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2008
Impact of Workspace Decompositions on Discrete Search Leading Continuous Exploration (DSLX) Motion Planning, Plaku E, Kavraki LE, Vardi MY , 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, Moll M, Kavraki LE , The Seventh Annual International Conference on Computational Systems Bioinformatics (CSB2008), (2008)

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids, Kristensen DM, Ward RM, Lisewski AM, Edrin S, Chen BY, Fofanov VY, Kimmel M, Lichtarge O , BMC Bioinformatics, Volume 9, Issue 17, (2008)

Robot Algorithms, Tsianos K, Halperin D, Kavraki L, Latombe J, Attalah M , Algorithms and Theory of Computation Handbook, (2008)

Special Issue on Self-Reconfiguring Modular Robots (Guest Editorial), Moll M, Rus D , 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 LE, 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 KE, Tsianos KI, Kavraki LE , First International Conference on Robot Communication and Coordination (ROBOCOMM 07), Oct. 15-17, Athens, Greece, (2007)

A Decentralized Planner that Guarantees the Safety of Communicating Vehicles with Complex Dynamics that Replan Online, Bekris KE, Tsianos KI, Kavraki LE , 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 HH, Tsai CJ, Wolfson HJ, 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 LE, Vardi MY , 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 BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE , 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, Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kimmel M, Lichtarge O, Kavraki LE , Computational Systems Bioinformatics Conference (CSB2007), p.343-355, (2007)

Distributed Computation of the knn Graph for Large High-Dimensional Point Sets, Plaku E, Kavraki LE , 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 LE, Vardi MY , 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 LE , Proteins: Structure, Function, and Bioinformatics, Volume 67, Number 4, p.897--907, (2007)

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

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

Hybrid Systems: From Verification to Falsification, Plaku E, Kavraki LE, Vardi MY, and Hermanns DWH , International Conference on Computer Aided Verification (CAV), Volume 4590, Berlin, Germany, p.468--481, (2007)

Modular Self-reconfigurable Robot Systems: Challenges and Opportunities for the Future, Yim M, Shen W-M, Salemi B, Rus D, Moll M, Lipson H, Klavins E , IEEE Robotics & Automation Magazine, March, Volume 14, Number 1, (2007)

Motion Planning, Kavraki LE, LaValle S, and Siciliano KOB , 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 CJ, Aleman C, Nussinov R , Biochemistry, Volume 46, Number 5, p.1205-1218, (2007)

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

On the Characterization of Protein Native State Ensembles, Shehu A, Kavraki LE, 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 KE, Kavraki LE , IEEE International Conference on Robotics and Automation (ICRA), Rome, Italy, p.3711-3716, (2007)

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

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

Roadmap Methods for Protein Folding, Moll M, Schwarz D, Kavraki LE, and Bystroff ZMC , Protein Structure Prediction: Methods and Protocols, Oct., (2007)

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

Sampling-based robot motion planning: Towards realistic applications, Tsianos KI, Sucan IA, Kavraki LE , Computer Science Review, August, Volume 1, Issue 1, p.2--11, (2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs, Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE , Journal of Computational Biology, Volume 14, Number 6, p.791-816, (2007)

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)

Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction, Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE , Systems Bioinformatics Conference (CSB), August, Volume 4, Stanford, CA, p.311-323, (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 AI, 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)

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

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

Exploiting Panoramic Vision for Angle-Based Robot Navigation, Bekris KE, Argyros AA, Kavraki LE, and Kleete DKR , Lecture Notes in Computer Science, Vol. 33, p.229-251, (2006)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction, Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE , Research in Computational Biology: 10th Annual International Conference (RECOMB), April, Venice, Italy, (2006)

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

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

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

Quantitative Analysis of Nearest Neighbors Search in High-Dimensional Sampling-based Motion Planning, Plaku E, Kavraki LE , 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 DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O , Protein Science, Volume 15, Number 6, p.1530-1536, (2006)

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

2005
A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: A single beta-sheet model with a small hydrohpobic core, Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R , Journal of Molecular Biology, Volume 345, Number 5, p.1213-1227, (2005)

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs, Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE , Pacific Symposium on Biocomputing, Hawaii, USA, (2005)

Computational approaches and tools for establishing structural models for short amyloid-forming peptides., Haspel N, Zanuy D, Tsai HH, Ma B, Wolfson H, Nussinov R, Sipe JD , Amyloid Proteins, Volume 1, p.301-318, (2005)

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

Fast Tree-Based Exploration of State Space for Robots with Dynamics, Ladd AM, Kavraki LE, and and van der Erdmann M. and Hsu ODMAF , Algorithmic Foundations of Robotics VI, p.297-312, (2005)