title: Computational methods to study kinetics of DNA replication.
abstract: New technologies such as DNA combing have led to the availability of large quantities of data that describe the state of DNA while undergoing replication in S phase. In this chapter, we describe methods used to extract various parameters of replication--fork velocity, origin initiation rate, fork density, numbers of potential and utilized origins--from such data. We first present a version of the technique that applies to "ideal" data. We then show how to deal with, a number of real-world complications, such as the asynchrony of starting times of a population of cells, the finite length of fragments used in the analysis, and the finite amount of DNA in a chromosome.
authors: Department of Physics, Simon Fraser University, Burnaby, BC, Canada.
authors: Scott Cheng-Hsin
authors: SC
authors: Yang
authors: Michel G
authors: MG
authors: Gauthier
authors: John
authors: J
authors: Bechhoefer
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004261:DNA Replication; D006801:Humans; D007700:Kinetics; D008856:Microscopy, Fluorescence; D008954:Models, Biological; D016196:S Phase