B.S. (1989) University of Crete, Greece
M.S. (1992) Stanford University
Ph.D. (1995) Stanford University
Robotics, Bioinformatics, Algorithms
Email: kavraki@rice.edu
Phone: 713-348-5737
Office: Duncan Hall, 3106
|
|
Lydia Kavraki
Noah Harding Professor of Computer Science and Bioengineering
Kavraki's Group Research Interests
In Robotics Kavraki's group works on motion planning with emphasis on high-dimensional systems, assembly planning, reasoning with sensing and control uncertainty, flexible object manipulation, physical modeling, probabilistic methods in robotics, the geometry of motion and the use of new enabling technologies such as MicroElectroMechanical Systems. We are also interested in problems arising in the intersection of robotics and sensor nets.
In Bioinformatics Kavraki's group develops computational tools on high-performance systems to model protein structure and function, understand biomolecular interactions and help analyze, in the long run, the molecular machinery of the cell. We integrate sequence information with three-dimensional structural information to capture, represent and exploit relevant molecular motion. Of particular interest are the identification of three-dimensional functional motifs in protein databases, docking of flexible molecules to flexible receptors, computer-assisted drug discovery, and the understanding and compact representation of structural changes in large biomolecular machines. We apply robotics and computational geometry methods to the above problems.
Both areas above involve real-world problems and fall into the broader category of physical computing. In both areas we seek to develop physical algorithms: algorithms that are capable of solving complex high-dimensional geometric problems arising in real-world applications (e.g., move a robot from A to B, predict a biomolecular complex). We believe that as computers become ubiquitous, we need to use computers to represent, simulate, and interact with the physical world. This is not an easy task, however. Algorithms for physical problems differ in significant ways from those for traditional (artificial world) problems. The latter algorithms have full control over and perfect access to the required data. In contrast, physical algorithms apply to objects in the real world which are subject to the independent and imperfectly modeled laws of nature. Our long term goal is to study the fundamental issues arising when algorithms are designed for problems in the physical world and to develop coherent solution frameworks which quantify, to the extent possible, the tradeoff between accuracy and performance present in solutions developed for realistic settings.
Selected Publications
Abstract
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. Moll and L.E. Kavraki "Path Planning for Minimal Energy Curves of Constant Length." 21st Annual Houston Conference on Biomedical Engineering Research (2004).
A. Shehu, C. Clementi and L.E. Kavraki "A Multiscale Framework for the Characterization of Protein Native States." (2008).
M. Moll and L.E. Kavraki "LabelHash: A Flexible and Extensible Method for Matching Structural Motifs." Nature Precedings (2008).
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).
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.
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.
A. Shehu, L.E. Kavraki, and C. Clementi "A Multiscale Characterization of Native Conformational States in Proteins." (January 6-11, 2008).
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).
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).
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).
A. Shehu, C. Clementi, and L.E. Kavraki "Sampling Biomolecular Conformations with Spatial and Energetic Constraints." 8th Johns Hopkins Folding Meeting (March 2005).
A. Heath, G.N. Bennett and L.E. Kavraki "Visualizing the Results of Metabolic Pathway Queries." (Sept. 21-24, 2008).
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.
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).
M. Moll, D.H. Bryant and L.E. Kavraki "A Flexible and Extensible Method for Matching Structural Motifs." (Oct. 3-4, 2008): 85.
Article
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.
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.
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.
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.
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.
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.
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.
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.
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.
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. Shehu, C. Clementi, and L.E. Kavraki "Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins." Algorithmica, 48 (2007): 303-327.
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.
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.
Lydia Kavraki "Algorithms in Robotics: The Motion Planning Perspective (Invited)." Frontiers of Engineering of the National Academy of Engineering (1999): 90-93.
Book
P.K. Agrawal, L. Kavraki, and M. Mason "Robotics: The Algorithmic Perspective." AK Peters (1998).
L. Kavraki, H. Choset, W. Burgard, S. Hutchinson, G. Kantor, K. Lynch, andn S. Thurn "Principles of Robot Motion: Theory, Algorithms, and Implementation." (2005).
Book chapter
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. Halperin, L.E. Kavraki, and J.C. Latombe "Robotics." Handbook of Discrete and Computational Geometry (2004): 1065-1094.
M. Teodoro, Kavraki, L. "Pharmacology." Handbook on Data Mining and Knowledge Discovery (2002): 808-816.
D. Halperin, L. Kavraki, and J.-C. Latombe "Robotics (Invited)." Handbook of Discrete and Computational Geometry (1997): 755-779.
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.
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.
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. Kavraki, and J.-C. Latombe "Robot Algorithms (Invited)." Algorithms and Theory of Computation Handbook, CRC Press (1999).
D. Schwarz and L.E. Kavraki "Protein-Ligand Interactions: Computational Docking." Encyclopedia of Life Scienes, Article #A4105, Wiley (2006).
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.
L. Kavraki and S. LaValle "Motion Planning." Springer Handbook of Robotics (2008): 109-131.
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.
Other
M. Zhang and L.E. Kavraki "A New Method for Fast and Accurate Computation of Molecular Conformations." Journal of Chemical Information and Computer Science (In press).
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.
A.M. Ladd, K. Bekris, A. Rudys, L.E. Kavraki, and D.S. Wallach "Robotics-Based Localization Sensing Using Wireless Ethernet." Journal on Special Topics in Mobile Networking and Applications (MONE) (2003).(In Press)
Refereed Article
A. Shehu, L.E. Kavraki, and C. Clementi "Unfolding the Fold of Cyclic Cysteine-rich Peptides." Protein Science, 17 (2008): 482-493.
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)
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.
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).
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 and L.E. Kavraki "Measure Theoretic Analysis of Probabilistic Path Planning." Transactions on Robotics and Automation, 20(2) (2004): 229-242.
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.
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.
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.
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.
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.
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.
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.
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.
F. Lamiraux and L.E. Kavraki "Planning Paths for Elastic Objects under Manipulation Constraints." International Journal of Robotics Research, 20(3) (2001): 188-208.
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.
P.W. Finn and L. Kavraki "Computational Approaches to Drug Design." Algorithmica, 25 (1999): 347-371.
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.
Refereed Conference Paper
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.
M. Moll and L.E. Kavraki "Matching of structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction." (August 2008).
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, 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.
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.
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, 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.
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.
R. Bohlin and L.E. Kavraki "Path Planning using Lazy PRM." Proceedings of the IEEE International Conference on Robotics and Automation (2000): 521-538.
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.
K. Tsianos, L.E. Kavraki "Replanning: A Powerful Planning Strategy for Hard Kinodynamic Problems." (October 2008): 1667-1672.
I.A. Sucan, J.F. Kruse, M. Yim and L.E. Kavraki "Reconfigurations for Modular Robots using Kinodynamic Motion Planning." (October 2008).
I.A. Sucan, J.F. Kruse, M. Yim and L.E. Kavraki "Kinodynamic Motion Planning with Hardware Demonstrations." (October 2008): 1661-1666.
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).
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.
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.
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).
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).
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).
A. Heath, L.E. Kavraki, and G. Balazsi "Biopolarity of the Saccharomyces Cerevisiae Genome." , paper #60540 (May 16-18, 2008).
L.E. Kavraki, F. Lamiraux, Ch. Holleman "Towards Planning for Flexible Objects." Robotics: The ALgorithmic Perspective (1998): 313-325.
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).
K. Bekris and L.E. Kavraki "Informed and Probabilistically Complete Search for Motion Planning under Differential Constraints." (July 2008).
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).
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.
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.
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.
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)
A. Ladd, L. Kavraki "Generalizing the Analysis of PRM." Proceedings of the 2002 IEEE International Conference on Robotics and Automation (ICRA) (2002): 2120-2125.
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. Ladd, L.E. Kavraki "Motion Planning in the Presence of Drift, Underactuation and Discrete System Changes." Robotics Science and Systems (2005).
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.E. Kavraki "Fast Tree-Based Exploration of State Space for Robots with Dynamics." Alrogithmic Foundations of Robotics VI, Springer STAR, 17 (2005): 297-312.
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.
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.
J. Phillips, A. Ladd, L. Kavraki "Simulated Knot Tying." Proceedings of the 2002 IEEE International Conference on Robotics and Automation (ICRA) (2002): 841-846.
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.
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).
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
M. Zhang and L.E. Kavraki "Efficiently Maintaining Molecular Conformations Using Local Frames." Currents in Computational Molecular Biology (2001): 97-98.
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.
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., 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.
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.
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.
Presentations
Conference Committee Member
Program committee member. "Int'l Workshop on the Algorithmic Foundations of Robotics 2006.".
Program committee member. "IEEE Int'l conf on Robotics and Automation 2006.".
Program committee member. "Robotics: Science and Systems, 2005.".
Program committee member. "IEEE Int'l Conf on Robotics and Automation, 2005.".
Invited Talk
Distinguished Speaker Series Guest. "Computing about the Physical World." Rensselaer Polytechnic Institute, Troy, New York. (December 9 2004)
"Modeling the Conformational Flexibility of Proteins." DIMACS Workshop on Computational Geometry, DIMACS Center, Rutgers University, Piscataway, New jersey. (November 14, 2002)
"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)
"Robotics Methods for Molecular Modeling and Computer-Assisted Drug Discovery." Rice University, Houston, Texas. (January 10, 2003)
"From Robots to Biomolecules: Computing Meets the Physical World." Corporate Affiliates Meeting, Rice University. (October 15, 2008)
"From Robots to Biomolecules: Designing Amazing New Medicines." Affiliates Meeting, Computer Science, Rice University, Houston, Texas. (October 3, 2002)
"Modeling the Conformational Flexibility of Proteins." Department of Computer Science, Case Western Reserve University, Cleveland, Ohio. (July 25, 2003)
"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)
"Engineering Receptor-Mediated Cellular Interacitons." Short Course on Advances in Tissue Engineering, Rice University. (August 15, 2007)
"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)
"Modeling the Conformational Flexibiity of Proteins." Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania. (August 8, 2003)
"Negotiating the Ideal Faculty Position." How to Obtain Funding, Rice Universtiy. (October 23, 2006)
"Receptor-Mediated Cellular Interactions." Short Course on Advances in Tissue Engineering, Rice University. (August 13, 2008)
"Robotics Methods in Drug discovery and Tissue engineering." Rice University, Houston, Texas. (August 14, 2002)
"Bioinformatics." Board of Trustees, Rice University, Houston, Texas. (May 22, 2002)
"From Robots to Biomolecules: Computing Meets the Physical World." Carnegie Mellon University, Pittsburgh, Pennsylvania. (January 27, 2004)
"Informed Search for Motion Planning under Differential Constraints." The AAAI-08 Workshop on Searching Artificial Intelligence and Robotics, Chicago, IL. (July 13-14, 2008)
"Robotics Methods in Drug Discovery and Tissue Engineering." Rice University, Houston, Texas. (August 15, 2003)
"A Robotics Engineering Approach to Drug Discovery." Department of Computer Science, Harvard University, Cambridge, Massachusetts. (September 25, 2003)
"A Robotics-Based Approach to Drug Discovery and Tissue Engineering." Tissue Engineering Growth International Conference and Exposition, Pittsburgh, Pennsylvania. (March 19, 2002)
"From Robots to Biomolecules: Computing Meets the Physical World." Rice Theoretical and Computational Biology Symposium, Houston, TX. (December 11, 2005)
"Motion Planning for Physical Systems." IEEE Galveston Bay Section and Joint Society Meerting, NASA-JSC, Clear Lake, TX. (June 19, 2008)
"Motion Planning for Physical Systems." Stanford Broad Area Colloquium, Dept. of Computer Science, Stanford University. (June 4, 2007)
"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, Duke University, Durham, North Carolina. (September 29, 2003)
"Engineering Receptor Mediated Cellular Processes." Advances in Tissue Engineering, Houston, Texas. (August 11, 2004)
"From Robots to Molecules: Applications of Physical Computing." Department of Chemical Engineering, Rice University, Houston, Texas. (January 31, 2002)
"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 with Dynamics." Dept of Computer Science, Washington University, St. Louis, MO. (December 9, 2005)
"Research in Computational Structural Biology." Retreat for Planning an NIH Roadmap Grant, Univeristy of Texas at Austin, Austin, TX. (August 26, 2006)
"Engineering Receptor-Mediated Cellular Interactions." Short Course on Advances in Tissue Engineering, Rice University. (August 16, 2006)
"Modeling the Conformational Flexibility of Proteins." Center for Biological Modeling and Science, Michigan State University, East Lansing, Michigan. (October 10, 2003)
"Physical Computing." CRAY Distinguished Lecture Series, University of Minnesota, Minneapolis, MN. (December 5, 2005)
"A Robotics-Inspired Approach to the Analysis of Molecular Flexibility and Function." Colloquium, Boston, MA. (February 7, 2008)
"Bioinformatics Research." King's College, Oxford University, Oxford. (March 6, 2006)
"Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps." International Symposium on Robotics and Automation, Siena, Italy. (October 20, 2003)
"Sampling-based Motion Planning: Recent Developments and Future Challenges." General Robotics, Automation, Sensing and Percention (GRASP) Laboratory, University of Pennsylvania. (November 18, 2005)
"A Robotics Engineering Approach to Drug Discovery." University of North Carolina, Chapel Hill, North Carolina. (November 10, 2003)
"From Robots to Biomolecules: Designing Amazing New Medicines." NSF-ADVANCE Lecture Series, Univ of New Mexico, Las Cruses, NM. (September 1, 2005)
"Recent Developments in Motion Planning." Distinguished Colloquium Series, Department of Computer Science, University of Toronto. (January 8, 2008)
"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)
"From Robots to Biomolecules to Drug Discovery." Baylor College of Medicine, Houston, Texas. (December 10, 2003)
"Geometry and Robotics Inspired Approaches to Structural Biology." Department of Computer Science, University of New Mexico, Las Cruses, NM. (August 31, 2005)
"Motion Planning: from Solving Puzzles to Driving Vehicles." Cognitive Mobile Robotics Technical Interchange Planning Meeting DARPA, Camden, NJ. (January 10, 2008)
"Engineering Receptor-Mediated Cellular Interactions." Short Course on Advances in Tissue Engineering, Rice University, Houston, TX. (August 10, 2005)
"Robots, Molecules, and Physical Computing." Dept. of Computer Science, University of Massachusetts at Amherst, Amherst. (November 6, 2008)
"Computational Drug Discovery." Alliance for Nanohealth Meeting, Houston, TX. (June 2, 2005)
"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)
"From Robotics to Biomolecules: Computing Meets the Physical World." Distinguished Speaker Series: National Science Foundation, Washington, DC. (April 6, 2005)
"Computer-Assisted Drug Design." Rice Alumni College, Rice University, Houston, TX. (February 25, 2005)
"Computational Modeling of Biomolecular Interactions." Molecular Medicine Symposium, The Univ of Texas System, Houston, TX. (February 22, 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)
Keynote Speaker
Keynote. "Computational Problems in Systems Biology." M.D. Anderson 61st Annual Symposium on Cancer Research, M.D. Anderson Cancer Center. (October 30, 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)
"Physical Computing." National Center for Women and information Technology, Annual Meeting, Urbana. (May 14, 2008)
Lecture
"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.
"Simulated Knot Typing." 2002 IEEE International Conference on Robotics and Automation (ICRA), . (May 2002) With J. Phillips, A. Ladd.
"Generalizing the Analysis of PRM." 2002 IEEE International Conference on Robotics and Automation (ICRA), . (May 2002) With A. Ladd.
"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.
Other
"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.
"Part Assembly Using Static and Dynamic Force Fields." IEEE/RSJ International Conference on Intelligent Robots and Systems, Takamastu, Japan. (November 2000) With J. Luo.
"Probabilistic Methods in Path Planning." Invited Colloquium, Department of Mathematics, Rice University, Houston, Texas. (September 30, 1999)
"Towards Planning for Flexible Objects." Third International Workshop on the Algorithmic Foundations of Robotics, Houston, Texas. (March 1998)
"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)
"A Two-Level Fuzzy PRM for Manipulation Planning." IEEE/RSJ International Conference on Intelligent Robots and Systems, Takamastu, Japan. (November 2000) With Ch. Nielsen.
"Computational Approaches to Drug Design." Invited Plenary Talk, International Joint Conference on Artificial Intelligence (IJCAI), . (August 3, 1999)
"Randomized Planning for Elastic Objects, Invited Presentation." Department of Industrial Engineering and Operations Research, University of California, Berkeley, California. (April 1998)
"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)
"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)
"Randomized Techniques for Robotics Problems, Invited Presentation." Department of Computer Science, University of Houston, Houston, Texas. (April 1998)
"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)
"Computational Tools for Problems in the Physical World." Annual Meeting of the Coalition for National Funding, Capital Hill, Washington DC. (June 25, 2007)
"Efficient Modeling of Molecular Conformations Using Local Frames." 19th Annual Houston Conference on Biomedical Engineering Research, Houston, Texas. (February 8, 2001)
"Planning Paths for a Flexible Surface Patch." IEEE International Conference on Robotics and Automation, Leuven. (May 1998)
"Planning the Motion of Molecules (Invited Talk)." ARO/NSF Workshop on Modeling Motion, Duke University. (August 7, 2000)
"Computational Approaches to drug Design and the RAPID Pharmacophore Identification System." Invited Colloquium, Department of Bioengineering, Rice University, Houston, Texas. (September 7, 1999)
"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.
"Planning for Rigid and Flexible Robots, Invited Presentation." Department of Computer Science, Stanford University, Stanford, California. (June 1998)
"Planning the Motion of Robots and Molecules: An Algorithmic Introduction (Invited Seminar)." University of Crete, Greece. (July 10 - 14, 2000)
"A Single Universal Force Can Uniquely Orient any Non-Symmetric Part." 9th International symposium of Robotics Research, Utah. (October 12, 1999)
"Part Manipulation Using Programmable Vector Fields." (Invited) Department of Computer Science, Texas A&M University, College Station, Texas. (October 26, 2001)
"Pharmacophore Identification in Computer-Assisted Drug Design (Invited Presentation)." European Biomolecular Institute, Cambridge, United Kingdom. (July 1998)
"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)
"An Introduction to Teaching in Engineering." Teaching Workshop, George R. Brown School of Engineering, Rice University, Houston, Texas. (August 21, 2001)
"Motion Planning: Current Approaches and Future Directions (Invited Symposium Talk)." IEEE International Conference on Robotics and Automation, San Francisco, California. (April 26, 2000)
"Part Orientation into One or Two Stable Equilibria using Programmable (Invited Talk)Force Fields." Xerox Parc, Palo Alto, CA. (1999)
"Robotics: Current Directions and Future Challenges (Invited Presentation)." Affiliates Meeting, Department of Computer Science, Rice University, Houston, Texas. (October 1998)
"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)
"Computational Approaches to Pharmaceutical Drug Design (Invited Presentation)." LAAS, Toulouse, France. (October 1998)
"Unique Part Orientation using Programmable Force Fields." Robotics Laboratory, Stanford University, Stanford, California. (June 1999)
"From Robots to Biomolecules: Designing Amazing New Medicines." Rice Engineering Reunion, Rice University, Houston, Texas. (May 11, 2001)
"Motion Planning in Robotics (Invited Speaker and Panelist)." Frontiers of Engineering Symposium, National Academy of Engineering, Washington, D.C.. (September 1998)
"Planning Paths for Flexible Objects under Manipulation Constraints." IEEE International Conference on Robotics and Automation, Detroit, Michigan. (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)
"Flexible Objects in Virtual Prototyping Applications." Workshop on Motion Support in Virtual Prototyping, Stanford University, Stanford, California. (May 1999)
"Towards Planning for Elastic Objects (Invited Colloquium)." University of Texas A&M, College Station, Texas. (April 1999)
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, IEEE Transactions on Robotics and Automation, (2002).
Editor for Special Issue, Int'l Journal of Robotics Research, (2005).
Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics, (2005).
Associate Editor, Computer Science Reviews, (2005).
Member of the Editorial Board, Advanced Robotics Series (STAR), (2005).
Associate Editor, Robotics Magazine, (2005).
Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics, (2007).
Associate Editor, Computer Science Reviews, (2007).
Member of the Editorial Board, Advanced Robotics Series (STAR), (2007).
Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics, (2008).
Associate Editor, Computer Science Reviews, (2008).
Associate Editor, Springer-Verlag Advanced Robotics Series, (2008).
Theses
Carole Nissoux, "External Reader and Examiner, Ph.D. Thesis, "Visibility et Methods Probabilistes Pour la Planification de Mouvement en Robotique" Centre Scientific de la Reserche National, Robotics Laboratory, LAAS-CNRS, France." (1999).
Jiangchun Luo, Master of Science. "Part Assembly Using Static and Dynamic Force Fields." (2000).(Thesis or Dissertation Director)
Christopher Holleman, Master of Science. "Path Planning with Medial Axis Hints." (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, 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)
Miguel Teodoro, Doctor of Philosophy. "Modeling Protein Flexibility Using Collective Modes of Motion: Applications to Drug design." (2003).(Thesis or Dissertation Director)
Andrew Ladd, Master of Science. "Analysis of Probabilistic Roadmap Methods for Motion Planning and Applications to Polygon Manipulation." (2003).(Thesis or Dissertation Director)
Scott Schaefer, Master of Science. "A Factored, Interpolatory Subdivision Scheme for Surfaces of Revolution." (2003).(Committee Member)
Fabin Gravot, Doctor of Philosophy. "External Reader and Examiner - Motion Planning Algorithms for General Closed-ChainMechanisms." (2004).
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)
Konstantinos Bekris, Master of Science. "Reactive Range-free Landmark Navigation without Scene Reconstruction." (2004).(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)
Jan 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)
Tao Ju, Doctor of Philosophy. "Building a D3 Atlas of the Mouse Brain." (2005).(Committee Member)
M. Schwarz, Master of Science in Computer Science. "Local Conformational Sesarch of Proteins Using the Expansive Spaces Search." (2005).(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)
Brian Chen, Doctor of Philosophy. "Geometry-based Methods for Protein Function Prediction." (2006).(Thesis or Dissertation Director)
Brian Chen, Ph.D. "Geometry Based Methods for Protein Function Prediction." (2007).(Thesis or Dissertation Director)
Andrew Ladd, Doctor of Philosophy. "Motion Planning for Physical Simulation." (2007).(Thesis or Dissertation Director)
David Kristensen, Ph. D. "Automated Protein functional Site Discovery; Structural Similarity and De Novo Approaches." (2007).(Committee Member)
Ajay Gulati, Ph. D. "Performance Virtualization and QoS in Shared Storage Systems." (2007).(Committee Member)
Endah Susilowati, Ph. D. "Specificity of Membrane Helix-helix Interactions by Mutagenesis and Structural Analysis." (2007).(Committee Member)
Maciej Kalisiak, Ph.D. "Efficient Motion Planning with Differential Constraints." (2007).(Committee Member)
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)
Herman Stamati, Master of Science. "Analysis of Molecular Motion using Non-Linear Dimensionality Reduction." (2007).(Thesis or Dissertation Director)
Amarda Shehu, Doctor of Philosophy. "Molecules in Motion:Computing Structural Flexibility." (2008).(Thesis or Dissertation Director)
Cuong Than, Master of Science. "Reconstruction of Phylogenetic Networks and Their Relationships with Trees and Branches." (2008).(Committee Member)
Viacheslav 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)
Adina Kilpatrick, Ph. D. "Structural Basis for Calmodulin-Mediated Regulation of the Ryanodine Receptor." (2008).(Committee Member)
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)
Derek Ruths, Doctor of Philosophy. "Deriving Executable Models of Biochemical Network Dynamics from Qualitative Data." (2009).(Committee Member)
|
