Scribe: S. Oak

Today's Talks

Nick Allen: Shortest common superstring
 
    References:
          Avrim Blum, Tao Jiang, Ming Li, John Tromp, and Mihalis Yannakakis
          Linear Approximation of Shortest Superstrings
           Journal of the ACM 41, July 1994, 630-647.

          S. Rao Kosaraju and Arthur L. Delcher
          Large-Scale Assembly of DNA Strings and Space-Efficient Construction of Suffix Trees
          ACM Symposium on Theory of Computing, 1995, 169-177.
 

Jason Zwolak: Modeling the cell cycle
 
    References:
          John J. Tyson, Bela Novak, Kathy Chen, and John Val
          Checkpoints in the cell cycle from a modeler's perspective
          Progress in Cell Cycle Research 1, 1995, 1-8.

          John J. Tyson, Bela Novak, Garrett M. Odell, Kathy Chen, and C. Dennis Thron
          Chemical kinetic theory: understanding cell-cycle regulation
          Trends in Biochemical Sciences 21, March 1996, 89-96.

Today's Topics

The Algorithm snapshot :

Make suffix tree

Eaxamine the suffix tree at depth d ( overlaps with atleast d matches)

If overlap is  ' w'  add the pair to priority queue.

Take K best strings.

Calculate the edit distance

Count the number and type of edits to have a consesus vote.

Modeling the cell cycle using differential equations.

Topics discussed

The Cell cycle consists of phases, viz, G1, S , G2, M.

The usage of Differential equations (Eulers method).

The neat & clear diagram for cell cycle is here

Today's Sources

• Setubal and Meidanis: Not Used
• Salzberg, Searls, and Kasif: Not Used.