Itay Lotan
PhD candidate
Advisor: Jean-Claude Latombe

Robotics Laboratory
Computer Science Department
Gates Building, Rm 114
Stanford University
Stanford, CA 94305-9010
Email: itayl@cs.stanford.edu
Office: (650) 725-6055

 
 
 

 

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):299317, 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

CV: [DOC][PDF]

 

Software

Efficient Monte Carlo simulation of proteins