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检索条件"丛书名=Advances in Bioinformatics and Computational Biology"

共 63 条记录，以下是21-30 订阅

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The distance between randomly constructed genomes

The distance between randomly constructed genomes

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Xu, Wei Univ Ottawa Dept Math & Stat Ottawa ON K1N 6N5 Canada

ISBN: (纸本)9781860947834

In this paper, we study the exact probability distribution of the number of cycles c in the breakpoint graph of two random genomes with n genes or markers and chi(1) and chi(2) linear chromosomes, respectively. The genomic distance d between the two genomes is d = n - c. In the limit we find that the expectation of d is n - 2(chi 1 chi 2)/2(chi 1)+2(chi 2)-1 - 1/2 ln n+min((chi 1),(chi 2))/chi 1+chi 2.

关键词： Probability distributions

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An effective promoter detection method using the adaboost algorithm

An effective promoter detection method using the adaboost al...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Xie, Xudong Wu, Shuanhu Lam, Kin-Man Yan, Hong City Univ Hong Kong Dept Elect Engn Hong Kong Hong Kong Peoples R China Tsinghua Univ Dept Elect Engn Beijing Peoples R China Yantai Univ Sch Comp Sci & Technol Yantai Peoples R China Hong Kong Polytech Univ Hong Kong Hong Kong Peoples R China Univ Sydney Sch Elect & Informat Engn Sydney NSW 2006 Australia

ISBN: (纸本)9781860947834

In this paper, an effective promoter detection algorithm, which is called PromoterExplorer, is proposed. In our approach, various features, i.e. local distribution of pentamers, positional CpG island features and digitized DNA sequence, are combined to build a high-dimensional input vector. A cascade AdaBoost based learning procedure is adopted to select the most "informative" or "discriminating" features to build a sequence of weak classifiers. A number of weak classifiers construct a strong classifier, which can achieve a better performance. In order to reduce the false positive, a cascade structure is used for detection. PromoterExplorer is tested based on large-scale DNA sequences from different databases, including EPD, Genbank and human chromosome 22. The proposed method consistently outperforms PromoterInspector and Dragon Promoter Finder.

关键词： DNA sequences

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A new strategy of geometrical biclustering for microarray data analysis*

A new strategy of geometrical biclustering for microarray da...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Zhao, Hongya Liew, Alan W. C. Yan, Hong City Univ Hong Kong Dept Elect & Engn Hong Kong Hong Kong Peoples R China City Univ Hong Kong Dept Comp Sci & Engn Hong Kong Hong Kong Peoples R China Univ Sydney Sch Elect & Informat Engn Sydney NSW 2006 Australia

ISBN: (纸本)9781860947834

In this paper, we present a new biclustering algorithm to provide the geometrical interpretation of similar microarray gene expression profiles. Different from standard clustering analyses, biclustering methodology can perform simultaneous classification on the row and column dimensions of a data matrix. The main object of the strategy is to reveal the submatrix, in which a subset of genes exhibits a consistent pattern over a subset of conditions. However, the search for such subsets is a computationally complex task. We propose a new algorithm, based on the Hough transform in the column-pair space to perform pattern identification. The algorithm is especially suitable for the biclustering analysis of large-scale microarray data. Our simulation studies show that the method is robust to noise and computationally efficient. Furthermore, we have applied it to a large database of gene expression profiles of multiple human organs and the resulting biclusters show clear biological meanings.

关键词： Hough transforms

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Semi-supervised pattern learning for extracting relations from bioscience texts

Semi-supervised pattern learning for extracting relations fr...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Ding, Shilin Huang, Minlie Zhu, Xiaoyan Tsinghua Univ Dept Comp Sci & Technol State Key Lab Intelligent Technol & Syst LITS Beijing 100084 Peoples R China

ISBN: (纸本)9781860947834

A variety of pattern-based methods have been exploited to extract biological relations from literatures. Many of them require significant domain-specific knowledge to build the patterns by hand, or a large amount of labeled data to learn the patterns automatically. In this paper, a semi-supervised model is presented to combine both unlabeled and labeled data for the pattern learning procedure. First, a large amount of unlabeled data is used to generate a raw pattern set. Then it is refined in the evaluating phase by incorporating the domain knowledge provided by a relatively small labeled data. Comparative results show that labeled data, when used in conjunction with the inexpensive unlabeled data, can considerably improve the learning accuracy.

关键词： Domain Knowledge

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Fitting protein chains to cubic lattice is NP-complete

Fitting protein chains to cubic lattice is NP-complete

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Manuch, Jan Gaur, Daya Ram Simon Fraser Univ Sch Comp Sci Burnaby BC V5A 1S6 Canada

ISBN: (纸本)9781860947834

It is known that folding a protein chain into the cubic lattice is an NP-complete problem. We consider a seemingly easier problem, given a 3D fold of a protein chain (coordinates of its C atoms), we want to find the closest lattice approximation of this fold. This problem has been studied under names such as "lattice approximation of a protein chain", "the protein chain fitting problem" and "building protein lattice models". We show that this problem is NP-complete for the cubic lattice with side 3.8 angstrom and the coordinate root mean-square deviation.

关键词： computational complexity

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Gene regulatory network inference via regression based topological refinement

Gene regulatory network inference via regression based topol...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Supper, Jochen Frohlich, Holger Zell, Andreas Ctr Bioinformat Tubingen ZBIT Sand 1 D-72076 Tubingen Germany

ISBN: (纸本)9781860947834

Inferring the structure of gene regulatory networks from gene expression data has attracted a growing interest during the last years. Several machine learning related methods, such as Bayesian networks, have been proposed to deal with this challenging problem. However, in many cases, network reconstructions purely based on gene expression data not lead to satisfactory results when comparing the obtained topology against a validation network. Therefore, in this paper we propose an "inverse" approach: Starting from a priori specified network topologies, we identify those parts of the network which are relevant for the gene expression data at hand. For this purpose, we employ linear ridge regression to predict the expression level of a given gene from its relevant regulators with high reliability. Calculated statistical significances of the resulting network topologies reveal that slight modifications of the pruned regulatory network enable an additional substantial improvement.

关键词： Network topology

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Metagenome analysis using megan

Metagenome analysis using megan

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Huson, Daniel H. Auch, Alexander F. Qi, Ji Schuster, Stephan C. Tubingen Univ Ctr Bioinformat Sand 14 D-72076 Tubingen Germany PennState Univ Ctr Comparat Genom Ctr Infect Dis Dynam Wartik Labs 310 University Pk PA USA

ISBN: (纸本)9781860947834

In metagenomics, the goal is to analyze the genomic content of a sample of organisms collected from a common habitat. One approach is to apply large-scale random shotgun sequencing techniques to obtain a collection of DNA reads from the sample. This data is then compared against databases of known sequences such as NCBI-nr or NCBI-nt, in an attempt to identify the taxonomical content of the sample. We introduce a new software called MEGAN (Meta Genome ANalyzer) that generates species profiles from such sequencing data by assigning reads to taxa of the NCBI taxonomy using a straight-forward assignment algorithm. The approach is illustrated by application to a number of datasets obtained using both sequencing-by-synthesis and Sanger sequencing technology, including metagenomic data from a mammoth bone, a portion of the Sargasso sea data set, and several complete microbial test genomes used for validation proposes.

关键词： Genome

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Two plus two does not equal three: Statistical tests for multiple genome comparison

Two plus two does not equal three: Statistical tests for mul...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Raghupathy, Narayanan Hoberman, Rose Durand, Dannie Carnegie Mellon Univ Dept Sci Biol Pittsburgh PA 15213 USA Carnegie Mellon Univ Dept Comp Sci Pittsburgh PA 15213 USA

ISBN: (纸本)9781860947834

Gene clusters that span three or more chromosomal regions are of increasing importance, yet statistical tests to validate such clusters are in their infancy. Current approaches either conduct several pairwise comparisons, or consider only the number of genes that occur in all the regions. In this paper, we provide statistical tests for clusters spanning exactly three regions based on genome models of typical comparative genomics problems, including analysis of conserved linkage within multiple species and identification of large-scale duplications. Our tests are the first to combine evidence from genes shared among all three regions and genes shared between pairs of regions. We show that our tests of clusters spanning three regions are more sensitive than existing approaches and can thus be used to identify more diverged homologous regions.

关键词： Statistical tests

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A global maximum likelihood super-quartet phylogeny method

A global maximum likelihood super-quartet phylogeny method

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Wang, P. Zhou, B. B. Taraeneh, M. Chu, D. Wang, C. Zomaya, A. Y. Brent, R. P. Univ Sydney Sch Informat Technol Sydney NSW 2006 Australia Australian Natl Univ Math Sci Inst Canberra ACT 0200 Australia

ISBN: (纸本)9781860947834

Extending the idea of our previous algorithm [17, 18] we developed a new sequential quartet-based phylogenetic tree construction method. This new algorithm reconstructs the phylogenetic tree iteratively by examining at each merge step every possible super-quartet which is formed by four subtrees instead of simple quartet in our previous algorithm. Because our new algorithm evaluates super-quartet trees, each of which may consist of more than four molecular sequences, it can effectively alleviate a traditional, but important problem of quartet errors encountered in the quartet-based methods. Experiment results show that our newly proposed algorithm is capable of achieving very high accuracy and solid consistency in reconstructing the phylogenetic trees on different sets of synthetic DNA data under various evolution circumstances.

关键词： Maximum likelihood

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Computing the quartet distance between evolutionary trees of bounded degree.

Computing the quartet distance between evolutionary trees of...

引用

5th Asia-Pacific bioinformatics Conference (APBC2007)

作者： Stissing, M. Pedersen, C. N. S. Mailund, T. Brodal, G. S. Fagerberg, R. Univ Aarhus Bioinformat Res Ctr Aarhus Denmark Univ Aarhus Dept Comp Sci Aarhus Denmark Univ Southern Denmark Dept Math & Comp Sci Odense Denmark

ISBN: (纸本)9781860947834

We present an algorithm for calculating the quartet distance between two evolutionary trees of bounded degree on a common set of n species. The previous best algorithm has running time O(d(2)n(2)) when considering trees, where no node is of more than degree d. The algorithm developed herein has running time O(d(9) n log n)) which makes it the first algorithm for computing the quartet distance between non-binary trees which has a sub-quadratic worst case running time.

关键词： Binary trees

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