Dan Gusfield

Dan Gusfield is Professor of Computer Science at the University of California, Davis. He is the coauthor of The Stable Marriage Problem: Structure and Algorithms (MIT Press) and author of Algorithms on Strings, Trees, and Sequences.

  • ReCombinatorics

    ReCombinatorics

    The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks

    Dan Gusfield

    Combinatorial structure and algorithms for deducing genetic recombination history, represented by ancestral recombination graphs and other networks, and their role in the emerging field of phylogenetic networks.

    In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems.

    Phylogenetic trees have been the traditional means to represent evolutionary history, but there is a growing realization that networks rather than trees are often needed, most notably for recent human history. This has led to the development of ARGs in population genetics and, more broadly, to phylogenetic networks. ReCombinatorics offers an in-depth, rigorous examination of current research on the combinatorial, graph-theoretic structure of ARGs and explicit phylogenetic networks, and algorithms to reconstruct or deduce information about those networks.

    ReCombinatorics, a groundbreaking contribution to the emerging field of phylogenetic networks, connects and unifies topics in population genetics and phylogenetics that have traditionally been discussed separately and considered to be unrelated. It covers the necessary combinatorial and algorithmic background material; the various biological phenomena; the mathematical, population genetic, and phylogenetic models that capture the essential elements of these phenomena; the combinatorial and algorithmic problems that derive from these models; the theoretical results that have been obtained; related software that has been developed; and some empirical testing of the software on simulated and real biological data.

    • Hardcover $64.00
  • The Stable Marriage Problem

    The Stable Marriage Problem

    Structure and Algorithms

    Dan Gusfield and Robert W. Irving

    This book probes the stable marriage problem and its variants as a rich source of problems and ideas that illustrate both the design and analysis of efficient algorithms. It covers the most recent structural and algorithmic work on stable matching problems, simplifies and unifies many earlier proofs, strengthens several earlier results, and presents new results and more efficient algorithms.The authors develop the structure of the set of stable matchings in the stable marriage problem in a more general and algebraic context than has been done previously; they discuss the problem's structure in terms of rings of sets, which allows many of the most useful features to be seen as features of a more general set of problems. The relationship between the structure of the stable marriage problem and the more general stable roommates problem is demonstrated, revealing many commonalities.The results the authors obtain provide an algorithmic response to the practical, and political, problems created by the asymmetry inherent in the Gale Shapley solutions, leading to alternative methods and better compromises than are provided by the Gale Shapley method. And, in contrast to Donald Knuth's earlier work which primarily focused on the application of mathematics to the analysis of algorithms, this book illustrates the productive and almost inseparable relationship between mathematical insight and the design of efficient algorithms.

    The Stable Marriage Problem is included in the Foundations of Computing Series, edited by Michael Garey and Albert Meyer.

    • Hardcover $45.00
    • Paperback $25.00