Biblio

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2010
Bhatia, A, Kavraki LE, Vardi MY.  2010.  Sampling-Based Motion Planning with Temporal Goals. IEEE International Conference on Robotics and Automation. :2689-2696.
Preprint PDF     
Stamati, H, Clementi C, Kavraki LE.  2010.  Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. Proteins. 78:223-235.
Abstract      Publisher's web site     
Bryant, DH, Moll M, Chen BY, Fofanov VY, Kavraki LE.  2010.  Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics. 11:242.
Abstract      Preprint PDF     Publisher's web site     
Heath, AP, Bennett GN, Kavraki LE.  2010.  Finding Metabolic Pathways Using Atom Tracking. Bioinformatics. 26:1548-1555.
Abstract      Publisher's web site     
Bhatia, A, Kavraki LE, Vardi MY.  2010.  Motion Planning with Hybrid Dynamics and Temporal Goals. IEEE Conference on Decision and Control.
Sucan, IA, Kavraki LE.  2010.  On the Implementation of Single-Query Sampling-Based Motion Planners. IEEE International Conference on Robotics and Automation. :2005-2011.
Preprint PDF     
Haspel, N, Moll M, Baker ML, Chiu W, Kavraki LE.  2010.  Tracing conformational changes in proteins. BMC Structural Biology. 10:S1.
Abstract      Preprint PDF     Publisher's web site     
2009
Sucan, IA, Kavraki LE.  2009.  On the Performance of Random Linear Projections for Sampling-Based Motion Planning. IEEE/RSJ International Conference on Intelligent Robots and Systems. :2434-2439.
Preprint PDF     
Rusu, R B, Sucan IA, Gerkey BP, Chitta S, Beetz M, Kavraki LE.  2009.  Real-Time Perception-Guided Motion Planning for a Personal Robot. IEEE/RSJ International Conference on Intelligent Robots and Systems. :4245-4252.
Preprint PDF     
Heath, AP, Kavraki LE.  2009.  Computational Challenges in Systems Biology. Computer Science Review. 3:1-17.
Abstract      Publisher's web site     
Plaku, E, Kavraki LE, Vardi MY.  2009.  Falsification of LTL Safety Properties in Hybrid Systems. Proc. of the Conf. on Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2009).
Abstract      Preprint PDF     
Plaku, E, Kavraki LE, Vardi MY.  2009.  Hybrid systems: from verification to falsification by combining motion planning and discrete search. Formal Methods in System Design. 34:157-182.
Abstract      Preprint PDF     Publisher's web site     
Haspel, N, Geisbrecht B, Lambris JD, Kavraki LE.  2009.  Multi-scale Characterization of the Energy Landscape of Proteins with Application to the C3d/Efb-C Complex. Proteins: Structure, function and bioinformatics. 78:1004-1014.
Publisher's web site     
Bekris, KE, Tsianos K, Kavraki LE.  2009.  Safe and Distributed Kinodynamic Replanning for Vehicular networks. ACM/Springer Mobile Networks and Applications (MONET). 14:292–308.
Abstract      Publisher's web site     
Haspel, N, Moll M, Baker ML, Chiu W, Kavraki LE.  2009.  Tracing Conformational Changes in Proteins. IEEE Intl. Conf. on Bioinformatics and Biomedicine Workshops (BIBMW).
Abstract      Preprint PDF     
2008
Plaku, E, Kavraki LE, Vardi MY.  2008.  Impact of Workspace Decompositions on Discrete Search Leading Continuous Exploration (DSLX) Motion Planning. IEEE International Conference on Robotics and Automation. :3751-3756.
Abstract     
Plaku, E, Kavraki LE, Vardi MY.  2008.  Discrete Search Leading Continuous Exploration for Kinodynamic Motion Planning. Robotics: Science and Systems. :326-333.
Abstract      Preprint PDF     Publisher's web site     
Tsianos, K, Kavraki LE.  2008.  Replanning: A powerful planning strategy for hard kinodynamic problems. IEEE/RSJ International Conference on Intelligent Robots and Systems. :1667-1672.
Abstract      Preprint PDF     
Haspel, N, Ricklin D, Geisbrecht B, Lambris JD, Kavraki LE.  2008.  Electrostatic Contributions Drive the Interaction Between Staphylococcus aureus Protein Efb-C and its Complement Target C3d.. Protein Science. 17(11):1894-1906.
Abstract      Publisher's web site     
Heath, AP, Balázsi G, Kavraki LE.  2008.  Bipolarity of the saccharomyces cerevisiae genome. International Conference on Bioinformatics and Biomedical Engineering (iCBBE). :330–333.
Abstract      Publisher's web site     
Plaku, E.  2008.  From High-Level Tasks to Low-Level Motions: Motion Planning for High-Dimensional Nonlinear Hybrid Robotic Systems. Department of Computer Science.
Abstract      Preprint PDF     
Bekris, KE.  2008.  Informed Planning and Safe Distributed Replanning under Physical Constraints. Department of Computer Science.
Abstract      Preprint PDF     
Sucan, IA, Kavraki LE.  2008.  Kinodynamic Motion Planning by Interior-Exterior Cell Exploration. International Workshop on the Algorithmic Foundations of Robotics.
Abstract      Preprint PDF     Publisher's web site     
Sucan, IA.  2008.  Kinodynamic Motion Planning for High-dimensional Physical Systems. Department of Computer Science.
Preprint PDF     
Sucan, IA, Kruse JF, Yim M, Kavraki LE.  2008.  Kinodynamic Motion Planning with Hardware Demonstrations. IEEE/RSJ International Conference on Intelligent Robots and Systems. :1661--1666.
Abstract      Preprint PDF     Publisher's web site     
Moll, M, Kavraki LE.  2008.  LabelHash: A Flexible and Extensible Method for Matching Structural Motifs. Automated Function Prediction / BioSapiens meeting (AFP-BioSapiens).
Preprint PDF     Publisher's web site     
Moll, M, Kavraki LE.  2008.  Matching of Structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction. The Seventh Annual International Conference on Computational Systems Bioinformatics (CSB2008). :157-168.
Abstract      Preprint PDF     Publisher's web site     
Shehu, A.  2008.  Molecules in Motion: Computing Structural Flexibility. Department of Computer Science.
Abstract      Preprint PDF     
Kristensen, DM, Ward MR, Lisewski AM, Edrin S, Chen BY, Fofanov VY, Kimmel M, Lichtarge O.  2008.  Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics. 9(17)
Abstract      Publisher's web site     
Sucan, IA, Kruse JF, Yim M, Kavraki LE.  2008.  Reconfiguration for modular robots using kinodynamic motion planning. ASME -- Dynamic Systems and Control.
Tsianos, K.  2008.  Replanning: A Powerful Planning Strategy for Systems with Differential Constraints. Department of Computer Science.
Abstract      Preprint PDF     
Tsianos, K, Halperin D, Kavraki LE, Latombe J-C, Attalah M.  2008.  Robot Algorithms. Algorithms and Theory of Computation Handbook.
Fofanov, VY, Chen BY, Bryant DH, Moll M, Lichtarge O, Kavraki LE, Kimmel M.  2008.  A Statistical Model to Correct Systematic Bias Introduced by Algorithmic Thresholds in Protein Structural Comparison Algorithms. IEEE Intl. Conf. on Bioinformatics and Biomedicine (BIBM).
Abstract      Preprint PDF     Publisher's web site     
Shehu, A, Kavraki LE, Clementi C.  2008.  Unfolding the Fold of Cyclic Cysteine-rich Peptides. Protein Science. 17(3):482-493.
Abstract      Publisher's web site     
2007
Bekris, KE, Tsianos K, Kavraki LE.  2007.  A Distributed Protocol for Safe Real-Time Planning of Communicating Vehicles with Second-Order Dynamics. First International Conference on Robot Communication and Coordination (ROBOCOMM 07).
Abstract      Preprint PDF     
Moll, M, Schwarz D, Kavraki LE.  2007.  Roadmap Methods for Protein Folding. Protein Structure Prediction: Methods and Protocols.
Abstract      Preprint PDF     Publisher's web site     
Tsianos, K, Sucan IA, Kavraki LE.  2007.  Sampling-based robot motion planning: Towards realistic applications. Computer Science Review. 1(1):2--11.
Abstract      Preprint PDF     Publisher's web site     
Heath, AP, Kavraki LE, Clementi C.  2007.  From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes. Proteins: Structure, Function and Bioinformatics. 68:646-661.
Abstract      Publisher's web site     
Bekris, KE, Kavraki LE.  2007.  Greedy but Safe Replanning under Kinodynamic Constraints. Intl. Conf. on Robotics and Automation. :704-710.
Abstract      Preprint PDF     Publisher's web site     
Bekris, KE, Tsianos K, Kavraki LE.  2007.  A Decentralized Planner that Guarantees the Safety of Communicating Vehicles with Complex Dynamics that Replan Online. IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems.
Abstract      Preprint PDF     
Stamati, H.  2007.  Analysis of Molecular Motion using Non-Linear Dimensionality Reduction. Department of Computer Science.
Abstract      Preprint PDF     
Chen, BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.  2007.  Cavity Scaling: Automated Refinement of Cavity-Aware Motifs in Protein Function Prediction. Journal of Bioinformatics and Computational Biology. 5:353-382.
Abstract      Preprint PDF     
Chen, BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kimmel M, Lichtarge O, Kavraki LE.  2007.  Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction. Computational Systems Bioinformatics Conference (CSB2007). :343-355.
Abstract      Preprint PDF     
Plaku, E, Kavraki LE.  2007.  Distributed Computation of the knn Graph for Large High-Dimensional Point Sets. Journal of Parallel and Distributed Computing. 67:346--359.
Abstract      Preprint PDF     Publisher's web site     
Plaku, E, Stamati H, Clementi C, Kavraki LE.  2007.  Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction. Proteins: Structure, Function, and Bioinformatics. 67:897--907.
Abstract      Publisher's web site     
Plaku, E, Kavraki LE, Vardi MY.  2007.  Hybrid Systems: From Verification to Falsification. International Conference on Computer Aided Verification (CAV). 4590:468--481.
Abstract      Preprint PDF     Publisher's web site     
Chen, BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE.  2007.  The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. Journal of Computational Biology. 14:791-816.
Abstract      Preprint PDF     Publisher's web site     
Plaku, E, Kavraki LE, Vardi MY.  2007.  A Motion Planner for a Hybrid Robotic System with Kinodynamic Constraints. IEEE International Conference on Robotics and Automation (ICRA). :692--697.
Abstract      Preprint PDF     Publisher's web site     
Kavraki, LE, LaValle SM.  2007.  Motion Planning. Handbook of Robotics.
Publisher's web site     
Plaku, E, Kavraki LE.  2007.  Nonlinear Dimensionality Reduction Using Approximate Nearest Neighbors. SIAM International Conference on Data Mining (SDM). :3711-3716.
Abstract      Preprint PDF     Publisher's web site