Biblio

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Thesis
Stamati H.  2007.  Analysis of Molecular Motion using Non-Linear Dimensionality Reduction. Department of Computer Science.
Abstract      Preprint PDF
Dhanik A.  2010.  Computational Modeling of Structural Heterogeneity in Folded Proteins. PhD Thesis
Dhanik A.  2005.  Development of a Palpable Virtual Nylon Thread and Handling of Bifurcations. Masters Thesis
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
Moll M.  1995.  Head-corner Parsing Using Typed Feature Structures.
Abstract      Preprint PDF
Bekris KE.  2008.  Informed Planning and Safe Distributed Replanning under Physical Constraints. Department of Computer Science.
Abstract      Preprint PDF
Sucan IA.  2008.  Kinodynamic Motion Planning for High-dimensional Physical Systems. Department of Computer Science.
Preprint PDF
Teodoro ML.  2003.  Modeling Protein Flexibility Using Collective Modes of Motion: Applications to Drug Design. :255.
Abstract      Preprint PDF
Shehu A.  2008.  Molecules in Motion: Computing Structural Flexibility. Department of Computer Science.
Abstract      Preprint PDF
Ladd AM.  2006.  Motion Planning for Physical Simulation. Department of Computer Science.
Preprint PDF
Tsianos K.  2008.  Replanning: A Powerful Planning Strategy for Systems with Differential Constraints. Department of Computer Science.
Abstract      Preprint PDF
Moll M.  2002.  Shape Reconstruction Using Active Tactile Sensors.
Abstract      Preprint PDF
Şucan IA.  2011.  Task and Motion Planning for Mobile Manipulators.
Abstract      Preprint PDF
Grady DK.  2011.  Unsynchronized Distributed Motion Planning with Safety Guarantees under Second-Order Dynamics.
Abstract      Preprint PDF
Report
Ter Doest H, Moll M, Bos R, Van de Burgt S, Nijholt A.  1996.  Language Engineering in Dialogue Systems.
Abstract      Preprint PDF
Moll M.  1996.  Mapping Science: Methods and Tools for the Automatic Creation of Semantic Maps of Large Corpora.
Moll M, Schwarz D, Heath AP, Kavraki LE.  2004.  On Flexible Docking Using Expansive Search.
Abstract      Preprint PDF
Kavraki LE.  1995.  On the Number of Equilibrium Placements of Mass Distributions in Elliptic Potential Fields.
Preprint PDF
Op den Akker R, Ter Doest H, Moll M, Nijholt A.  1995.  Parsing in Dialogue Systems using Typed Feature Structures.
Abstract      Preprint PDF
Moll M, Erdmann MA.  2001.  Shape Reconstruction in a Planar Dynamic Environment.
Abstract      Preprint PDF
Journal Article
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.
     Publisher's web site     
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.
     Publisher's web site     
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     
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     
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     
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     
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     
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     
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     
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
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     
Finn PW, Kavraki LE.  1999.  Computational Approaches to Drug Design. Algorithmica. 25:347-371.
Preprint PDF
Heath AP, Kavraki LE.  2009.  Computational Challenges in Systems Biology. Computer Science Review. 3:1-17.
Abstract      Preprint PDF     Publisher's web site     
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     
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     
Yao P, Dhanik A, Marz N, Propper R, Kou C, Liu G, van den Bedem H, Latombe JC, Landsbergz IH, Altman RB.  2008.  Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 5:534-545.
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     
White RW, Richardson M, Bilenko M, Heath AP.  2008.  Enhancing web search by promoting multiple search engine use. SIGIR ’08: Proceedings of the 31st annual international ACM SIGIR conference on research and development in information retrieval. :43-50.
     Publisher's web site     
Plaku E, Kavraki L, Vardi M.  2012.  Falsification of LTL safety properties in hybrid systems. International Journal on Software Tools for Technology Transfer (STTT).
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     
Heath AP, Bennett GN, Kavraki LE.  2010.  Finding Metabolic Pathways Using Atom Tracking. Bioinformatics. 26:1548-1555.
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