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2008

Impact of Workspace Decompositions on Discrete Search Leading Continuous Exploration (DSLX) Motion Planning, Plaku, E.; Kavraki, L. E.; Vardi, M. Y. , IEEE International Conference on Robotics and Automation, Pasadena, CA, (2008)

Matching of Structural Motifs Using Hashing on Residue Labels and Geometric Filtering for Protein Function Prediction, Mark Moll; Lydia E. Kavraki , The Seventh Annual International Conference on Computational Systems Bioinformatics (CSB2008), (2008)

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids, David M. Kristensen; R. Matthew Ward; Andreas Martin Lisewski; Serkan Edrin; Brian Y Chen; Viacheslav Y Fofanov; Marek Kimmel; Olivier Lichtarge , BMC Bioinformatics, Volume 9, Issue 17, (2008)

Robot Algorithms, Konstantinos Tsianos; Dan Halperin; Lydia Kavraki; Jean-Claude Latombe , Algorithms and Theory of Computation Handbook, (2008)

Special Issue on Self-Reconfiguring Modular Robots (Guest Editorial), Mark Moll; Daniela Rus , Intl. J. of Robotics Research, Volume 27, Issue 3/4, p.277-278, (2008)

Unfolding the Fold of Cyclic Cysteine-rich Peptides, Shehu, A.; Kavraki, L. E.; Clementi, C. , Protein Science, Volume 17, Issue 3, p.482-493, (2008)

2007

A Distributed Protocol for Safe Real-Time Planning of Communicating Vehicles with Second-Order Dynamics, Bekris, K. E.; Tsianos, K. I.; Kavraki, L. E. , First International Conference on Robot Communication and Coordination (ROBOCOMM 07), Oct. 15-17, Athens, Greece, (2007)

Roadmap Methods for Protein Folding, Moll, M.; Schwarz, D.; Kavraki, L. E. , Protein Structure Prediction: Methods and Protocols, Oct., (2007)

Modular Self-reconfigurable Robot Systems: Challenges and Opportunities for the Future, Yim, Mark; Shen, Wei-Min; Salemi, Benham; Rus, Daniela; Moll, Mark; Lipson, Hod; Klavins, Eric , IEEE Robotics & Automation Magazine, March, Volume 14, Number 1, (2007)

Sampling-based robot motion planning: Towards realistic applications, Tsianos, K. I.; Sucan, I. A.; Kavraki, L. E. , Computer Science Review, August, Volume 1, Issue 1, p.2--11, (2007)

From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes, Heath, A. P.; Kavraki, L. E.; Clementi, C. , Proteins: Structure, Function and Bioinformatics, Aug, Volume 68, Number 3, p.646-661, (2007)

Greedy but Safe Replanning under Kinodynamic Constraints, Bekris, K. E.; Kavraki, L. E. , Intl. Conf. on Robotics and Automation, April, Rome, Italy, p.704-710, (2007)

A Decentralized Planner that Guarantees the Safety of Communicating Vehicles with Complex Dynamics that Replan Online, Bekris, K. E.; Tsianos, K. I.; Kavraki, L. E. , IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, 29 Oct./2 Nov., San Diego, CA, (2007)

A hierarchical protein folding scheme based on the building block folding model., Haspel, N.; Wainreb, G.; Inbar, Y.; Tsai, H. H.; Tsai, C. J.; Wolfson, H. J.; Nussinov, R. , Methods in Molecular Biology, Volume 350, Totowa, NJ, p.189-204, (2007)

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

Cavity Scaling: Automated Refinement of Cavity-Aware Motifs in Protein Function Prediction, Chen, B. Y.; Bryant, D. H.; Fofanov, V. Y.; Kristensen, D. M.; Cruess, A. E.; Kimmel, M.; Lichtarge, O.; Kavraki, L. E. , Journal of Bioinformatics and Computational Biology, Volume 5, Number 2a, p.353-382, (2007)

Changing the charge distribution of beta-helical based nanostructures can provide the conditions for charge transfer, Haspel, N.; Zanuy, D.; Zheng, J.; Aleman, C.; Wolfson, H.; Nussinov, R. , Biophysics Journal, Volume 93, Issue 1, p.245-253, (2007)

Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity for Function Prediction, Brian Y. Chen; Drew H. Bryant; Amanda E. Cruess; Joseph H. Bylund; Viacheslav Y. Fofanov; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki , Computational Systems Bioinformatics Conference (CSB2007), p.343-355, (2007)

Distributed Computation of the knn Graph for Large High-Dimensional Point Sets, Plaku, E.; Kavraki, L. E. , Journal of Parallel and Distributed Computing, Volume 67, Number 3, p.346--359, (2007)

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

Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction, Plaku, E.; Stamati, H.; Clementi, C.; Kavraki, L. E. , Proteins: Structure, Function, and Bioinformatics, Volume 67, Number 4, p.897--907, (2007)

Hybrid Systems: From Verification to Falsification, Plaku, E.; Kavraki, L. E.; Vardi, M. Y. , International Conference on Computer Aided Verification (CAV), Volume 4590, Berlin, Germany, p.468--481, (2007)

Motion Planning, Kavraki, L. E.; LaValle, S. , Advanced Series in Robotics, p.In Press, (2007)

Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues., Zheng, J.; Zanuy, D.; Haspel, N.; Tsai, C. J.; Aleman, C.; Nussinov, R. , Biochemistry, Volume 46, Number 5, p.1205-1218, (2007)

Nonlinear Dimensionality Reduction Using Approximate Nearest Neighbors, Plaku, E.; Kavraki, L. E. , SIAM International Conference on Data Mining (SDM), Minneapolis, Minnesota, p.3711-3716, (2007)

On the Characterization of Protein Native State Ensembles, Shehu, A.; Kavraki, L. E.; Clementi, C. , Biophysical Journal, Volume 92, Number 5, p.1503-1511, (2007)

OOPS for Motion Planning: An Online Open-source Programming System, Plaku, E.; Bekris, K. E.; Kavraki, L. E. , IEEE International Conference on Robotics and Automation (ICRA), Rome, Italy, p.3711-3716, (2007)

Protein-Ligand Interactions: Computational Docking, Schwarz, D.; Kavraki, L. E. , Encyclopedia of Life Sciences, p.Article #A4105, (2007)

Principles of nanostructure design with protein building blocks, Tsai, C. J.; Zheng, J.; Zanuy, D.; Haspel, N.; Nussinov, R. , Proteins, Volume 68, Number 1, p.1-12, (2007)

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins, Shehu, A.; Clementi, C.; Kavraki, L. E. , Algorithmica, Volume 48, Issue 4, p.303-327, (2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs, Chen, B. Y.; Fofanov, V. Y.; Bryant, D. H.; Dodson, B. D.; Kristensen, D. M.; Lisewski, A. M.; Kimmel, M.; Lichtarge, O.; Kavraki, L. E. , Journal of Computational Biology, Volume 14, Number 6, p.791-816, (2007)

2006

Distributed Control of the Center of Mass of a Modular Robot, Moll, Mark; Will, Peter; Krivokon, Maks; Shen, Wei-Min , Proc. 2006 IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, October, Beijing, China, p.4710--4715, (2006)

SUPERBOT: A Deployable, Multi-Functional, and Modular Self-Reconfigurable Robotic System, Salemi, Behnam; Moll, Mark; Shen, Wei-Min , Proc. 2006 IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems, oct, Beijing, China, p.3636--3641, (2006)

Evaluation of Algorithms for Bearing-Only SLAM, Bekris, K. E.; Glick, M.; Kavraki, L. E. , Proceedings of The IEEE International Conference on Robotics and Automation (ICRA), May, Orlando, FL, p.1937-1944, (2006)

Low-dimensional Free-energy Landscapes of Protein-Folding Reactions by Nonlinear Dimensionality Reduction, Das, P.; Moll, M.; Stamati, H.; Kavraki, L. E.; Clementi, C. , Proceedings of the National Academy of Sciences, June 17, Volume 103, Number 26, p.9885-9890, (2006)

Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction, Chen, B. Y.; Bryant, D. H.; Fofanov, V. Y; Kristensen, D. M.; Cruess, A. E.; Kimmel, M.; Lichtarge, O.; Kavraki, L. E. , Systems Bioinformatics Conference (CSB), August, Volume 4, Stanford, CA, p.311-323, (2006)

Path Planning for Deformable Linear Objects, Moll, M.; Kavraki, L. E. , IEEE Transactions on Robotics, Aug., Volume 22, Number 4, p.625-636, (2006)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction, Chen, B. Y.; Fofanov, V. Y; Bryant, D. H.; Dodson, B. D.; Kristensen, D. M.; Lisewski, A. M.; Kimmel, M.; Lichtarge, O.; Kavraki, L. E. , Research in Computational Biology: 10th Annual International Conference (RECOMB), April, Venice, Italy, (2006)

A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly, Wainreb, G.; Haspel, N.; Wolfson, H.; Nussinov, R. , Bioinformatics, Volume 22, p.1343-1352, (2006)

Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids, Aleman, C.; Zanuy, D.; Jimenez, A. I.; Cativiela, C.; Haspel, N.; Zheng, J.; Casanovas, J.; Wolfson, H.; Nussinov, R. , Physical Biology, Volume 3, Number 1, p.54-62, (2006)

De-novo tubular nanostructure design based on self-assembly of beta-helical protein motifs, Haspel, N.; Zanuy, D.; Aleman, C.; Wolfson, H.; Nussinov, R. , Structure, Volume 14, p.1137-1148, (2006)

Exploiting Panoramic Vision for Angle-Based Robot Navigation, Bekris, K. E.; Argyros, A. A.; Kavraki, L. E. , Lecture Notes in Computer Science, Vol. 33, p.229-251, (2006)

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

Quantitative Analysis of Nearest Neighbors Search in High-Dimensional Sampling-based Motion Planning, Plaku, E.; Kavraki, L. E. , Workshop on Algorithmic Foundations of Robotics (WAFR), New York, NY, (2006)

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

2005

Motion Planning in the Presence of Drift, Underactuation and Discrete System Changes, Ladd, A. M.; Kavraki, L. E. , Robotics: Science and Systems I, June, Boston, MA, p.233-241, (2005)

Principles of Robot Motion: Theory, Algorithms, and Implementation, Choset, H.; Burgard, W.; Hutchinson, S.; Kantor, G.; Kavraki, L. E.; Lynch, K.; Thrun, S. , June, (2005)

Robotics-Based Location Sensing using Wireless Ethernet (Invited), Ladd, A. M.; Bekris, K. E.; Rudys, A.; Marceau, G.; Kavraki, L. E.; Wallach, D. S. , Wireless Networks (The Journal of Mobile Communication, Computation and Information), January, Volume 11, Number 1-2, p.189-204, (2005)

Distributed Sampling-Based Roadmap of Trees for Large-Scale Motion Planning, Plaku, E.; Kavraki, L. E. , IEEE International Conference on Robotics and Automation, April, Barcelona, Spain, p.3879-3884, (2005)

Path Planning for Variable Resolution Minimal-Energy Curves of Constant Length, Moll, M.; Kavraki, L. E. , Proc. 2005 IEEE Intl. Conf. on Robotics and Automation, April, Barcelona, Spain, p.2143-2147, (2005)