Discrete Mathematical Biology Working Seminar

Introduction

  • M.S. Waterman and T.F. Smith. RNA Secondary Structure: A Complete Mathematical Analysis. Math Biosci, 42(3-4): 257-266, 1987.
  • R. Nussinov, G. Pieczenik, J.R. Griggs and D.J. Kleitman. Algorithms for Loop Matchings. SIAM J Appl Math, 35(1): 68-82, 1978.

Sampling


Metrics


Kinetics


Combinatorics


Suboptimal structures

  • R. Giegerich, B. Voss, and M. Rehmsmeier. Abstract shapes of RNA. Nucleic Acids Res, 32(16): 4843-4851, 2004.
  • B. Voss, R. Giegerich, and M. Rehmsmeier. Complete probabilistic analysis of RNA shapes. BMC Biology, 4(5): Epub, 2006.
  • S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49(2): 145-65, 1999.

  • SHAPE


    Stochastic models