PhD candidate
Advisor: Jean-Claude Latombe
Computer Science Department
Gates Building, Rm 114
Stanford University
Stanford, CA 94305-9010
Email: itayl@cs.stanford.edu
Office: (650) 725-6055
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Itay Lotan PhD candidate Advisor: Jean-Claude Latombe Computer Science Department Gates Building, Rm 114 Stanford University Stanford, CA 94305-9010 Email: itayl@cs.stanford.edu Office: (650) 725-6055 |
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| Reasearch |
My research lies at the intersection of robotics and computational geometry with computational structural biology and protein crystallography. I investigate various computational methods to sample protein conformations, simulate pathways, find structural similarities, and compute structures from electron density maps. The methods I develop take advantage of the fact that proteins are long kinematic chains, by using efficient techniques from the field of robotics .
| Publications |
Journal Articles
Algorithm and Data Structures for
Efficient Energy Maintenance during Monte Carlo Simulation of Proteins
I. Lotan, F. Schwarzer, D. Halperin and J.-C
Latombe. J. of Computational Biology. To appear.
Approximation of Protein Structure for Fast
Similarity Measures
I. Lotan and F. Schwarzer. . J. of Computational
Biology., 11(2-3):299–317, 2004.
Automated protein model completion: an inverse kinematics
approach
H. van den Bedem, I. Lotan, J.-C Latombe, and A. M.
Deacon. . Acta Cryst. D, 2004. Submitted.
Conference Articles
Computing Protein Structures from Electron
Density Maps: The Missing Loop
Problem.
I. Lotan, H. van den Bedem, A.M. Deacon and
J.-C Latombe. Submitted to 6th Workshop on Algorithmic
Foundations of Robotics (WAFR `04)
[Powerpoint slides]
Efficient Energy Computation for
Monte-Carlo Simulation of Proteins
I. Lotan, F. Schwarzer and J.-C Latombe, ,
Workshop on Algorithms for Bioinformatics (WABI `03), 2003
[Powerpoint Slides]
Approximation of Protein Structure for
Fast Similarity Measures
F. Schwarzer and I. Lotan. . Proc. of
Conference on Research in Computational Molecular Biology (RECOMB `03), 2003
pp 267-276
[Powerpoint Slides]
Efficient Maintenace and Self-Collision
Testing for Kinematic Chains.
I. Lotan, F. Schwarzer, D. Halperin and J.-C
Latombe. Proc. Symposium on Computational Geometry (SoCG `02), 2002 pp.
43-52
[Powerpoint Slides]
Skiplist-Based Concurrent Priority Queues.
I. Lotan and N. Shavit. International
Parallel and Distributed Processing Symposium (IPDPS `00). 2000, pp.
263-268 [Powerpoint Slides]
Ph.D. Thesis
Algorithms exploiting the
chain structure of proteins
Stanford University, Computer Science Dept., Aug. 2004
[Oral
defense Powerpoint slides]
| Teaching |
I have been a Teaching Assistant for the following classes:
Fall 2000: CS205 Mathematical Methods for Computer Vision, Robotics, and Graphics
Spring 2002: CS326A Motion Planning
spring 2004: CS273 Algorithms for Structure
and Motion in Biology
| Links |
| Software |
Efficient Monte Carlo simulation of proteins