1. "Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy," by Luay Nakhleh, Craig R. Linder, Bernard M.E. Moret, Jerry Sun, Anneke Padolina, Anna Tholse, Ruth Timme, and Tandy Warnow. This paper develops a formal model of phylogenetic networks, motivated by hybrid speciation and lateral gene transfer. It provides efficient algorithms for problems defined on the model, and perhaps most important, it establishes that an efficient method for comparing the topologies of phylogenetic networks produces a metric score. That result will facilitate the careful comparison of phylogenetic networks and the methods that construct and estimate them.
2. "Biclustering Algorithms for Biological Data Analysis: A Survey," by Sara Madeira and Arlindo L. Oliveira. This paper surveys algorithms and applications for biclustering of biological data. Biclustering algorithms are increasingly used in bioinformatics and computational biology to reveal important correlations and possible causal relations. The most notable example is in analyzing gene expression data from microarray experiments. This impressive, comprehensive survey partitions the methods according to the type of biclusters they seek, and by the algorithmic ideas that underly them. It will be very helpful to users and researchers in understanding the issues and the recent progress in the area of biclustering algorithms.
3. "Sequencing-by-Hybridization Revisited: The Analog-Spectrum Proposal," by Franco Preparata. This paper revisits the question of the practicality of DNA sequencing by hybridization. It argues that the digital-spectrum model, which has been the basis for for past work on SBH, should be replaced by an analog-spectrum model that more closely reflects biochemical reality. That change leads to the conclusion that SBH could be a practical way to sequence DNA. As stated in the abstract, "the theoretical proposal presented in this paper should be a convincing stimulus for the needed biotechnological work."
4. "Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach," by Matthias Höchsmann, Björn Voss, and Robert Giegerich. This paper presents a method to align multiple RNA secondary structures without the need for sequence similarity. This not only provides a useful way to compare many RNA molecules, but also develops a robust data structure for holding multiple RNA structure information.
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