Biblio

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Gipson B, Zeng XY, Stahlberg H, Wouts R.  2007.  2dx – User Friendly Image Processing ( and Merging ) for 2D Crystals. Microscopy and Microanalysis. 13:160–161.
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Gipson B, Zeng X, Stahlberg H.  2008.  2dx-Automated 3D structure reconstruction from 2D crystal data. Microscopy and Microanalysis. :1290-1291.
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Gipson B, Zeng X, Stahlberg H.  2007.  2dx_merge : Data management and merging for 2D crystal images. Journal of Structural Biology. 160:375–384.
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Gipson B, Zeng X, Zhang ZY, Stahlberg H.  2007.  2dx–user-friendly image processing for 2D crystals.. Journal of structural biology. 157:64–72.
Abstract           Publisher's web site     
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Schenk AD, Casta D, Gipson B, Arheit M, Zeng X, Stahlberg H.  2010.  3D Reconstruction from 2D Crystal Image and Diffraction Data. Cryo-EM, Part B: 3-D Reconstruction. 482:101-129.
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Sucan IA, Kavraki LE.  2012.  Accounting for Uncertainty in Simultaneous Task and Motion Planning Using Task Motion Multigraphs. IEEE International Conference on Robotics and Automation. :4822-4828.
Abstract      Preprint PDF
Yao H, Kristensen DM, Mihalek I, Sowa M, Shaw C, Kimmel M, Kavraki LE, Lichtarge O.  2003.  An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures. Journal of Molecular Biology. 326:255-261.
Abstract           Publisher's web site     
Heath AP, Bennett GN, Kavraki LE.  2011.  An Algorithm for Efficient Identification of Branched Metabolic Pathways. Journal of Computational Biology. 18:1575-1597.
Abstract      Preprint PDF     Publisher's web site     
Agrawal PK, Guibas LJ, Edelsbrunner H, Erickson J, Isard M, Har-Peled S, Hershberger J, Jensen C, Kavraki LE, Koehl P et al..  2002.  Algorithmic Issues in Modeling Motion. ACM Computing Surveys. 34:550-572.
Abstract           Publisher's web site     
Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE.  2005.  Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. Pacific Symposium on Biocomputing.
Kavraki LE.  1999.  Algorithms in Robotics: The Motion Planning Perspective. Frontiers of Engineering Publication. :90-93.
Moll M, Goldberg KY, Erdmann MA, Fearing RS.  2002.  Aligning Parts for Micro Assemblies. Assembly Automation. 22:46--54.
Abstract      Preprint PDF     Publisher's web site     
Stamati H.  2007.  Analysis of Molecular Motion using Non-Linear Dimensionality Reduction. Department of Computer Science.
Abstract      Preprint PDF
Kavraki LE, Kolountzakis MN, Latombe J-C.  1998.  Analysis of Probabilistic Roadmaps for Path Planning. IEEE Transactions on Robotics and Automation. 14(1):166-171.
Abstract      Preprint PDF     Publisher's web site     
Kavraki LE, Kolountzakis MN, Latombe J-C.  1996.  Analysis of Probabilistic Roadmaps for Path Planning. Proceeedings of The 1996 International Conference on Robotics and Automation (ICRA 1996). :3020-3026.
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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     
Bekris KE, Argyros AA, Kavraki LE.  2004.  Angle-Based Methods for Mobile Robot Navigation: Reaching the Entire Plane. Proceedings of The IEEE International Conference on Robotics and Automation (ICRA). :2373--2378.
Abstract      Preprint PDF     Publisher's web site     
Luna R, Şucan IA, Moll M, Kavraki LE.  2013.  Anytime Solution Optimization for Sampling-Based Motion Planning. IEEE International Conference on Robotics and Automation.
Abstract      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     
Zhang M, Kavraki LE.  2002.  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). :2182-2183.
Abstract           Publisher's web site     
Grady DK, Bekris KE, Kavraki LE.  2011.  Asynchronous Distributed Motion Planning with Safety Guarantees under Second-Order Dynamics. Algorithmic Foundations of Robotics IX. 68:53-70.
Abstract      Preprint PDF     Publisher's web site     
Dhanik A, McMurray JS, Kavraki LE.  2012.  AUTODOCK-based Incremental Docking Protocol to Improve Docking of Large Ligands. IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). :48-55.
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Grady DK, Moll M, Kavraki L.  2013.  Automated Model Approximation for Robotic Navigation with POMDPs. IEEE International Conference on Robotics and Automation.
Abstract      Preprint PDF
Zeng X, Gipson B, Zheng ZY, Renault L, Stahlberg H.  2007.  Automatic lattice determination for two-dimensional crystal images.. Journal of structural biology. 160:353–61.
Abstract           Publisher's web site     
Gipson B, Masiel D, Browning N, Spence J, Mitsuoka K, Stahlberg H.  2011.  Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals. Physical Review E. 84(1)
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Dhanik A, McMurray JS, Kavraki LE.  2012.  Binding Modes of Peptidomimetics Designed to Inhibit STAT3. PLoS ONE. 7(12):e51603.
Abstract      Preprint PDF     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     
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Moll M, Miikkulainen R, Abbey J.  1994.  The Capacity of Convergence-Zone Episodic Memory. Proc. 12th Natl. Conf. on Artificial Intelligence. :68--73.
Abstract      Preprint PDF     Publisher's web site     
Hsu D, Kavraki LE, Latombe J-C, Motwani R, Rolim J.  1999.  Capturing the Connectivity of High-Dimensional Geometric Spaces by Parallelizable Random Sampling Techniques. Parallel and Distributed Processing. 1388:330-340.
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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, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.  2006.  Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction. Systems Bioinformatics Conference (CSB). 4:311-323.
Abstract           Publisher's web site     
Sucan IA, Kalakrishnan M, Chitta S.  2010.  Combining Planning Techniques for Manipulation Using Realtime Perception. IEEE International Conference on Robotics and Automation. :2895-2901.
Preprint PDF     Publisher's web site     
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
Kavraki LE.  1995.  Computation of Configuration Space Obstacles Using the Fast Fourier Transform. IEEE Transactions on Robotics and Automation. 11:408-413.
Abstract      Preprint PDF     Publisher's web site     
Kavraki LE.  1993.  Computation of configuration-space obstacles using the fast Fourier transform. IEEE International Conference on Robotics and Automation. 3:255-261.
Abstract           Publisher's web site     
Finn PW, Kavraki LE.  1999.  Computational Approaches to Drug Design. Algorithmica. 25:347-371.
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Heath AP, Kavraki LE.  2009.  Computational Challenges in Systems Biology. Computer Science Review. 3:1-17.
Abstract      Preprint PDF     Publisher's web site     
Dhanik A.  2010.  Computational Modeling of Structural Heterogeneity in Folded Proteins. PhD Thesis
Gipson B, Hsu D, Kavraki LE, Latombe J-C.  2012.  Computational Models of Proteins Kinematics and Dynamics: Beyond Simulation. Annual Reviews of Analytical Chemistry. 5:273-291.
Abstract      Preprint PDF     Publisher's web site     
Teodoro ML, Kavraki LE.  2003.  Conformational Flexibility Models for the Receptor in Structure Based Drug Design. Current Pharmaceutical Design. 9:1419-1431.
Abstract      Preprint PDF     Publisher's web site     
Moll M, Miikkulainen R.  1997.  Convergence-Zone Episodic Memory: Analysis and Simulations. Neural Networks. 10:1017--1036.
Abstract      Preprint PDF     Publisher's web site     
Yin J, Dhanik A, Hsu D, Wang Y.  2004.  The Creation of a Music-driven Digital Violinist. ACM international conference on Multimedia. :476-479.
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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
Brock O, Kavraki LE.  2001.  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). :1469-1475.
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Anshelevich E, Owens S, Lamiraux F, Kavraki LE.  2000.  Deformable Volumes in Path Planning Applications. Proceedings of The IEEE International Conference on Robotics and Automation (ICRA). 3:2290-2295.
Abstract      Preprint PDF     Publisher's web site     
Dhanik A.  2005.  Development of a Palpable Virtual Nylon Thread and Handling of Bifurcations. Masters Thesis
Teodoro ML, Jr. GPN, Kavraki LE.  2002.  A Dimensionality Reduction Approach to Modeling Protein Flexibility. Proceedings of the 2002 ACM International Conference on Research in Computational Biology (RECOMB 2002). :299-308.
Abstract           Publisher's web site     
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     
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     
Moll M, Will P, Krivokon M, Shen W-M.  2006.  Distributed Control of the Center of Mass of a Modular Robot. Proc. 2006 IEEE/RSJ Intl. Conf. on Intelligent Robots and Systems. :4710--4715.
Abstract      Preprint PDF     Publisher's web site