Publications resulting from book chapters

Example 1.16 has been studied in detail by Fienberg, Hersh, Rinaldo and Zhou in a forthcoming book chapter.
The methods from chapters 5,6 and 7 were extended and resulted in a paper on Parametric alignment of Drosophila genomes in PloS Computational Biology.
Conjectures 8.1 and 8.3 have been solved by Cynthia Vinzant. A paper is forthcoming.
Chapter 9 was extended and a publication on Bounds on the number of inference functions of a graphical model will appear in Statistica Sinica.
A complete version of the results in Chapter 10 were published in the paper Viterbi Sequences and Polytopes, published in the Journal of Symbolic Computation.
The results in Chapter 14 were developed and published in the paper A Mutagenic Tree Hidden Markov Model for Longitudinal Clonal HIV Sequence Data in the journal Biostatistics.
The results on generalized neighbor joining from Chapter 18 were extended and published in the paper Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates in the journal Molecular Biology and Evolution.
The ideas in Chapter 19 led to the paper Performance of a new invariants method on homogeneous and non-homogeneous quartet trees in the journal Molecular Biology and Evolution.
Chapter 21 inspired the paper Phylogenetic Profiling of Insertions and Deletions that appeared in RECOMB 2006.