Models of DNA replication timing in interphase nuclei: an exercise in inferring process from state

Patterns of spots, produced by fluorescence in situ hybridization, can be used to infer the order and timing of replication of DNA sequences in S-phase nuclei, sampled randomly from asynchronous cell populations. We describe statistical models that provide estimates of replication timings and completion rates and of their standard errors. By applying the technique to experimental data from diploid cell lines, we show how it can be used to compare the replication timings either of different sequences on the same chromosome, or of the same sequence on a pair of homologous chromosomes.