Kavraki Lab Webpage: http://www.kavrakilab.org includes descriptions of research work and full list of publications.

     
    Selected Publications
     Abstracts
     

    A. Dhanik, J. McMurray, and L.E. Kavraki, "Experimentally measured versus computationally predicted binding scores of phosphopeptide inhibitors of Stat3: a comparative study", 22nd American Peptide Symposium, June, 2011.

     
     

    A.P. Heath, S. Neira, G. Bennett, and L.E. Kavraki, "Search Tools for Metabolic Pathway Discovery and Analysis", Annual Conference of the Society for Industrial Microbiology, July, 2011.

     
     

    L.E. Kavraki, "Look Before you Leap: Predictive Sensing and Opportunistic Navigation", Workshop on Progress and Open Problems in Motion Planning, IEEE/RSJ International Conference on Intelligent Robotics and Systems, September 30, 2011. 

     
     

    M. Moll, D.H. Bryant, and L.E. Kavraki, "Labelhash: A fast, versatile substructure matching tool for functional annotation and modeling variability within protein families", Protein Structure Initiative 2010 NIGMS Workshop: Enabling Technologies in Structure and Function, (Bethesda, MD), 2010.

     
     

    N. Haspel, M. Moll, M.L.Baker, W. Chiu, and L.E. Kavraki, "Tracing conformational changes in proteins", Proteins Structure Initiative 2010 NIGMS Workshop: Enabling Technologies in Structure and Fuction, (Bethesda, MD), 2010.

     
     

    A.H. Heath, G.M. Bennett, and L.E. Kavraki, "Finding Metabolic Pathways Using Full Atom Tracking", The 19th Keck Center Annual Research Conference, October 29-30, 2009, Houston, TX, p. 59.

     
     

    A. Heath, G.N. Bennett and L.E. Kavraki "Visualizing the Results of Metabolic Pathway Queries."  (Sept. 21-24, 2008)

     
     

    A. Heath, L.E. Kavraki, and G. Balazsi "Understanding the Role of Housekeeping and Stress-Related Genes in Transcription-Regulatory Networks."  (March 10-14, 2008)

     
     

    A. Shehu, C. Clementi and L.E. Kavraki "A Multiscale Framework for the Characterization of Protein Native States."  (2008)

     
     

    A. Shehu, L.E. Kavraki, and C. Clementi "A Multiscale Characterization of Native Conformational States in Proteins."  (January 6-11, 2008)

     
     

    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, J.D. Lambris "Novel insights into target specifications and molecular mechanisms for two potent complement evasion proteins from Staphylococcus aureus - Basel, Switzerland."  (Sept. 28, 2008)

     
     

    M. Moll and L.E. Kavraki "LabelHash: A Flexible and Extensible Method for Matching Structural Motifs." Nature Precedings (2008)

     
     

    M. Moll, D.H. Bryant and L.E. Kavraki "A Flexible and Extensible Method for Matching Structural Motifs."  (Oct. 3-4, 2008) : 85.

     
     

    A. Shehu, L.E. Kavraki, and C. Clementi "Detailed Conformational Characterization of the Native State of Cyclic Cysteine-Rich Peptides Using Minimal Information." 12th Structural Biology Symposium (May 18-19, 2007) : 142.

     
     

    B.Y. Chen, D.H. Bryant, J. Bylund, A. Cruess, D.M. Kristenson, V.Y. Fofanov, M. Moll, M. Kimmel, O. Lichtarge, L.E. Kavraki "Representations of Structural Motifs for Protein Function Prediction." ISMB/ECCB 2007 (July 19-20, 2007)

     
     

    H. Stamati, C. Clementi, and L.E. Kavraki "Analysis of Molecular Motion using Non-Linear Dimensionality Reduction." 23rd Annual Houston Conference on Biomedical Engineering Research (February 2007) : 258.

     
     

    K.E. Bekris, A. Ladd, and L.E. Kavraki "Efficient Motion Planners for Systems with Dynamics." Workshop on Collision-Free Motion Planning for Dynamical Systems, IEEE Intl. Conf. on Robotics and Automation (April 2007)

     
     

    K.E. Bekris, K. Tsianos, and L.E. Kavraki "Real-Time Kinodynamic Planning: Physically Realistic, Faster, Safer, and Distributed." Workshop on Algorithmic Motion Planning for Autonomous Robots in Challenging Environments, IEEE Intl. Conf. on Intelligent Robots and Systems (November 2007)

     
     

    A. Shehu, C. Clementi and L.E. Kavraki "A Computational Method for Capturing Structured and Properties in Proteins." 23rd Annual Houston Conference on Biomedical Engineering Reseach (2006/Feb) : 96.

     
     

    A. Shehu, C. Clementi and L.E. Kavraki "A Method to Model Conformational Ensembles of Proteins at Equilibrium." 11th Strctural Biology Symposium (2006/May) : 134.

     
     

    A. Shehu, C. Clementi and L.E. Kavraki "Advances at Predicting Protein Conformational Ensembles at Equlibrium: A Multi-scaling Approach." 62nd Southwest Regioal Meeting of the American Chemical Society (2006/Oct) : 442.

     
     

    A. Shehu, C. Clementi, and L.E. Kavraki "Advances at Predicting Protein Conformational Ensembles at Equilibrium: A Multi-scaling approach." Keck Center 16th Annual Research Conference (2006/Oct) : 50.

     
     

    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." 23rd Annual Houston Conference on Biomedical Engineering Reseach (2006/Feb)

     
     

    B.Y. Chen, V.Y. Fofanov, D.H. Bryant, B.D. Dodson, D.M. Kristensen, M. Kimmel, O. Lichtarge, and L.E. Kavraki "Geometric Uniqueness Refines Motifs for Protein Structure Prediction." 11th Structural Biology Symposium (2006/May) : 110.

     
     

    H. Stamati. P. Das, M. Moll, C. Clementi and L. Kavraki "Analysis of Free Energy Surfaces of Large Protien Motions Through Non-linear Dimensionality Reduction." Keck Center 16th Annual Research Conference (2006/Oct) : 52.

     
     

    A. Shehu, C. Clementi, and L.E. Kavraki "Sampling Biomolecular Conformations with Spatial and Energetic Constraints." 8th Johns Hopkins Folding Meeting (March 2005)

     
     

    M. Moll and L.E. Kavraki "Path Planning for Sutures Using Minimal Energy Curves." 22nd Annual Houston Conference on Biomedical Engineering Research (February 2005) : 223.

     
     

    M. Moll and L.E. Kavraki "Path Planning for Minimal Energy Curves of Constant Length." 21st Annual Houston Conference on Biomedical Engineering Research (2004)

     
     

    B. Chen, D. Kristensen, A. Christian, O. Lichtarge, and L.E. Kavraki "Structural Pattern Matching for Functional Annotation of Proteins." 20th Annual Houston Conference on Biomedical Engineering Research (2003)

     
     

    M.L. Teodoro, G.N. Phillips, Jr., and L.E. Kavraki "A Dimensionality Reduction Approach to Modeling Protein Flexibility." 20th Annual Houston Conference on Biomedical Engineering Research (2003)

     
     Refereed articles
     

    A. Bhatia, M. Maly, L.E. Kavraki and M.Y. Vardi, "Motion Planning with Complex Goals", IEEE Robotics and Automation Magazine, September 2011, 55-64. 

     
     

    A.P. Heath, G.N. Bennett, and L.E. Kavraki, "An Algorithm for Efficient Identification of Branched Metabolic Pathways", Journal of Computational Biology, November 2011, 18(11): 1575-1597.

     
     

    A.P. Heath, G.N. Bennett, and L.E. Kavraki, "Finding Metabolic Pathways Using Atom Tracking", Bioinformatics, 2010, 26: 1548-1555.

     
     

    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, 2010, 11:242.

     
     

    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, 2010, 26(3): 469-482

     
     

    H. Stamati, C. Clementi, and L.E. Kavraki, "Application of Non-Linear Dimensionality Reduction to Characterize the Conformational Landscape of Small Peptides", Proteins: Stucture, Function, and Bioinformatics, 2010, 2(1): 223-225.

     
     

    M. Moll, D.H. Bryant, and L.E. Kavraki, "The LabelHash Algorithms for Substructure Matching", BMC Bioinformatics, 2010, 11:5555.

     
     

    M. Moll, J. Bordeaux, and L.E. Kavraki, "Teaching Robot Motion Planning", Computers in Education (Special Issue on Novel Approaches to Robotics Education), 2010, 20(3): 50-59.

     
     

    N. Haspel, M. Moll, M.L. Baker, W. Chiu, and L.E. Kavraki, "Tracing Conformational Changes in Proteins", BMC Structural Biology, 2010, 10:S1. 

     
     

    A. Heath and L.E. Kavraki "Computational Challenges in Systems Biology." Computer Science Review, 3(1): 1-17.

     
     

    A. Shehu, L.E. Kavraki, and C. Clementi "Multiscale Characterization of Protein Conformational Ensembles." Proteins: Structure, Function, and Bioinformatics, 76(4): 837-851.

     
     

    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, 34(2): 157-182.

     
     

    K. Bekris, K. Tsianos, and L.E. Kavraki "Safe and Distributed Kinodynamic Replanning for Vehicular Networks." ACM/Springer Mobile Networks and Applications (MONET), 14(3): 292-308.

     
     

    A. Shehu, L.E. Kavraki, and C. Clementi "Unfolding the Fold of Cyclic Cysteine-rich Peptides." Protein Science, 17 (2008) : 482-493.

     
     

    D.M. Kristensen, R.M. Ward, A.M. Lisewski, S. Erdin, B.Y. Chen, V.Y. Fofanov, M. Kimmel, L.E. Kavraki and O. Lichtarge "Prediction of Enzyme Function Based on 3D Templates of Evolutionary Important Aminoacid Motifs." BMC Bioinformatics, 9:17 (2008)

     
     

    N. Haspel, D. Ricklin, B.V. Geisbrecht, L.E. Kavraki and J.D. Lambris "Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d." Protein Science, 17(11) (2008) : 1894-1906.

     
     

    A. Shehu, C. Clementi, and L.E. Kavraki "Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins." Algorithmica, 48 (2007) : 303-327.

     
     

    A. Shehu, L.E. Kavraki, and C. Clementi "On the characterization of Protein Native State Ensembles." Biophysical Journal, 92 (5) (2007) : 1503-1511.

     
     

    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, 68 (3) (2007) : 646-661.

     
     

    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, 5 (2a) (2007) : 353-382.

     
     

    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, 14 (6) (2007) : 791-816.

     
     

    E. Plaku, H. Stamati, C.Clementi, L.E. Kavraki "Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction." Proteins: Structure, Function, and Bioinformatics, 67 (2007) : 897-907.

     
     

    E. Plaku, and L.E. Kavraki "Distributed Computation of the knn Graph for Large High-Dimensional Point Sets." Journal of Parallel and Distributed Computing, 67 (2007) : 346-359.

     
     

    K.I. Tsianos, I.A. Sucan, L.E. Kavraki "Sampling-based Robot Motion Planning: Towards Realistic Applications." Computer Science Reviews, 1 (1) (2007) : 2-11.

     
     

    A. Shehu, C. Clementi, and L.E. Kavraki "Modeling Protein Conformational Ensembles: From Missing Loops to Equilibrium Fluctuations." Protiens: Structure, Function, and Bioinformatics, 65(1), 65 (1) (2006) : 164-179.

     
     

    D.M. Kristensen, B.Y. Chen, V.Y. Fofanov, R.M. Ward, A.M. Lisewski, M. Kimmel, L.E. Kavraki, and O. Lichtarge "Recurrent Use of Evolutionary Importance for Functional Annotation of Protiens Based on Local Structural Similarity." Protein Science, 15 (6) (2006) : 1530-1536.

     
     

    M. Moll and L.E. Kavraki "Path Planning for Deformable Linear Objects." IEEE Transactions on Robotics, 22 (4) (2006) : 625-636.

     
     

    P. Das, M. Moll, H. Stamati, L.E. Kavraki, and C. Clementi "Low-dimensional Free-energy Landscapes of Protien-folding Reactions By Nonlinear Dimensionality Reduction." Procceding of the National Axademy of Sciences, USA, 103(26), 103 (26) (2006-Jun-17) : 9885-9890.

     
     

    A.A. Argyros, K.E. Bekris, S.C. Orfanoudakis, L.E. Kavraki "Robot Homing by Exploiting Panoramic Vision." Autonomous Robots, 19 (1) (2005) : 7-25.

     
     

    A.A. Ladd, K. Bekris, A. Rudys, L.E. Kavraki, D.S. Wallach "Robotics-Based Localization Sensing Using Witeless Ethernet." Wireless Networks, 11(1-2) (2005) : 189-204.

     
     

    E. Plaku, K.E. Bekris, B.Y. Chen, A.M. Ladd, L.E. Kavraki "Sampling-Based Roadmap of Trees for Parallel Motion Planning." IEEE Transactions on Robotics, 21 (4) (2005) : 597-608.

     
     

    M. Zhang, R.A. White, L. Wang, R. Goldman, L.E. Kavraki, B. Hassett "Improving Conformational Searches by Geometric Screening." Bioinformatics, 21 (5) (2005) : 624-630.

     
     

    A.A. Argyros, K.E. Bekris, S.C. Orfanoudakis, and L.E. Kavraki "Robot Homing by Exploring Panoramic Vision." Autonomous Robots Journal (2005) In Press

     
     

    A.M. Ladd and L.E. Kavraki "Measure Theoretic Analysis of Probabilistic Path Planning." Transactions on Robotics and Automation, 20(2) (2004) : 229-242.

     
     

    A.M. Ladd and L.E. Kavraki "Using Motion Planning for Knot Untangling." Transactions on Robotics, 20(3) (2004) : 555-558.

     
     

    A.M. Ladd, K. Bekris, A. Rudys, D.S. Wallach, and L.E. Kavraki "On the Feasibilty of Using Wireless Ethernet for Indoor Localization." IEEE Transactions on Robotics, 20(3) (2004) : 555-558.

     
     

    A.M. Ladd, K. Bekris, A. Rudys, L.E. Kavraki, and D.S. Wallach "Robotics-Based Localization Sensing Wireless Ethernet." Wireless Networks (The Journal of Mobile Communication, Computation and Information (2005) In Press

     
     

    A.M. Ladd and L.E. Kavraki "Using Motion Planning for Knot Untangling." International Journal of Robotics Research (2003) In Press

     
     

    H. Yao, D. Kristensen, I. Mihalek, M. Sowa, Ch. Shaw, M. Kimmel, L.E. Kavraki, and O. Lichtarge "An Accurate, Scalable Method to Identify Functional Sites in Protein Structures." Journal of Molecular Biology, 326(1) (2003) : 255-261.

     
     

    M. Teodoro and L.E. Kavraki "Pharmacology." Handbook on Data Mining and Knowledge Discovery (In Press)

     
     

    M.L. Teodoro and L.E. Kavraki "Conformational Flexibility Models for the Receptor in Structure Based Drug Design." Current Pharmaceutical Design, 9 (2003) : 1419-1431.

     
     

    M.L. Teodoro, G.N. Phillips, and L.E. Kavraki "Understanding Protein Flexibility through Dimensionality Reduction." Journal of Computational Biology, 10(3-4) (2003) : 617-634.

     
     

    A. Ladd, L. Kavraki "Analysis of Probabilistic Roadmap Methods for Path Planning." IEEE Transactions on Robotics and AutomationSubmitted

     
     

    M. Zhang, L. Kavraki "A New Method for Fast and accurate Computation of Molecular Conformations." Journal of Chemical Information and Comuter Sciences, 42(1) (2002) : 64-70.

     
     

    P.K. Agarwal et al "Algorithmic Issues in Modeling Motion." ACM Computing Surveys, 34(4) (2002) : 550-572.

     
     

    F. Lamiraux and L.E. Kavraki "Planning Paths for Elastic Objects under Manipulation Constraints." International Journal of Robotics Research, 20(3) (2001) : 188-208.

     
     

    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, 20(8) (2001) : 635-659.

     
     

    J. Yakey, S.M. LaValle, and L.E. Kavraki "Randomized Path Planning for Linkages with Closed Kinematic Chains." IEEE Transactions on Robotics and Automation, 17(6) (2001) : 951-959.

     
     

    K.-F. Bohringer, B.R. Donald, L.E. Kavraki, and F. Lamiraux "Part Orientation to One and Two Stable Equilibria Using Programmable Force Fields." IEEE Transactions on Robotics and Automation, 16 (2) (2000) : 157-170.

     
     

    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, 22(9) (2000) : 731-747.

     
     

    P.W. Finn and L. Kavraki "Computational Approaches to Drug Design." Algorithmica, 25 (1999) : 347-371.

     
     

    P.W. Finn, L. Kavraki, J.C. Latombe, S. Venkatasubramanian, C. Shelton, and A. Yao "RAPID: Randomized Pharmacophore Identification." Computational Geometry: Theory and Applications, 10 (1998) : 263-272.

     
     

    L. Kavraki, J.-C. Latombe, R. Motwani, and P. Raghavan "Randomized Query Processing in Robot Path Planning (Invited)." Journal of Computer and System Sciences, 57(1) (1999) : 50-60.

     
     

    L. Kavraki, M. Kolountzakis, and J.-C. Latombe "Analysis of Probabilistic Roadmaps for Path Planning." Proceedings of the IEEE Transactions on Robotics and Automation, 14/1 (1998) : 166-171.

     
     

    P. Finn, L. Kavraki, J.-C. Latombe, S. Venkatasubramanian, C. Shelton and A. Yao "RAPID: Randomized Pharmacophore Indentification." Computational Geometry: Theory and Applications, 10 (1998) : 263-272.

     
     Articles
     

    A. Dhanik, J.S. McMurray, and L.E. Kavraki, “DINC: A New AutoDock Based Protocol for Docking
    Large Ligands,” BMC Structural Biology, 2013, 13(S1):S11.

     
     

    B. Gipson, M. Moll, and L.E. Kavraki, “SIMS: A hybrid method for rapid conformational analysis,”
    PLOS ONE, 2013, 8:e68826

     
     

    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, June 6 2013,
    9(6):e1003087

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi, “Falsification of LTL Safety Properties in Hybrid Systems,”
    Springer International Journal on Software Tools for Technology Transfer (STTT), 2013, 55(4): 305-
    320. (Invited Paper)

     
     

    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, 2013, 23(4): 332-348.

     
     

    A. Dhanik, J.S. McMurray, and L.E. Kavraki, “Binding Modes of Peptidomimetics Designed to Inhibit STAT3,” PLoS ONE, 7(12):e51603

     
     

    A. Shehu, L.E. Kavraki, “Modeling Structures and Motions of Loops in Protein Molecules,” Entropy, 2012, 14(2): 252-290.

     
     

    B. Gipson, D. Hsu, L.E. Kavraki, and J.-C. Latombe, “Computational Models of Proteins Kinematics and Dynamics: Beyond Simulation,” Annual Review of Analytical Chemistry, 2012, 5: 273-291. On-line version appeared April 9, 2012.

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi, "Falsification of LTL Satefy Properties in Hydrid Systems," Springer International Journal on Software Tools for Technology Transfer (STTT), 2012, May 23rd (on-line), DOI: 10.1007/s10009-012-0233-2.

     
     

    I.A. Sucan and L.E. Kavraki, “A Sampling-Based Tree Planner for Systems with Complex Dynamics,” IEEE Transactions on Robotics, 2012, 28(1): 116-131.

     
     

    I.A. Sucan, M. Moll, and L.E. Kavraki, “The Open Motion Planning Library,” IEEE Robotics Magazine, 2012, 19(4): 72-82.

     
     

    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, 2012, 31(2), 129-150.

     
     

    Lydia Kavraki "Algorithms in Robotics: The Motion Planning Perspective (Invited)." Frontiers of Engineering of the National Academy of Engineering (1999) : 90-93.

     
     Books
     

    Dhanik and L.E. Kavraki, "Protein-Ligand Interactions: Computational Docking" Encyclopedia of Life Sciences, Wiley & Sons Ltd: Chichester, 2012, #A24027, DOI: 10.1002/9780470015902.a0004105.pub2.

     
     

    H. Choset, W. Burgard, S. Hutchinson, G. Kantor, L.E. Kavraki, K. Lynch, and S. Thurn "Principles of Robot Motion: Theory, Algorithms and Implementation." MIT Press (2005) In Press

     
     

    L. Kavraki and J.C. Latombe "Probabilistic Roadmaps for Robot Path Planning." : 33-53.

     
     

    P.K. Agrawal, L. Kavraki, and M. Mason "Robotics: The Algorithmic Perspective." AK Peters (1998)

     
     Book chapters
     

    K. Tsianos, D. Halperin, L.E. Kavraki, and J.C. Latombe, "Robot Algorithms", Algorithms and Theory of Computation Handbook, M. Attalah (ed), CRC Press, 2010, Chapter 4.

     
     

    K. Tsianos, D. Halperin, L.E. Kavraki, and J.C. Latombe "Robot Algorithms." Algorithms and Theory of Computation Handbook (2009) In Press

     
     

    L. Kavraki and S. LaValle "Motion Planning." Springer Handbook of Robotics (2008) : 109-131.

     
     

    M. Moll, D. Schwarz, and L.E. Kavraki "Roadmap Methods for Protein Folding." Methods in Molecular Biology, Protein structure Prediction (2nd edition), 413 (2007) : 219-238.

     
     

    D. Schwarz and L.E. Kavraki "Protein-Ligand Interactions: Computational Docking." Encyclopedia of Life Scienes, Article #A4105, Wiley (2006)

     
     

    K.E. Bekris, A.A. Argyros, L.E. Kavraki "Exploiting Panoramic Vision for Angle-Based Robot Navigation." Springer, Series: Computational Imaging and Vision, Vol33, 2006, 229-251 (2006)

     
     

    D. Halperin, L.E. Kavraki, and J.C. Latombe "Robotics." Handbook of Discrete and Computational Geometry (2004) : 1065-1094.

     
     

    D. Halperin, J.C. Latombe, L. Kavraki "Robotics." Handbook of Discrete and Computational Geometry (2003) In Press

     
     

    M. Teodoro, Kavraki, L. "Pharmacology." Handbook on Data Mining and Knowledge Discovery (2002) : 808-816.

     
     

    R. Bohlin and L.E. Kavraki "A Randomized Algorithm for Robot Path Planning Based on Lazy Evaluation." (Invited) Handbook on Randomized Computing (2001) : 221-249.

     
     

    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 Force Fields (Invited)." Distributed Manipulation, Kluwer (2000) : 1-29.

     
     

    D. Halperin, L. Kavraki, and J.-C. Latombe "Robot Algorithms (Invited)." Algorithms and Theory of Computation Handbook, CRC Press (1999)

     
     

    D. Hsu, J.C. Latombe, R. Motwani, and L. Kavraki "Capturing the Connectivity of High-Dimensinal Spaces by Parallelizable Random Sampling Techniques." Advances in Randomized and Parallel Computing, Kluwer (1999) : 159-182.

     
     

    D. Halperin, L. Kavraki, and J.-C. Latombe "Robotics (Invited)." Handbook of Discrete and Computational Geometry (1997) : 755-779.

     
     

    L.E. Kavraki and J.C. Latombe "Probabilistic Roadmaps for Robot Path Planning (Invited)." Practical Motion Planning in Robotics: Current Approaches and Future Directions, John Wiley (1998) : 33-53.

     
     Refereed conference papers
     

    A. Dhanik, J. McMurray, and L.E. Kavraki, "On modeling peptidomimetics in complex with the SH2 domain of Stat3", 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 30 - September 3, Boston, MA, 2011.

     
     

    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), Lecture Notes in Computer Science, 6577: 70-82, 2011.

     
     

    I.A. Sucan, L.E. Kavraki, "Mobile Manipulation: Encoding Motion Planning Options Using Task Motion Multigraphs", IEEE International Conference on Robotics and Automation (ICRA), 5492-5498, Shanghai, China, 2011.

     
     

    I.A. Sucan, L.E. Kavraki, "On the Advantages of Using Motion Multigraphs for Efficient Mobile Manipulation", IEEE/RSJ International Conference on Intelligent Robots and Systems, San Francisco, CA, 2011.

     
     

    M. Moll, I.A. Sucan, J. Bordeaux, and L.E. Kavraki, "Teaching Motion Planning concepts to Undergraduate Students", IEEE Workshop on Advanced Robotics and Its Social Impacts, October 2-4, Half Moon Bay, CA, 2011.

     
     

    A. Bhatia, L.E. Kavraki, M.Y. Vardi, "Sampling-Based Motion Planning with Temporal Goals", IEEE International Conference on Robotics and Automation, Anchorage, AL, May 2010, 2689-2696.

     
     

    A. Bhatia, L.E. Kavraki, and M.Y. Vardi, "Motion Planning with Hybrid Dynamics and Temporal Goals", IEEE International Conference on Decision and Control, Atlanta, GA, December 2010, 1108-1115.

     
     

    D.K. Grady, K.E. Berkis, and L.E. Kavraki, "Asynchronous Distributed Motion Planning with Safety Guarantees under Second-Order Dynamics", Springer Tracts in Advanced Robotics, STAR 68, Algorithmic Foundations of Robotics IX, D. Hsu, V. Isler, J.C. Latombe, and M.C. Lin (eds), 2010, 53-70.

     
     

    I.A. Sucan and L.E. Kavraki, "On the Implementation of Single-Query Sampling-Based Motion Planners", IEEE International Conference on Robotics and Automation, Anchoage, AL, May 2010, 2005-2011.

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi "Falsification of LTL Safety Properties in Hybrid Systems." Proceedings of the 15th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS) (March/2009)

     
     

    I.A. Sucan and L.E. Kavraki "On the Performance of Random Linear Projections." 2009 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS) (October/2009)

     
     

    N. Haspel, M. Moll, M. Baker, W. Chiu, and L.E. Kavraki "Tracing Conformational Changes in Proteins." Proceedings of the IEEE Conference on Bioinformatics and Biomedicine (2009)

     
     

    R. Rusu, I.A. Sucan, B. Gerkey, S. Chitta, M. Beetz, and L.E. Kavraki "Real-time Perception-Guided Motion Planning for a Personal Robot." 2009 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS) (October/2009)

     
     

    A. Heath, L.E. Kavraki, and G. Balazsi "Biopolarity of the Saccharomyces Cerevisiae Genome." , paper #60540 (May 16-18, 2008)

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi "Impact of Workspace Decompositions on Discrete Search Leading Continuous Exploration (DSLX) on Motion Planning."  (May 2008)

     
     

    E. Plaku, and L.E. Kavraki "Quantitative Analysis of Nearest-Neighbors Search in High-Dimensional Sampling-Based Motion Planning." Springer-Verlag Series on Advanced Robotics (2008) : 3-18.

     
     

    I.A. Sucan, J.F. Kruse, M. Yim and L.E. Kavraki "Kinodynamic Motion Planning with Hardware Demonstrations."  (October 2008) : 1661-1666.

     
     

    I.A. Sucan, J.F. Kruse, M. Yim and L.E. Kavraki "Reconfigurations for Modular Robots using Kinodynamic Motion Planning."  (October 2008)

     
     

    K. Bekris and L.E. Kavraki "Informed and Probabilistically Complete Search for Motion Planning under Differential Constraints."  (July 2008)

     
     

    K. Tsianos, L.E. Kavraki "Replanning: A Powerful Planning Strategy for Hard Kinodynamic Problems."  (October 2008) : 1667-1672.

     
     

    M. Moll and L.E. Kavraki "Matching of structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction."  (August 2008)

     
     

    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 Structure Prediction."  (November 2008) : 1-8.

     
     

    B.Y. Chen, D.H. Bryant, A.Cruess, J. Bylund, V.Y. Fofanov, D. Kristensen, M. Kimmel, O. Lichtarge, and L.E. Kavraki "Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction." Computational Systems Bioinformatics (CSB) (2007)

     
     

    E. Plaku, K. Bekris, and L.E. Kavraki "OOPS for Motion Planning: An Online Open Source Programming System." IEEE International Conference on Robotics and Automation (April 2007) : 3711-3716.

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi "A Motion Planner for a Hybrid Robotic System with Kinodynamic Constraints." IEEE International Conference on Robotics and Automation (April 2007) : 692-697.

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi "Discrete Search Leading Continuous Exploration for Kinodynamic Motion Planning." Robotics: Science and Systems (RSS) (June 2007)

     
     

    E. Plaku, L.E. Kavraki, and M.Y. Vardi "Hybrid systems: From Verification to Falsification." International Conference on Computer Aided Verification (CAV), 4590 (July 2007)

     
     

    E. Plaku, and L.E. Kavraki "Nonlinear Dimensionality Reduction Using Approximate Nearest Neighbors." SIAM International Conference on Data Mining (SDM) (April 2007) : 692-697.

     
     

    K. Bekris and L.E. Kavraki "Greedy but Safe Replanning under Kinodynamic Constraints." IEEE International Conference on Robotics and Automation (April 2007) : 704-710.

     
     

    K.E. Bekris, K. Tsianos, and L.E. Kavraki "A Decentralized Planner that Guarantees the Safety of Communicating Vehicles with Complex Dynamics that Replan Online." IEEE/RSJ Intl. Conference on Intelligent Robots and Systems (November 2007)

     
     

    K.E. Bekris, K. Tsianos, and L.E. Kavraki "A Distributed Protocol for Safe Real-Time Planning of Communicating Vehicles with Second-Order Dynamics." Intl. Conference on Robot Communication and Coordination (ROBOCOMM) (October 2007)

     
     

    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 Reduces False Positives in Protein Function Prediction." Computational Systems Bioinformatics (CSB) Series on Advances in Bioinformatics and Computational Biology, Vol 4 (2006/Aug) : 311-323.

     
     

    B.Y. Chen, V.Y. Fofanov, D.H. Bryant, B.D. Dodson, D.M. Kristen, A.M. Lisewski, M. Kimmel, O. Lichtarge, and L.E. Kavraki "Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction." Research in Computational Biology: 10th Annual International Comference (RECOMB) (2006/April) : 500-515.

     
     

    E. Plaku and L.E. Kavraki "Quantitative Analysis of Nearest-Neighbors Search in High-Dimensional Sampling-Bases Motion Planning." 7th Workshop on the algorithmic Foundations of Robotics (2006/June)

     
     

    K. Bekis, M. Glick and L.E. Kavraki "Evaluation of Algoithms for Bearing-Only SLAM." IEEE Press (2006/June) : 1937-1944.

     
     

    A. Ladd, L.E. Kavraki "Fast Tree-Based Exploration of State Space for Robots with Dynamics." Alrogithmic Foundations of Robotics VI, Springer STAR, 17 (2005) : 297-312.

     
     

    A. Ladd, L.E. Kavraki "Motion Planning in the Presence of Drift, Underactuation and Discrete System Changes." Robotics Science and Systems (2005)

     
     

    B.Y. Chen, V.Y. Fofanov, D.M.Kristensen, M. Kimmel, O. Lichtarge, L.E. Kavraki "Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs." Proceedings of the Pacific Symposium on Biocomputing, World Scientific (2005) : 334-345.

     
     

    E. Plaku, L.E. Kavraki "Distributed Sampling-Based Roadmap of Trees for Large-Scale Motion Planning." Proceedings of the IEEE Int'l Conf on Robotics and Automation, IEEE Press (2005) : 3879-3884.

     
     

    M. Akinc, K.E. Bekris, A.Y. Chen, A.M. Ladd, E. Plaku, L.E. Kavraki "Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps (Invited)." Proceedings of Robotics Research: The 11th Int'l Symposium, Spinger STAR, 15 (2005) : 80-89.

     
     

    M. Moll, L.E. Kavraki "Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length." Proceedings of the IEEE Int'l Conf on Robotics and Automation, IEEE Press (2005) : 2143-2147.

     
     

    A. Haeberlen, E. Flannery, A.M. Ladd, A. Rudys, D.S. Wallach, and L.E. Kavraki "Practical and Robust Localization over Large-Scale 802.11 Wireless Networks." International Conference on Mobile Computing and Networking - MOBICOM 2004 (2004)

     
     

    J.M. Phillips, N. Bedrossian, and L.E. Kavraki "Guided Expansive Spaces Trees: A Search Strategy for Motion- and Cost-Constrained State Spaces." Proceedings of the International Conference of Robotics and Automation (ICRA) (2004) : 2968-2973.

     
     

    K.E. Bekris, A.A. Argyros, and L.E. Kavraki "New Methods for Reaching the Entire Plane with Angle-Based Navigation." Proceedings of the International Conference of Robotics and Automation (ICRA) (2004) : 2373-2378.

     
     

    M. Akinc, K.E. Bekris, A.Y. Chen, A.M. Ladd, E. Plaku, and L.E. Kavraki "Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps." Proceedings of the International Symposium on Robotics Research (2005) In Press

     
     

    M. Moll and L.E. Kavraki "Path Planning for Minimal Energy Curves of Constant Length." Proceedings of the International Conference of Robotics and Automation (ICRA) (2004) : 2826-2831.

     
     

    A.M. Ladd and L.E. Kavraki "Motion Planning for Knot Untangling." Algorithmic Foundations of Robotics V, Springer Tracts in Advanced Robotics (2004) : 7-23.

     
     

    J.M. Phillips, L.E. Kavraki, and N. Bedrossian "Probabilistic Optimization Applied to Spacecraft Rendezvous and Docking." 13th AAS/AIAA Space Flight Mechanics Meeting (2003)

     
     

    J.M. Phillips, L.E. Kavraki, and N. Bedrossian "Spacecraft Rendezvous and Docking with Real-Time Randomized Optimization." AIAA Guidance, Navigation and Control Conference (2003)

     
     

    K.E. Bekris, A.Y. Chen, A.M. Ladd, E. Plaku, and L.E. Kavraki "Multiple Query Probabilistic Roadmap Planning Using Single Query Planning Primitives." 2003 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS) (2003) : 656-661.

     
     

    A. Ladd, K. Bekris, A. Rudys, G. Marceau, D. Wallach, L. Kavraki "Robotics-Based Location Sensing using Wireless Ethernet." Proceedings of the Eighth ACM International Conference on Mobile Computing and Networking - MOBICOM (2002) : 227-238.

     
     

    A. Ladd, L. Kavraki "Generalizing the Analysis of PRM." Proceedings of the 2002 IEEE International Conference on Robotics and Automation (ICRA) (2002) : 2120-2125.

     
     

    A. Ladd, k. Bekris, G. marceau, A. Rudys, D. Wallach, L. Kavraki "Using Wireless Internet for Localization." Proceedings of the 2002 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS) (2002) : 402-408.

     
     

    Andrew Ladd, L. Kavraki "Motion Planning for Knot Untangling." Proceedings of the International Workshop on the Algorithmic Foundations of Robotics (WAFR) (Dec. 2002) In Press

     
     

    J. Phillips, A. Ladd, L. Kavraki "Simulated Knot Tying." Proceedings of the 2002 IEEE International Conference on Robotics and Automation (ICRA) (2002) : 841-846.

     
     

    M. Teodoro, G.N. Phillips, Jr., L.E. Kavraki "A Dimensionality Reduction Approach to Modeling Protein Flexibility." Proceedings of the 2002 ACM international conference on Research in Comutational Biology (RECOMB) (2002) : 299-308.

     
     

    M. Zhang, L. Kavraki "Solving Molecular Inverse Kinematics Problems for Protein Folding and Drug design." Currents in Computational Molecular Biology (2002) : 214-215.

     
     

    Ming Zhang, L. Kavraki "Approximating Solutions of Molecular Inverse Kinematics Problems by Subdivision." Proceedings of 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) : 2182-2183.

     
     

    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." Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA) (2001) : 1079-1085.

     
     

    A. Sudsang and L.E. Kavraki "Part Orientation with a Force Field: Orienting Multiple Shapes using a Single Field." Proceedings of the 2001 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS) (2001) : 208-213.

     
     

    M. Teodoro, G.N. Phillips, Jr., and L.E. Kavraki "Molecular Docking: A Problem with Thousands of Degrees of Freedom (Invited)." Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA) (2001) : 960-966.

     
     

    M. Zhang and L.E. Kavraki "Efficiently Maintaining Molecular Conformations Using Local Frames." Currents in Computational Molecular Biology (2001) : 97-98.

     
     

    O. Brock and L.E. Kavraki "Decomposition-Based Motion Planning: A Framework for Real-Time Motion Planning in High-Dimensional Configuration Places." Proceedings of the 2001 IEEE International Conference on Robotics and Automation (ICRA) (2001) : 1469-1475.

     
     

    C. Holleman and L.E. Kavraki "A Framework for Using the Workspace Medial Axis in PRM Planners." The IEEE International Conference on Robotics and Automation (2000) : 1408-1413.

     
     

    Ch. Nielsen and L.E. Kavraki "A Two-Level Fuzzy PRM for Manipulation Planning." Proceedings of the IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (2000) : 1716-1722.

     
     

    E. Anshelevich, S. Owens, F. Lamiraux, and L.E. Kavraki "Deformable Volumes in Path Planning Applications." Proceedings of the IEEE International Conference on Robotics and Automation (2000) : 2290-2295.

     
     

    F. Lamiraux and L.E. Kavraki "Positioning and Orienting Symmetric and Non-Symmetric Parts Using Radial and Constant Force Fields." Proceedings of the International Workshop on the Algorithmic Foundations of Robotics (WAFR) (2000)

     
     

    F. Lamiraux and L.E. Kavraki "Positioning and Orienting a Class of Symmetric Parts Using a Combination of a Unit-Radial and Constant Force Fields." Proceedings of the IEEE International Conference on Robotics and Automation (2000) : 178-183.

     
     

    J. Luo and L.E. Kavraki "Static and Dynamic Force Fields for Assembly Planning." Proceedings of the ITTE/RSJ International Conference on Intelligent Robots and Systems (IROS) (2000) : 1468-1474.

     
     

    M. Teodoro, G. Phillips, and L.E. Kavraki "Singular Value Decomposition of Protein Conformational Motions: Applications to HIV-1 Protease." Currents in Computational Molecular Biology (2000) : 198-199.

     
     

    O. Brock and L.E. Kavraki "Towards Real-Time Motion Planning in High-Dimensional Spaces." Proceedings of the International Symposium on Robotics and Automation, Monterey, Mexico (2000) : 81-86.

     
     

    R. Bohlin and L.E. Kavraki "Path Planning using Lazy PRM." Proceedings of the IEEE International Conference on Robotics and Automation (2000) : 521-538.

     
     

    T. Danner and L.E. Kavraki "Randomized Planning for Short Inspection Paths." Proceedings of the IEEE International Conference on Robotics and Automation (2000) : 971-976.

     
     

    D. Donald, K. Bohringer, L. Kavraki, and F. Lamiraux "A Single Universal Force Field can Uniquely Orient any Non-Symmetric Part." Robotics Research (1999) : 395-402.

     
     

    F. Lamiraux and L. Kavraki "Path Planning for Elastic Plates under Manipulation Constraints." Proceedings of the International Conference on Robotics and Automation (1999) : 151-156.

     
     

    L. Guibas, R. Holleman, and L. Kavraki "A Probabilistic Roadmap Planner for Flexible Objects with a Workspace Medial-Axis Based Sampling Approach." Proceedings of the IEEE/RSJ International Conference on Robots and Systems (IROS) (1999) : 254-260.

     
     

    S. Lavalle, J. Yakey, and L. Kavraki "A Probabilistic Roadmap Approach for Systems with Closed Kinematic Chains." Proceedings of the International Conference on Robotics and Automation (1999) : 1671-1677.

     
     

    S. Lavalle, P. Finn, L. Kavraki, and J.-C. Latombe "Efficient Database Screening for Rational Drug Design Using Pharmacophore-Constrained Conformational Search." Proceedings of the Third ACM International Conference Computational Biology (RECOMB) (1999) : 250-259.

     
     

    D. Hsu, L. Kavraki, J.-C. Latombe, R. Motwani, and S. Sorkin "On Finding Narrow Passages with Probabilistic Roadmap Planners." Robotics: The Algorithmic Perspective, A.K. Peters (1998) : 141-153.

     
     

    D. Hsu, L. Kavraki, J.-C. Latombe, and Rajeev Motwani "Capturing the Connectivity of High-Dimensional Geometric Spaces by Parallelizable Random Sampling Techniques." Parallel and Distributed Processing, Springer Verlag Lecture Notes in Computer Science, 1388 (1998) : 330-340.

     
     

    L.E. Kavraki "Geometry and the Discovery of New Ligands (Invited)." Algorithms for Robotic Motion and Manipulation (1997) : 435-448.

     
     

    L.E. Kavraki "Part Orientation with Programmable Vector Fields: Two Equilibria for Most Parts." Proceedings of the IEEE International Conference on Robotics and Automation (1997) : 2446-2452.

     
     

    L.E. Kavraki, F. Lamiraux, Ch. Holleman "Towards Planning for Flexible Objects." Robotics: The ALgorithmic Perspective (1998) : 313-325.

     
     

    R. Holleman, L. Kavraki, and Joe Warren "Planning Paths for a Flexible Surface Patch." Proceedings of the IEEE International Conference on Robotics and Automation (1998)

     
     Conference papers
     

    B. Gipson, M. Moll, and L.E. Kavraki, “Resolution Independent Density Estimation for Motion Planning
    in High-Dimensional Spaces,” IEEE International Conference on Robotics and Automation, IEEE
    Press, May 6-10, Karlsruhe, Germany, 2013, 2429-2435

     
     

    D. Grady, M. Moll, and L.E. Kavraki, “Anytime Solution Optimization for Sampling-Based Motion Planning,”
    Proc. IEEE International Conference on Robotics and Automation, IEEE Press, International
    Conference on Robotics and Automation, May 6-10, Karlsruhe, Germany, 2013, 78-84

     
     

    D. Grady, M. Moll, and L.E. Kavraki, “Combining a POMDP Abstraction with Replanning to Solve
    Complex, Position-Dependent Sensing Tasks,” Proc. of the AAAI Fall Symposium, AAAI Press, FS-13-02, November 15-17, Arlington, VA, 2013

     
     

    M. Maly, M. Lahijanian, L.E. Kavraki, H. Kress-Gazit, and M.Y. Vardi, “Iterative Temporal Motion Planning
    for Hybrid Systems in Partially Unknown Environments,” Proc. of 16th International Conference
    on Hybrid Systems: Computation and Control, ACM Press, April 9-11, Philadelphia, PA, USA, 2013,
    353-362.

     
     

    R. Luna, I. Sucan, M. Moll, and L.E. Kavraki, “Anytime Solution Optimization for Sampling-Based
    Motion Planning,” IEEE International Conference on Robotics and Automation, IEEE Press, May
    6-10, Karlsruhe, Germany, 2013, 5053-5059.

     
     

    A. Dhanik, J. McMurray, and L.E. Kavraki, “An AutoDock-based Incremental Docking Protocol to Im­prove Docking of Large Ligands,” Computational structural Bioinformatics Workshop at the 2012 IEEE International Conference on BioInformation and BioMedicine, IEEE Press, October 4-7, Philadel­phia, PA, 2012, 48-55.

     
     

    A. Dhanik, J. McMurray, and L.E. Kavraki, "Computational Modeling Of Peptidomimetics In Complex With The Sh2 Domain Of Cancer Target Stat3" Innovations in Cancer Prevention and Research, October 24-25, Austin, TX  2012.

     
     

    B. Gipson, M. Moll, D. Ricklin, J.D. Lambris, and L.E. Kavraki, “On the Conformational Flexibility of C3b: A Molecular Insight into Activation and Transformation of a Major Complement Effector,” Im­munobiology, 217, 1129-1222, 2012.

     
     

    D.K. Grady. M. Moll, C. Hedge, A.C. Sankaranarayanan, R.G. Baraniuk, and L.E. Kavraki, “Multi-Robot Target Verification with Reachability Constraints,” IEEE International Symposium on Safety, Security, and Rescue Robotics, College Station, TX, November 5-8, 2012.

     
     

    D.K. Grady. M. Moll, C. Hedge, A.C. Sankaranarayanan, R.G. Baraniuk, and L.E. Kavraki, “Multi-Objective Sensor-Based Replanning for a Car-Like Robot,” IEEE International Symposium on Safety, Security, and Rescue Robotics, College Station, TX, November 5-8, 2012.

     
     

    I.A. Sucan and L.E. Kavraki, “Accounting for Uncertainty in Simultaneous Task and Motion Planning Us­ing Task Motion Multigraphs,” IEEE International Conference on Robotics and Automation (ICRA), May 14-18, Minneapolis, MN, 2012, 4822-4828.

     
     

    M.R. Maly and L.E. Kavraki, “Low-Dimensional Projections for SyCLoP,” IEEE/RSJ International Conference on Intelligent Robots and Systems, October 7-12, Vilamoura, Portugal, 2012, 420-425.

     

     
    Presentations
     Conference Committee Member
     

    Program committee member.  "IEEE Int'l Conf on Robotics and Automation, 2005."

     
     

    Program committee member.  "IEEE Int'l conf on Robotics and Automation 2006."

     
     

    Program committee member.  "Int'l Workshop on the Algorithmic Foundations of Robotics 2006."

     
     

    Program committee member.  "Robotics: Science and Systems, 2005."

     
     Invited Papers
     

    Annual Review of Analytical Chemistry, 2012

     
     

    Encyclopedia of Life Sciences, 2012

     
     

    Entropy, 2012

     
     

    International Journal of Robotics Research, 2012

     
     

    International Journal on Software Tools for Technology Transfer, 2012

     
     

    On the Analysis of Protein Flexibility and Function, Invited Talk, Department of Computer Science, National University of Singapore, Singapore, December 16, 2010.

     
     

    "ACM/Springer Mobile Networks and Applications Journal (MONET)." (2009)

     
     

    "Algorithms and Theory of Computation Handbook."

     
     

    "Formal Methods in System Design." (2009)

     
     Invited Talks
     

    Applications of Computational Biology to Tissue Engineering, Bioengineering Graduate Group Special Seminar, University of California Davis, March 11, 2013.

     
     

    Automatic Functional Annotation of Proteins, Computer Science Distinguished Lecture Series, The Department of Computer Science, George Mason University, March 20, 2013.

     
     

    Computing for the Physical World, Grace Hopper Distinguished Lecture Series, School of Engineering
    and Applied Sciences, University of Pennsylvania, Philadelphia, PA, November 5, 2013.

     
     

    From Robots to Biomolecules: Computing for the Physical World, Invited Plenary Talk, International
    Joint Conference on Neural Networks, Dallas, TX, August 7, 2013.

     
     

    Motion Planning for Complex Systems, George A. Bekey Distinguished Lecture, Viterbi School of Engineering,
    University of Southern California, Lost Angeles, CA, September 19, 2013.

     
     

    Physical Computing, Invited Talk, Center for Computational and Integrative Biomedical Research (CIBR) Seminar Series, Baylor School of Medicine, Houston, TX, April 17, 2013.

     
     

    Robot Motion Planning, Fourth Annual STEM Research Symposium, co-hosted by the Society of Hispanic Professional Engineers, the National Society of Black Engineers, the Empowering Leadership Alliance of Rice University, and the Richard Tapia Center for Excellence and Equity, Houston, TX, November 9, 2013.

     
     

    Temporal Logic Motion Planning for Robots with Complex Dynamics, Invited Talk, 4rth Workshop on Formal Methods for Robotics and Automation, Robotics Science and Systems, Berlin, Germany, June 27, 2013.

     
     

    Plenary Speaker, The International Joint Conference on Neural Networks, Dallas, August 7, 2013.

     
     

    The Open Motion Planning Library, Invited Talk,Workshop on Motion Planning for Mobile Manipulation:
    State-of-the-art Methods and Tools, International Conference on Robotics and Automation, Karlsruhe,
    Germany, May 10, 2013.

     
     

    Applications of Systems Biology to Tissue Engineering, Invited Talk, Advances in Tissue Engineering, Houston, TX, August 8, 2012

     
     

    Functional Annotation of Proteins, Invited Lecture, Lipari School on Pharmacogenomics, Lipari, Italy, June 13, 2012

     
     

    Motion Planning for Hybrid Systems, Invited Seminar, Foundation for Research and Technology, Hellas (FORTH), Heraklion, Crete, Greece, June 15, 2012

     
     

    On the Analysis of Protein Flexibility, Invited Lecture, Lipari School on Pharmacogenomics, Lipari, Italy, June 12, 2012

     
     

    On the Analysis of Proteins, Invited Lecture, Lipari School on Pharmacogenomics, Lipari, Italy, June 12, 2012

     
     

    Sampling-Based Planning for Robotics and Biology, Distinguished Lecture Series, Department of Com­puter Science, Lehigh University, Allentown, PA, March 20, 2012

     
     

    Sampling-based Motion Planning for Robotic Assistants, Dexterous Robotics Laboratory, NASA/Johnson Space Center Distinguished Seminar Series, March 9, 2012

     
     

    Future Faculty Workshop, Rice University, “Understanding the Tenure Process,” September 10, 2012

     
     

    Applications of Computational Biology and Systems Biology to Tissue Engineering, Invited Talk, Advances in Tissue Engineering, Houston, TX, August 10, 2011.

     
     

    Motion Planning Applications, The Air Force Research Labratory, Invited Talk, Arllington, VA, October 14, 2011.

     
     

    Motion Planning for Physical Systems, Invited Talk, Institute for Informatics and Telematics, Center for Research and Technology, Thessaloniki, Greece, June 6, 2011.

     
     

    Motion Planning for Physical Systems, Computer & Information Science and Engineering (CISE), Distinguished Lecture Series, National Science Foundation (NSF), Arlington, VA, October 13, 2011.

     
     

    Motion Planning with Temporal Constraints, Robotics Seminar, Carnegie Mellon University, PA, December 2, 2011.

     
     

    Robotic Motion Planning, IEEE Robotics & Automation Society Washington/NoVa Chapter, Invited Talk, Mitre Corporation, McLean, VA, October 14, 2011.

     
     

    Finding Metabolic Pathways using Atom Tracking, Invited Talk, The 85th Annual AAAS-SWARM Conference, Houston, TX, April 9, 2010.

     
     

    Motion Planning with High-Level Temporal Goals, Colloquium, Department of Aeronautical Engineering, Texas A&M University, College Station, TX, October 14, 2010.

     
     

    Motion Planning with High-Level Temporal Goals, Invited Talk, Workshop on Formal Methods for Robotics and Automation, Anchorage, AL, May 3, 2010.

     

     
     

    Motion Planning, Invited Colloquium, Departments of Mechanical Engineering and Computer Science, The University of Texas at Arlington, Arlington, TX, April 26, 2010.

     
     

    Planning for Multiple Agents under Contraints, MURI Meeting on Opportunistic Sensing, University of Maryland, October 28, 2010.

     
     

    Robotics Inspired and Dimension Reduction Methods for the Analysis of Protein Flexibility and Function, Biocomputation Forum, Asia University, Taichung, Taiwan, November 12, 2010. 

     
     

    Robotics-inspired Methods for the Analysis of Proein Flexibility, Invited Talk, Symposium on Computational Biology, 2010 SIAM Conference on Discrete Mathematics, Austin, TX, June 17, 2010.

     
     

    Systems Biology for Tissue Engineering, Invited Talk, Advances in Tissue Engineering, Houston, TX, August 11, 2010.

     
     

    "Algorithmic Robotics, Invited Talk, Meeting of the Robotics Club, Houston, TX." (Sept. 4)

     
     

    "Computational Structural Biology and Systems Biology for Tissue Engineering, Invited Talk, Advances in Tissue Engineering, Houston, TX." (August 12)

     
     

    "Falsification of Safety Properties expressed in Linear Temporal Logic in Hybrid Systems, Invited Talk, Workshop on Formal Methods in Robotics and Automation, International Conference on Robotics and Automation, Kobe, Japan." (May 12)

     
     

    "Motion Planning for Autonomous Robotic Systems, Invited Talk, Max Planck Symposium on Autonomous Systems: State-of-the-Art and Perspectives, Tubingen, Germany." (January 20)

     
     

    "Motion Planning for Physical Systems, Colloquium, Department of Computer Science, Univ. of California Santa Barbara, CA." (February 24)

     
     

    "OOPSMP: An Object-Oriented Programming System for Motion Planning, Invited Talk, Workshop on Open Source Sofeware n Robotics, International Conference on Robotics and Automation, Kobe, Japan." (May 17)

     
     

    "On the Analysis of Molecular Flexibility and Function, Colloquium, Department of Mechanical Engineering, Univ. of California Santa Barbara, CA." (February 23)

     
     

    "On the Characterization of Protein Flexibility, Biological Physics Seminar, Department of Physics, Arizona State Univ., Phoenix, AR." (January 21)

     
     

    "On the Role of Motion Planning for Automation, Invited Talk, Workshop on Algorithmic Automation, Robotics: Science and Systems, Seattle, WA." (June 28)

     
     

    "Robotics-Inspired and Dimension Reduction Methods for the Analysis of Protein Flexibility and Function, Protein Structure, Invited Talk, Planning and Kinematics Workshop, Robotics: Science and Systems, Seattle, WA." (June 29)

     
     

    "A Robotics-Inspired Approach to the Analysis of Molecular Flexibility and Function." Colloquium, Boston, MA. (February 7, 2008)

     
     

    "From Robots to Biomolecules: Computing Meets the Physical World." Corporate Affiliates Meeting, Rice University. (October 15, 2008)

     
     

    "Informed Search for Motion Planning under Differential Constraints." The AAAI-08 Workshop on Searching Artificial Intelligence and Robotics, Chicago, IL. (July 13-14, 2008)

     
     

    "Motion Planning and Physic-Based Simulation for Robotics Automation." Workshop on Algorithmic Automation, International Conference on Robotics and Automation. (Pasadena) With May 20, 2008

     
     

    "Motion Planning for Physical Systems." IEEE Galveston Bay Section and Joint Society Meerting, NASA-JSC, Clear Lake, TX. (June 19, 2008)

     
     

    "Motion Planning: from Solving Puzzles to Driving Vehicles." Cognitive Mobile Robotics Technical Interchange Planning Meeting DARPA, Camden, NJ. (January 10, 2008)

     
     

    "Recent Developments in Motion Planning." Distinguished Colloquium Series, Department of Computer Science, University of Toronto. (January 8, 2008)

     
     

    "Receptor-Mediated Cellular Interactions." Short Course on Advances in Tissue Engineering, Rice University. (August 13, 2008)

     
     

    "Robots, Molecules, and Physical Computing." Dept. of Computer Science, University of Massachusetts at Amherst, Amherst. (November 6, 2008)

     
     

    "Engineering Receptor-Mediated Cellular Interacitons." Short Course on Advances in Tissue Engineering, Rice University. (August 15, 2007)

     
     

    "Motion Planning for Physical Systems." Stanford Broad Area Colloquium, Dept. of Computer Science, Stanford University. (June 4, 2007)

     
     

    "Physical Realism in Motion Planning." Workshop on Algorithmic Motion Planning for Autonomous Robots in Challengning Environments, IEEE/RSJ 2007 International Conference on Intelligent Robots and Systems, (November 29, 2007)

     
     

    "Bioinformatics Research." King's College, Oxford University, Oxford. (March 6, 2006)

     
     

    "Engineering Receptor-Mediated Cellular Interactions." Short Course on Advances in Tissue Engineering, Rice University. (August 16, 2006)

     
     

    "Negotiating the Ideal Faculty Position." How to Obtain Funding, Rice Universtiy. (October 23, 2006)

     
     

    "Physical and Biological Computing Group at Rice: NSF-Funded Research." Presentation during the visit of the NSF Director Dr. Arden Bement, Rice University. (November 9, 2006)

     
     

    "Research in Computational Structural Biology." Retreat for Planning an NIH Roadmap Grant, Univeristy of Texas at Austin, Austin, TX. (August 26, 2006)

     
     

    "The Computer Science Behind Your Science and the Science Behind Computer Science." Symposium organized by the Computing Research Association at the 2006 American Association for the Advancement of Science (AAAS) Annual Meeting, St Louis, MO. (February 17, 2006)

     
     

    "Algorithms for Structural Comparison and Statistical Analysis of Three Dimensional Protein Motifs." DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition, DIMACS, Rutgers University. (June 13, 2005)

     
     

    "Computational Drug Discovery." Alliance for Nanohealth Meeting, Houston, TX. (June 2, 2005)

     
     

    "Computational Modeling of Biomolecular Interactions." Molecular Medicine Symposium, The Univ of Texas System, Houston, TX. (February 22, 2005)

     
     

    "Computer-Assisted Drug Design." Rice Alumni College, Rice University, Houston, TX. (February 25, 2005)

     
     

    "Engineering Receptor-Mediated Cellular Interactions." Short Course on Advances in Tissue Engineering, Rice University, Houston, TX. (August 10, 2005)

     
     

    "From Robotics to Biomolecules: Computing Meets the Physical World." Distinguished Speaker Series: National Science Foundation, Washington, DC. (April 6, 2005)

     
     

    "From Robots to Biomolecules: Computing Meets the Physical World." New Professor Lecture Series, School of Engineering, Rice University, Houston, TX. (February 7, 2005)

     
     

    "From Robots to Biomolecules: Computing Meets the Physical World." W.M. Keck Center for Computational and Structural Biology Seminar Series, Houston, TX. (January 28, 2005)

     
     

    "From Robots to Biomolecules: Computing Meets the Physical World." Rice Theoretical and Computational Biology Symposium, Houston, TX. (December 11, 2005)

     
     

    "From Robots to Biomolecules: Designing Amazing New Medicines." NSF-ADVANCE Lecture Series, Univ of New Mexico, Las Cruses, NM. (September 1, 2005)

     
     

    "Geometry and Robotics Inspired Approaches to Structural Biology." Department of Computer Science, University of New Mexico, Las Cruses, NM. (August 31, 2005)

     
     

    "Motion Planning with Dynamics." Dept of Computer Science, Washington University, St. Louis, MO. (December 9, 2005)

     
     

    "Physical Computing." CRAY Distinguished Lecture Series, University of Minnesota, Minneapolis, MN. (December 5, 2005)

     
     

    "Sampling-based Motion Planning: Recent Developments and Future Challenges." General Robotics, Automation, Sensing and Percention (GRASP) Laboratory, University of Pennsylvania. (November 18, 2005)

     
     

    Distinguished Speaker Series Guest.  "Computing about the Physical World." Rensselaer Polytechnic Institute, Troy, New York. (December 9 2004)

     
     

    "Engineering Receptor Mediated Cellular Processes." Advances in Tissue Engineering, Houston, Texas. (August 11, 2004)

     
     

    "From Robots to Biomolecules: Computing Meets the Physical World." Carnegie Mellon University, Pittsburgh, Pennsylvania. (January 27, 2004)

     
     

    "Geometry and Robotics Inspired Approaches in Structural Biology." The Gulf Coast Center for Computational Cancer Research, M.D. Anderson Cancer Center, Houston, Texas. (September 7, 2004)

     
     

    "Robots and Biomolecules: Computing about the Physical World." The Texas Academy of Science, Engineering and Medicine Conference, San Antonio, Texas. (January 7, 2004)

     
     

    "A Robotics Engineering Approach to Drug Discovery." Department of Computer Science, Harvard University, Cambridge, Massachusetts. (September 25, 2003)

     
     

    "A Robotics Engineering Approach to Drug Discovery." Department of Computer Science, Duke University, Durham, North Carolina. (September 29, 2003)

     
     

    "A Robotics Engineering Approach to Drug Discovery." University of North Carolina, Chapel Hill, North Carolina. (November 10, 2003)

     
     

    "From Robots to Biomolecules to Drug Discovery." Baylor College of Medicine, Houston, Texas. (December 10, 2003)

     
     

    "Modeling the Conformational Flexibiity of Proteins." Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania. (August 8, 2003)

     
     

    "Modeling the Conformational Flexibility of Proteins." Center for Biological Modeling and Science, Michigan State University, East Lansing, Michigan. (October 10, 2003)

     
     

    "Modeling the Conformational Flexibility of Proteins." Department of Computer Science, Case Western Reserve University, Cleveland, Ohio. (July 25, 2003)

     
     

    "Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps." International Symposium on Robotics and Automation, Siena, Italy. (October 20, 2003)

     
     

    "Robotics Methods for Molecular Modeling and Computer-Assisted Drug Discovery." Rice University, Houston, Texas. (January 10, 2003)

     
     

    "Robotics Methods in Drug Discovery and Tissue Engineering." Rice University, Houston, Texas. (August 15, 2003)

     
     

    "A Robotics-Based Approach to Drug Discovery and Tissue Engineering." Tissue Engineering Growth International Conference and Exposition, Pittsburgh, Pennsylvania. (March 19, 2002)

     
     

    "Bioinformatics." Board of Trustees, Rice University, Houston, Texas. (May 22, 2002)

     
     

    "From Robots to Biomolecules: Designing Amazing New Medicines." Affiliates Meeting, Computer Science, Rice University, Houston, Texas. (October 3, 2002)

     
     

    "From Robots to Molecules: Applications of Physical Computing." Department of Chemical Engineering, Rice University, Houston, Texas. (January 31, 2002)

     
     

    "Modeling the Conformational Flexibility of Proteins." DIMACS Workshop on Computational Geometry, DIMACS Center, Rutgers University, Piscataway, New jersey. (November 14, 2002)

     
     

    "Robotics Methods in Drug discovery and Tissue engineering." Rice University, Houston, Texas. (August 14, 2002)

     
     Keynote Speaker
     

    From Robots to Molecules: Computing for the Physical World, Plenary Speaker, National Center for Women & Information Technology Meeting, Houston, March 24, 2012

     
     

    Keynote.  "Computational Problems in Systems Biology." M.D. Anderson 61st Annual Symposium on Cancer Research, M.D. Anderson Cancer Center. (October 30, 2008)

     
     

    "Physical Computing." National Center for Women and information Technology, Annual Meeting, Urbana. (May 14, 2008)

     
     

    Keynote Speaker.  "From Robots to Biomolecules: Computing Meets the Physical World." Grace Hopper Celebration of Women in Computing Conference, Chicago, Illinois. (October 8, 2004)

     
     Lectures
     

    George A. Bekey Distinguished Lecturer, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, September 19, 2013.

     
     

    Distinguished Lecturer, Lipari School on Pharmacogenomics, Lipari, Italy, June 12-13, 2012

     
     

    Distinguished Lecturer, NASA Johnson Space Center Distinguished Lecture Series, March 9, 2012

     
     

    Planning for Physical Systems, Invited Lecture, Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, March 23, 2010.

     
     

    "Motion Planning for Physical Systems, Distinguished Colloquium Series." University of British Columbia, Vancouver, Canada. (November 4, 2007)

     
     

    "Approximating solutions of Molecular Inverse Kinematics Problems by Subdivision." The 24th International Conference of the IEEE Engineering in Medicine and Biology society (EMBs) and the Annual Meeting of the Biomedical Engineering Society (BMES), Houston, Texas. (October 23, 2002) With M. Zhang

     
     

    "Dimensionality Reduction Approach to Modeling Protein Flexibility." 2002 ACM International Conference on Research in Computational Biology (RECOMB), (April 2002) With M. Teodoro, G.N. Phillips, Jr.

     
     

    "Generalizing the Analysis of PRM." 2002 IEEE International Conference on Robotics and Automation (ICRA), (May 2002) With A. Ladd

     
     

    "Simulated Knot Typing." 2002 IEEE International Conference on Robotics and Automation (ICRA), (May 2002) With J. Phillips, A. Ladd

     
     Other
     

    Invited Participant, Workshop on Key Challenges in the Inplementation of Convergence, Sept. 16 - 17, 2013 National Academy of Sciences, Washington DC.

     
     

    Distinguished Lecturer.  "Institute of Electrical and Electronics Engineers, Robotics and Automation Society (IEEE RAS)." (2009)

     
     

    Co-Chair.  "The 19th Keck Center Annual Research Conference." Houston, Texas.

     
     

    "Computational Tools for Problems in the Physical World." Annual Meeting of the Coalition for National Funding, Capital Hill, Washington DC. (June 25, 2007)

     
     

    "A Geometric Approach to Designing a Programmable Force Field with a Unique Stable Equilibrium for Parts in the Plane." 2001 IEEE International Conference on Robotics and Automation (ICRA), Seoul, Korea. (May 25, 2001)

     
     

    "An Introduction to Teaching in Engineering." Teaching Workshop, George R. Brown School of Engineering, Rice University, Houston, Texas. (August 21, 2001)

     
     

    "Application of Robotics Principles to Drug Discovery and Tissue Engineering." (Invited Talk) Short Course on Advances in Tissue Engineering, Rice University, Houston, Texas. (August 17, 2001)

     
     

    "Decomposition-Based Motion Planning: A Framework for Real-Time Motion Planning in High-Dimensional Configuration Places." 2001 IEEE International Conference on Robotics and Automation (ICRA), Seoul, Korea. (May 24, 2001) With Co-author: O. Brock

     
     

    "Efficient Modeling of Molecular Conformations Using Local Frames." 19th Annual Houston Conference on Biomedical Engineering Research, Houston, Texas. (February 8, 2001)

     
     

    "From Robots to Biomolecules: Designing Amazing New Medicines." Rice Engineering Reunion, Rice University, Houston, Texas. (May 11, 2001)

     
     

    "Molecular Docking: A Problem with Thousands of Degrees of Freedom (Invited)." 2001 IEEE International Conference on Robotics and Automation (ICRA), Seoul, Korea. (May 24, 2001)

     
     

    "Orienting Multiple Shapes Using a Single Field." 2001 IEEE/RJS International Conference on Intelligent Robots and Systems (IROS), (November 2001) With Co-author: A. Sudsang

     
     

    "Part Manipulation Using Programmable Vector Fields." (Invited) Department of Computer Science, Texas A&M University, College Station, Texas. (October 26, 2001)

     
     

    "A Two-Level Fuzzy PRM for Manipulation Planning." IEEE/RSJ International Conference on Intelligent Robots and Systems, Takamastu, Japan. (November 2000) With Ch. Nielsen

     
     

    "Motion Planning: Current Approaches and Future Directions (Invited Symposium Talk)." IEEE International Conference on Robotics and Automation, San Francisco, California. (April 26, 2000)

     
     

    "Part Assembly Using Static and Dynamic Force Fields." IEEE/RSJ International Conference on Intelligent Robots and Systems, Takamastu, Japan. (November 2000) With J. Luo

     
     

    "Planning the Motion of Molecules (Invited Talk)." ARO/NSF Workshop on Modeling Motion, Duke University. (August 7, 2000)

     
     

    "Planning the Motion of Robots and Molecules: An Algorithmic Introduction (Invited Seminar)." University of Crete, Greece. (July 10 - 14, 2000)

     
     

    "Probabilistic Roadmap Planners: Current Approaches and Future Directions (Invited Talk)." NSF/EU Workshop on Key Research Issues and Opportunities in Motion Planning, Toulouse, France. (July 21, 2000)

     
     

    "Towards Real-Time Motion Planning in High Diemensional Spaces." International Symposium on Robotics and Automation, Monterrey, Mexico. (November 2000) With O. Brock

     
     

    "A Probabilistic Roadmap Planner for Flexible Objects with a Workspace Medial-Axis Based Sampling Approach." IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), Kyongju, Korea. (October 18, 1999)

     
     

    "A Single Universal Force Can Uniquely Orient any Non-Symmetric Part." 9th International symposium of Robotics Research, Utah. (October 12, 1999)

     
     

    "Computational Approaches to Drug Design." Invited Plenary Talk, International Joint Conference on Artificial Intelligence (IJCAI), (August 3, 1999)

     
     

    "Computational Approaches to drug Design and the RAPID Pharmacophore Identification System." Invited Colloquium, Department of Bioengineering, Rice University, Houston, Texas. (September 7, 1999)

     
     

    "Computer-Assisted Pharmaceutical Drug Design: Current Computational Approaches and Future Challenges." Invited Distinguished Lecture, Lecture Series in Biomedical Informatics, University of Wisconsin, Wisconsin. (November 5, 1999)

     
     

    "Flexible Objects in Virtual Prototyping Applications." Workshop on Motion Support in Virtual Prototyping, Stanford University, Stanford, California. (May 1999)

     
     

    "Orientation into One Stable Equilibrium Using Programmable Force Fields ." Invited Presentation, Workshop on Distributed Manipulation, IEEE International Conference on Robotics and Automation, Detroit, Michigan. (May 1999)

     
     

    "Part Orientation into One or Two Stable Equilibria using Programmable (Invited Talk)Force Fields." Xerox Parc, Palo Alto, CA. (1999)

     
     

    "Planning Paths for Flexible Objects under Manipulation Constraints." IEEE International Conference on Robotics and Automation, Detroit, Michigan. (May 1999)

     
     

    "Probabilistic Methods in Path Planning." Invited Colloquium, Department of Mathematics, Rice University, Houston, Texas. (September 30, 1999)

     
     

    "Towards Planning for Elastic Objects (Invited Colloquium)." University of Texas A&M, College Station, Texas. (April 1999)

     
     

    "Unique Part Orientation using Programmable Force Fields." Robotics Laboratory, Stanford University, Stanford, California. (June 1999)

     
     

    "Computational Approaches to Pharmaceutical Drug Design (Invited Presentation)." LAAS, Toulouse, France. (October 1998)

     
     

    "Motion Planning in Robotics (Invited Speaker and Panelist)." Frontiers of Engineering Symposium, National Academy of Engineering, Washington, D.C.. (September 1998)

     
     

    "Pharmacophore Identification in Computer-Assisted Drug Design (Invited Presentation)." European Biomolecular Institute, Cambridge, United Kingdom. (July 1998)

     
     

    "Planning Paths for a Flexible Surface Patch." IEEE International Conference on Robotics and Automation, Leuven. (May 1998)

     
     

    "Planning for Rigid and Flexible Robots, Invited Presentation." Department of Computer Science, Stanford University, Stanford, California. (June 1998)

     
     

    "Randomized Planning for Elastic Objects, Invited Presentation." Department of Industrial Engineering and Operations Research, University of California, Berkeley, California. (April 1998)

     
     

    "Randomized Techniques for Robotics Problems, Invited Presentation." Department of Computer Science, University of Houston, Houston, Texas. (April 1998)

     
     

    "Robotics: Current Directions and Future Challenges (Invited Presentation)." Affiliates Meeting, Department of Computer Science, Rice University, Houston, Texas. (October 1998)

     
     

    "Towards Planning for Flexible Objects." Third International Workshop on the Algorithmic Foundations of Robotics, Houston, Texas. (March 1998)

     
     Seminar Speaker
     

    "Computational Issues in Structural Systems Biology." M.D Anderson Cancer Center, Cancer Systems Biology Symposium, (December 14, 2006)

     
     

    "Planning for Physical Simulation." Colloquium, Dept. of Informatics and Telecommunications, National University of Athens, Athens, Greece. (October 19, 2006)

     
     

    "Sampling-Base Motion Planners: Recent Developments and Future Challenges." Colloquium, Institute of Computer Science, Foundation for Research and Technology, Hellas, Iraklion, Crete. (October 16, 2006)

     
    Editorial Positions
     Associate Editor, Computer Science Review. Elsevier. (2013 - 2013)

     Associate Editor, International Journal of Robotics Research. (2013 - 2013)

     Associate Editor, Big Data, Mary Ann Liebert Inc. (2013 - 2013)

     Associate Editor, International Journal of Robotics Research. (2012 - 2012)

     Associate Editor, Computer Science Reviews. (2012 - 2012)

     Associate Editor, ACM/IEEE Transactions on Computational Biology and Bioinformatics. (2012 - 2012)

     Associate Editor, Computer Science Review. Elsevier. (2009 - 2009)

     Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2009 - 2009)

     Associate Editor, The International Journal of Robotics Research. (2009 - 2009)

     Member of the Editorial Board, Technology, Imperial College Press and World Scientific (ICP/WSPC). (2013 - 2013)

     Member of the Editorial Board, Springer Tracts in Advanced Robotics (STAR). (2013 - 2013)

     Member of the Editorial Board, Springer Tracts in Advanced Robotics (STAR). (2012 - 2012)

     Member of the Editorial Board, Advanced Robotics Series. Springer-Verlag. (2009 - 2009)

     Other, International Journal of Robotics Research. (2009 - 2009)

     Other, Journal of Artificial Intelligence. (2009 - 2009)

     Other, Algorithmica. (2009 - 2009)

     Other, Automatica. (2009 - 2009)

     Other, ACM Solid Modeling Conference. (2009 - 2009)

     Other, AAAI National Conference on Artificial Intelligence. (2009 - 2009)

     Other, Journal of Robotic Systems. (2009 - 2009)

     Other, Biophysical Journal. (2009 - 2009)

     Other, Academy of Finland. (2009 - 2009)

     Other, Israel Science Foundation. (2009 - 2009)

     Other, Welcome Trust. (2009 - 2009)

     Other, Natioan Institutes of Health (NIH) Panels. (2009 - 2009)

     Other, IEEE International Conference on Robotics and Automation. (2009 - 2009)

     Other, IEEE Transactions on Robotics and Automation. (2009 - 2009)

     Other, Computatinal Geometry: Theory and Applications. (2009 - 2009)

     Other, ACM International Conference on Research in Computational Biology. (2009 - 2009)

     Other, Journal of Computer Graphics. (2009 - 2009)

     Other, Journal of Graphical Models and Image Processing. (2009 - 2009)

     Other, United Engineering Foundation. (2009 - 2009)

     Other, IEEE/RSJ International Conference on Intelligent Robots and Systems. (2009 - 2009)

     Other, International Joint Conference on Artificial Intelligence. (2009 - 2009)

     Other, International Symposium on Assembly and Task Planning. (2009 - 2009)

     Other, International Symposium for Robotics Research. (2009 - 2009)

     Other, International Conference on Informatics in Control, Automation and Robotics. (2009 - 2009)

     Other, Journal of Mechanical Design. (2009 - 2009)

     Other, IEEE Computer Society Bioinformatics Conference. (2009 - 2009)

     Other, IEEE Transactions on Systems, Man and Cybernetics. (2009 - 2009)

     Other, Artificial Intelligence Journal. (2009 - 2009)

     Other, International Journal of Robotics and Automation (IASTED). (2009 - 2009)

     Other, Journal of Computer-Aided Molecular Design. (2009 - 2009)

     Other, Encyclopedia of Electrical and Electronics Engineering. (2009 - 2009)

     Other, The Netherlands Computer Science Research Foundation. (2009 - 2009)

     Other, Greek Ministry of Education, Research Science Foundation. (2009 - 2009)

     Other, Radcliffe Institute. (2009 - 2009)

     Other, National Science Foundation (NSF) Panels. (2009 - 2009)

     Other, SIAM Journal on Control and Optimization. (2009 - 2009)

     Other, SIAM Journal on Computing. (2009 - 2009)

     Other, National Conference on Artificial Intelligence. (2009 - 2009)

     Other, International Workshop on Algorithmic Foundations of Robotics. (2009 - 2009)

     Other, Journal of Computational Biology. (2009 - 2009)

     Other, ACM International Symposium on Computational Geometry. (2009 - 2009)

     Other, ACM Crossroads Magazine. (2009 - 2009)

     Other, Hong-Kong Research Grants Council. (2009 - 2009)

     Other, European Research Council. (2009 - 2009)

     Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2007 - 2007)

     Associate Editor, IEEE Transactions on Robotics and Automation. IEEE Transactions on Robotics and Automation. (2001 - 2001)

     Editor for Special Issue, Int'l Journal of Robotics Research. (2005 - 2005)

     Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2008 - 2008)

     Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics. (2005 - 2005)

     Associate Editor, Computer Science Reviews. (2007 - 2007)

     Associate Editor, Computer Science Reviews. Elsevier. (2008 - 2008)

     Member of the Editorial Board, Advanced Robotics Series (STAR). Springer-Verlag. (2007 - 2007)

     Associate Editor, Computer Science Reviews. Elsevier. (2005 - 2005)

     Associate Editor, Springer-Verlag Advanced Robotics Series. (2008 - 2008)

     Member of the Editorial Board, Advanced Robotics Series (STAR). Springer-Verlag. (2005 - 2005)

     Associate Editor, Robotics Magazine. IEEE Press. (2005 - 2005)

    Supervised Theses & Dissertations
     Christopher Holleman, Master of Science Path Planning with Medial Axis Hints. (2000) (Thesis or Dissertation Director)

     Jiangchun Luo, Master of Science Part Assembly Using Static and Dynamic Force Fields. (2000) (Thesis or Dissertation Director)

     Andrew Ladd, Master of Science Analysis of Probabilistic Roadmap Methods for Motion Planning and Applications to Polygon Manipulation. (2002) (Thesis or Dissertation Director)

     Miguel Teodoro, Doctor of Philosophy Modeling Protein Flexibility Using Collective Modes of Motion: Applications to Drug design. (2003) (Thesis or Dissertation Director)

     Miguel Teodoro, Master of Science Molecular Conformational Sampling Using Collective Coordinate Expansive Spaces. (2003) (Thesis or Dissertation Director)

     Brian Chen, Master of Science Structural Pattern Matching for Functional Annotation of Proteins. (2003) (Thesis or Dissertation Director)

     Scott Schaefer, Master of Science A Factored, Interpolatory Subdivision Scheme for Surfaces of Revolution. (2003) (Committee Member)

     Andrew M. Ladd, Master of Science Analysis of Probabilistic Roadmap Methods for Motion Planning and Applications to Polygon Manipulation. (2003) (Thesis or Dissertation Director)

     Konstantinos Bekris, Master of Science Reactive Range-free Landmark Navigation without Scene Reconstruction. (2004) (Thesis or Dissertation Director)

     Ming Li, Doctor of Philosophy New Algorithms for Pathway Computation. (2004) (Committee Member)

     Ajay Gulati, Master of Science in Computer Science Scheduling with QoS in Parallel I/O Systems. (2004) (Committee Member)

     Jan Philipp Hakenberg, Master of Science in Computer Science Smooth Subdivision for Mixed Volumetric Meshes. (2005) (Committee Member)

     Mili Shah, Doctor of Philosophy Reduced Representations for Symmetric Molecules. (2005) (Committee Member)

     M. David Schwarz, Master of Science in Computer Science Local Conformational Sesarch of Proteins Using the Expansive Spaces Search. (2005) (Thesis or Dissertation Director)

     Armada Shehu, Master of Science in Computer Science Sampling Biomolecular Conformations with Spatial and Energetic Constraints. (2005) (Thesis or Dissertation Director)

     Derek Ruths, Master of Science in Computer Science Applications of Phylogenetic Incongruence to Detecting and Reconstructing Recombination and Horizontal Gene Transfer. (2005) (Committee Member)

     Tao Ju, Doctor of Philosophy Building a D3 Atlas of the Mouse Brain. (2005) (Committee Member)

     Brian Chen, Doctor of Philosophy Geometry-based Methods for Protein Function Prediction. (2006) (Thesis or Dissertation Director)

     Allison Heath, M.S. Towards multiscale Protein Simulations: Moving from Coarse-Grain to All-Atom Models. (2006) (Thesis or Dissertation Director)

     Maciej Kalisiak, Ph.D. Efficient Motion Planning with Differential Constraints. (2007) (Committee Member)

     Endah Susilowati, Ph. D. Specificity of Membrane Helix-helix Interactions by Mutagenesis and Structural Analysis. (2007) (Committee Member)

     Herman Stamati, Master of Science Analysis of Molecular Motion using Non-Linear Dimensionality Reduction. (2007) (Thesis or Dissertation Director)

     Brian Chen, Ph.D. Geometry Based Methods for Protein Function Prediction. (2007) (Thesis or Dissertation Director)

     Costas Panayiotakis, Ph. D. Motion Analysis and Modeling for Activity Recognition and 3-D Animation based on Geometrical and Video Processing Algorithms. (2007) (Committee Member)

     Mili Shah, Ph. D. Reduced Representations for Symmetric Molecules. (2007) (Committee Member)

     Ajay Gulati, Ph. D. Performance Virtualization and QoS in Shared Storage Systems. (2007) (Committee Member)

     David Kristensen, Ph. D. Automated Protein functional Site Discovery; Structural Similarity and De Novo Approaches. (2007) (Committee Member)

     Andrew M. Ladd, Doctor of Philosophy Motion Planning for Physical Simulation. (2007) (Thesis or Dissertation Director)

     Konstantinos Bekris, Doctor of Philosophy Informend Planning and Safe Distributed Replanning under Physical Constraints. (2008) (Thesis or Dissertation Director)

     Erion Plaku, Doctor of Philosophy From High-Level Tasks to Low-Level Motions: Motion Planning for High-Domensional Nonlinear Hybrid Robotic Systems. (2008) (Thesis or Dissertation Director)

     Cuong V. Than, Master of Science Reconstruction of Phylogenetic Networks and Their Relationships with Trees and Branches. (2008) (Committee Member)

     Amarda Shehu, Doctor of Philosophy Molecules in Motion:Computing Structural Flexibility. (2008) (Thesis or Dissertation Director)

     Adina Kilpatrick, Ph. D. Structural Basis for Calmodulin-Mediated Regulation of the Ryanodine Receptor. (2008) (Committee Member)

     Viacheslav Y. Fofanov, Ph. D. Statistical Models in Protein Structural Alignments. (2008) (Committee Member)

     Abhishek Gupta, Ph. D. Disturbance Observer Based Closed loop Control of Haptic Interfaces. (2008) (Committee Member)

     Derek Ruths, Doctor of Philosophy Deriving Executable Models of Biochemical Network Dynamics from Qualitative Data. (2009) (Committee Member)

     Konstantinos Tsianos, Master of Science Planning with Complex Dynamics Constraints. (2009) (Thesis or Dissertation Director)

     Junjie (George) Zhang, Ph.D. Modeling of Chaperonins. (2009) (Committee Member)

     Jeffrey R Kilpatrick, Master of Science Methods for detecting multi-locus genotype-phenotype association. (2010) (Committee Member)

     Allison Park Heath, Ph.D. Computational Discovery and Analysis of Metabolic Pathway. (2010) (Thesis or Dissertation Director)

     Devin Grady, Master of Science Motion Planning with Temporal Constraints. (2010) (Thesis or Dissertation Director)

     Natalie Berestovsky, Master of Science On the Modeling of Signaling Networks with Petri Nets. (2011) (Committee Member)

     Troy Ruths, Master of Science A Sequence-Based, Population Genetic Model of Regulatory Pathway Evolution. (2011) (Committee Member)

     Devin Kieber Grady, Master of Science Unsynchronized Distributed Motion Planning with Safety Guarantees under Second-Order Dynamics. (2011) (Thesis or Dissertation Director)

     Ioan Alexandru Sucan, Doctor of Philosophy Task and Motion Planning for Mobile Manipulators. (2011) (Thesis or Dissertation Director)

     Ioan Sucan, Ph.D. Task and Motion Planning for Mobile Manipulation. (2011) (Thesis or Dissertation Director)

     Ioan Sucan, Ph.D. Kinodynamic Motion Planning for High-dimensional Physical Systems. (2011) (Thesis or Dissertation Director)

     Keren Lasker, Doctoral Structure Determination of Macromolecular Assemblies by Data Integration, Application to the 26S Proteasome. (2012) (Committee Member)

     Drew Bryant, Ph.D. Protein Function Prediction. (2012) (Thesis or Dissertation Director)

     Jeff Chyan, MS, Examining the Use of Homology Models in Predicting Kinase Binding Afinity. (2013) (Thesis or Dissertation Director)

     Troy Ruths, Ph.D, Population Regulomics: Applying population genetics to the cis-regulome. (2013) (Committee Member)

     Natalie Berestovsky, Ph.D, Toward Integrated Computational Models of Cellular Networks. (2013) (Committee Member)

     Kristin Yvonne Rozier, Doctoral Explicit or Symbolic Transltion of Linear Temporal Logic to Automata. (2013) (Committee Member)

     Drew Bryant, Doctoral Redundancy-aware learning of protein structure-function relationships. (2013) (Thesis or Dissertation Director)

     Devin Kieber Grady, Ph.D, Motion Planning with Uncertain Information in Robotic Tasks. (2014) (Thesis or Dissertation Director)

     Rossitza Irobalieva, Ph.D, PhD Thesis. (Committee Member)

     Corey Hyrc, PhD Thesis. (Committee Member)

     Risa Myers, MS, Ordinal Regression over Time Series Data, with an Application to Classifying Patient Vital Sign Quality (2013). (Committee Member)

     Yun Yu, Ph.D, Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. (Committee Member)

     Christine Peterson, Ph.D, Bayesian Graphical Models for Biological Network Inference (2013). (Committee Member)

     Rahul Kumar, Learning to Highlighten Relevant Text in Binary Classified Documents. (Committee Member)

     Matt Maly, MS Temporal Logic Motion Planning in Partially Unknown Environments. (Thesis or Dissertation Director)

    Awards, Prizes, & Fellowships
     Fellow, American Association for the Advancement of Science (AAAS), (2012)

     Fellow, Association for Computing Machinery (ACM), (2010)

     World Open Source Softward Challenge Grand Prize for OMPL (Open Motion Planning Library), 2012, (2012)

     BioHoustonís 2012, Women in Science Award, Women in Science Award (2012)

     Fellow, Institute of Electrical and Electronics Engineers (IEEE), Institute of Electrical and Electronics Engineers (2012)

     Member, The Academy of Medicine, Engineering and Science of Texas, (2012)

     Elected Member, Institute of Medicine (IOM) of the National Academies, Institute of Medicine (IOM) of the National Academies (2012)

     Fellow, Institute of Electrical and Electronic Engineers (IEEE), (2011)

     Fellow, Association for the Advancement of Artificial Intelligence (AAAI), Advancement of Artificial Intelligence (AAAI) (2008)

     Program Committee Member, "Robotics: Science and Systems", (2005)

     Program Committee Member, " IEEE International Conference on Robotics and Automation ", (2005)

     Founding Member and Advisory Board, "Robotics: Science and Systems", (2005)

     Mentor CRA, (2005)

     Program Committee Member, ACM International Conference on Research in Computational Molecular Biology, (2004)

     Fellow, World Technology Network, World Technology Network (2004)

     Program Committee Member, IEEE International Conference on Robotics and Automation, (2004)

     Charles Duncan Award for Outstanding Academic Achievement, Rice University (2004)

     Program Committee Member, International Conference on Infromatics in Control, Automation and Robotics, (2004)

     Fellow, American Institute for Medical and Biological Engineering, American Institute for Medical and Biological Engineering (2004)

     Sloan Fellow, Sloan Foundation (2000-2002)

     Brilliant 10 Scientists, in Popular Science Magazine (2002)

     100 World's Top Young Innovators, MIT's Technology Review Magazine (2002)

     Member, American Association for the Advancement of Science,

     Member, Association for Computing Machinery,

     Member, Houston Chapter of IEEE,

     Member, IEEE Robotics and Automation Society,

     Member, Institute of Electrical and Electronic Engineers (IEEE),

     Paper invited to Handbook on Data Mining and Knowledge Discovery, Oxford University Press (2001)

     Paper invited to 2001 IEEE International Conference on Robotics and Automation, Seoul, Korea, (2001)

     Paper invited to Handbook of Randomized Computing, Kluwer Academic Publishing (2001)

     Paper invited to Handbook of Discrete and Computational Geometry, CRC Press (2002)

     Finalist, Best Conference Paper Award, IEEE International Conference on Robotics and Automation (2001)

     Member, Houston Society for Engineering in Medicine and Biology,

     Member, American Society for Engineering Education,

     Member, Faculty Operating Committee, MD/Ph.D. Program, Baylor College of Medicine, (2001)

     Executive Committee Member, Graduate Program in Structural and Computational Biology and Molecular Biophysics (SCBMB), Baylor College of Medicine, (2001)

     Administrative Committee (AdCom), IEEE Robotics and Automation Society

     Program Committee, ACM International Conference on Computational Molecular Biology (2002)

     Program Committee, Workshop on Algorithmic Foundations of Robotics (2002)

     Program Committee, IEEE International Conference on Robotics and Automation (2001 & 2002)

     Program Committee, IEEE/RSJ International Conference on Intelligent Robots and Systems (2001)

     Association for Computing Machiney Grace Murray Hopper Award, (2001)

     Member, Biomedical Engineering Society,

     Member, Biomedical Engineering Society

     Member, Institute of Electrical and Electronic Engineers and IEEE Robotics and Automation Society

     NSF CAREER Award, (1997-2000)

     Fellow, Whitaker Foundation, (2000)

     Sloan Fellow, (2000)

     Program Committee, IEEE International Conference on Robotics and Automation (2000 and 2001)

     Organizer and Chair, Developments in Probabilistic Motion Planning, Symposium during the IEEE International Conference on Robotics and Automation, San Francisco, Californi (April 2000)

     Award for second best poster, Fourth ACM International Conference on Computational Biology (RECOMB) (April 2000)

     Invited Plenary Speaker, International Joint Conference on Artificial Intelligence (IJCAI) (August 1 - 6, 1999)

     Invited Distinguished Lecturer, Distinguished Lecture Series in Biomedical Informatics, University of Wisconsin, Madison, Wisconsin (November 5, 1999)

     Invited Speaker, Workshop on Motion Support for Virtual Prototyping, Stanford University, Stanford, California (1999)

     Finalist, Phi Beta Kappa Teaching Award (1999)

     Invited Lecturer, Workshop on Distributed Manipulation, International Conference on Robotics and Automation, Detroit, Michigan (May 11-15, 1999)

     Invited Lecturer, Symposium on Computer Visition and Robotics, Center for Discrete Mathematics and Theoretical Computer Science, Rutgers University, New Brunswick, New (March 21 - 23, 1999)

     Invited Participant, National Science Foundation Meeting on the Directions of the CAREER Program (January 1999)

     Career Award, National Science Foundation (1997 - 2002)

     Member, IEEE Robotics and Automation Society

     Program Committee Member, IEEE International Conference on Robotics and Automation (1999)

     Organizer and Chair, AAAI Spring Symposium on Search Techniques forProblem Solving under Uncertainty and Incomplete Information (March 1999)