Itay Lotan PhD candidate Advisor: JeanClaude Latombe Robotics Laboratory 

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(23):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 6^{th} Workshop on Algorithmic
Foundations of Robotics (WAFR `04)
[Powerpoint slides]
Efficient Energy Computation for
MonteCarlo 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 267276
[Powerpoint Slides]
Efficient Maintenace and SelfCollision
Testing for Kinematic Chains.
I. Lotan, F. Schwarzer, D. Halperin and J.C
Latombe. Proc. Symposium on Computational Geometry (SoCG `02), 2002 pp.
4352
[Powerpoint Slides]
SkiplistBased Concurrent Priority Queues.
I. Lotan and N. Shavit. International
Parallel and Distributed Processing Symposium (IPDPS `00). 2000, pp.
263268 [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 