Advisor: Jean-Claude Latombe
Computer Science Department
Gates Building, Rm 114
Stanford, CA 94305-9010
Office: (650) 725-6055
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 .
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
I. Lotan and F. Schwarzer. . J. of Computational Biology., 11(2-3):299–317, 2004.
Automated protein model completion: an inverse kinematics
H. van den Bedem, I. Lotan, J.-C Latombe, and A. M. Deacon. . Acta Cryst. D, 2004. Submitted.
Computing Protein Structures from Electron
Density Maps: The Missing Loop
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]
Algorithms exploiting the
chain structure of proteins
Stanford University, Computer Science Dept., Aug. 2004 [Oral defense Powerpoint slides]
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
Efficient Monte Carlo simulation of proteins