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Comparative genomics : RECOMB 2006 International Workshop, RECOMB-CG 2006, Montreal, Canada, September 24-26, 2006, Proceedings (Lecture Notes in Bioinformatics 4205)
Bourque G., Mabrouk N., Springer-Verlag New York, Inc., Secaucus, NJ, 2006. 231 pp. Type: Book (9783540445296)
Date Reviewed: May 2 2007

Comparative genomics is an exciting new field of bioinformatics dealing with problems of vital importance for many areas in biology. The annual RECOMB Satellite Workshop on Comparative Genomics is an important forum covering all aspects of this field. This volume contains the 17 fully refereed papers presented at the fourth meeting, held in Montreal in September 2006.

The paper by Behzadi and Vingron focuses on multidomain proteins, and proposes a general approach to analyzing their composition. The paper by Song and others studies the vital issue of homology identification, and offers several new solutions that are fully evaluated using known benchmarks. A comprehensive model for genome evolution is the subject of the paper by Wojtowicz and Tiuryn; they conclude that the resulting distribution is a linear combination of logarithmic distributions. The paper by Adam and others and the one by Angibaud and others present very interesting genomic analysis methods based on common intervals. The important contribution by Gaul and Blanchette deals with ordering partially assembled genomes, offering a wealth of theoretical results and software that can help the research community further the state of the art. The paper by Bertrand and others presents methods for inferring an evolutionary history of a gene family, accounting for both tandem duplications and inversions. The paper by Parida is well written and offers important results on computational methods for the problem of reconstructing phylogeny trees. The paper by Coulombe-Huntington and Majewski deals with genome-wide analysis of “intron loss and gain events,” working on four mammalian species (human, mouse, rat, and dog): this is the largest-scale analysis for intron dynamics and is fully presented in the book. The work by Diallo and others focuses on the important Indel maximum likelihood problem; the proposed new solution is fully analyzed and compared against existing methods. The papers by Evans and others and Banerjee and Califano present methods to assess compensatory mutations within “transcription factor binding sites.” Full discussions are presented regarding both the related fundamental phenomena, as well as the performance of the proposed solutions. The concluding contribution by Than and others is highly interesting, as it focuses on “horizontal gene transfer,” a process that has recently led to disagreements between researchers.

Unavoidably, many papers in this volume discuss the important computer science subproblems that underlie many applications in genomic studies. Thus, the paper by Blin and others deals with inferring positional homologs, and focuses on a computational analysis of the corresponding algorithms. The paper by Xu and others analyzes related fundamental problems in graph theory. The paper by Ozery-Flato and Shamir focuses on the major subproblem of finding a shortest sequence of genome rearrangements that sorts one genome into another, while the contribution by Blin and others details analyses of theoretical results and algorithms related to this specific problem: “Given a reference genome characterized by a total order O and a related genome characterized by a partial order P, find a total order coherent with P minimizing the breakpoint distance with respect to O.”

It is obvious that all of the contributions in this volume are highly important papers bound to strongly influence current research in comparative genomics and in many related subjects. Thus, I consider this book essential for libraries aiming to support research in any field of bioinformatics.

Reviewer:  Nickolas S. Sapidis Review #: CR134216 (0804-0349)
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