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This is a collection of expository articles about various topics at the interface between enumerative combinatorics and stochastic processes. These articles expand on a course of lectures given at the École d’Été de Probabilités de St. Flour in July 2002. The articles are called ’chapters ’ and numbered according to the order of these chapters in a printed volume to appear in Springer Lecture Notes in Mathematics. Each chapter is fairly self-contained, so readers with adequate background can start reading any chapter, with occasional consultation of earlier chapters as necessary. Following this Chapter 0, there are 10 chapters, each divided into sections. Most sections conclude with some Exercises. Those for which I don’t know solutions are called Problems. Acknowledgments Much of the research reviewed here was done jointly with David Aldous. Much credit is due to him, especially for the big picture of continuum approximations to large combinatorial structures. Thanks also to my other collaborators in this work, especially Jean Bertoin, Michael Camarri, Steven

content or few deletions can be assumed. Since conserved duplicated regions are present in many Chloroplast genomes, the inference of inverted repeats is needed in ancestral genome reconstruction. We apply GRAPPA-IR to reconstruct ancestral chloroplast genomes containing duplicated genes. A test of GRAPPA

Abstract. We present a comparative genomics approach for inferring ancestral genome organization and evolutionary scenarios, based on present-day genomes represented as ordered gene sequences with duplicates. We develop our methodology for a model of evolution restricted to duplication and loss

PATHOPHYSIOLOGY OF LISTERIA INFECTION.............................................................................................586

-only claim, we suggest, is motivated by Chomsky’s recent approach to syntax, the Minimalist Program, which de-emphasizes the same aspects of language. The approach, however, is sufficiently problematic that it cannot be used to support claims about evolution. We contest other arguments from Chomsky

Similarity search is a very important operation in multimedia databases and other database applications involving complex objects, and involves finding objects in a data set S similar to a query object q, based on some similarity measure. In this article, we focus on methods for similarity search that make the general assumption that similarity is represented with a distance metric d. Existing methods for handling similarity search in this setting typically fall into one of two classes. The first directly indexes the objects based on distances (distance-based indexing), while the second is based on mapping to a vector space (mapping-based approach). The main part of this article is dedicated to a survey of distance-based indexing methods, but we also briefly outline how search occurs in mapping-based methods. We also present a general framework for performing search based on distances, and present algorithms for common types of queries that operate on an arbitrary “search hierarchy. ” These algorithms can be applied on each of the methods presented, provided a suitable search hierarchy is defined.

languages. The starting point is the observation that both premotor area F5 in monkeys and Broca's area in humans contain a "mirror system" active for both execution and observation of manual actions, and that F5 and Broca's area are homologous brain regions. This grounded the mirror

single locus, in a randomly mating population of constant size, for mutation models in which the distribution of the type of a mutant does not depend on the type of the progenitor allele; this includes any model with only two alleles. The new method is applied to ancestral inference for the two allele