Showing papers by "Boris Mirkin published in 2006"
National Institutes of Health1, Birkbeck, University of London2, United States Department of Energy3, North Carolina State University4, United States Department of Agriculture5, Utah State University6, University of Nebraska–Lincoln7, University of Minnesota8, University of Wisconsin-Madison9, University of California, San Diego10, University of California, Davis11, University of Idaho12
TL;DR: Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
Abstract: Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
1,314 citations
TL;DR: The results show that the character level representation of emails and classes facilitated by the suffix tree can significantly improve classification accuracy when compared with the currently popular methods, such as naive Bayes.
Abstract: We present an approach to email filtering based on the suffix tree data structure. A method for the scoring of emails using the suffix tree is developed and a number of scoring and score normalisation functions are tested. Our results show that the character level representation of emails and classes facilitated by the suffix tree can significantly improve classification accuracy when compared with the currently popular methods, such as naive Bayes. We believe the method can be extended to the classification of documents in other domains.
48 citations
TL;DR: Methods for imputation of missing data in the so-called least-squares approximation approach, a non-parametric computationally efficient multidimensional technique, are experimentally compared and it appears that NN-based versions almost always outperform their global counterparts.
35 citations
01 Dec 2006
TL;DR: A Lyapunov-Krasovskii type functional with "virtual" adaptation gain is introduced to design the adaptation algorithms and to prove stability in a class of linear dynamic systems with state delay.
Abstract: In this paper, we develop a simple adaptive control scheme for a class of linear dynamic systems with state delay which is robust with respect to an unknown plant delay and to an external disturbance with unknown bounds. A Lyapunov-Krasovskii type functional with "virtual" adaptation gain is introduced to design the adaptation algorithms and to prove stability.
5 citations
01 Sep 2006
TL;DR: This work investigates the automatic aggregation of motif-defined homologous protein families for further reconstruction of their evolutionary histories and proposes a method that utilises only parameters that can be adjusted by using the data.
Abstract: Protein families can be used to reconstruct evolutionary histories of organisms. The accuracy of protein assignment to such families is critical for the success of such studies. Here we investigate the automatic aggregation of motif-defined homologous protein families for further reconstruction of their evolutionary histories. We propose a method that utilises only parameters that can be adjusted by using the data. The building blocks of the method include: (a) a majority rule for combining protein homologous neighbourhood lists into that for a family, and (b) a robust clustering procedure whose only parameter, the similarity shift, can be estimated from information on proteins with known function. The method is applied to a herpesvirus protein dataset leading to insights into the composition of ancestors of herpesvirus superfamilies. Comparison of the computational reconstructions with more comprehensive analyses also show how alignment-based between-protein similarity scoring can be improved by using data on gene arrangements.
4 citations