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检索条件"任意字段=Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004"

共 371 条记录，以下是51-60 订阅

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A knowledge base for computational pathway reconstruction

A knowledge base for computational pathway reconstruction

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Peng Wang Zhengchang Su Phuongan Dam Ying Xu Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology University of Georgia USA

ISBN: (纸本)0769521940

The Synechococcus WH8102 knowledge base (http://***/WH8J02) is a Web based relational database developed to facilitate computational effort to reconstruct regulatory pathways and serve as a gateway for biologist to access the data. It is the repertoire that integrates a variety of knowledge derived both from literature and computational prediction. Those data are organized in hierarchical fashion. The basic building blocks are functional annotation and structure prediction of individual molecule. Those data are then organized into clusters based on computationally predicted operon, regulon and molecular complexes. Finally all data are complied into pathways derived from combined efforts of literature mining and computational prediction. A number of tools have been developed to facilitate the data retrieval including a SQL query engineer and several viewers to browse genome, molecular complexes and pathways.

关键词： bioinformatics Genomics Biology computing Relational databases Proteins Visual databases computational systems biology Information retrieval Displays Laboratories

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An intelligent digital library system for biologists

An intelligent digital library system for biologists

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： J. Stone Xindong Wu M. Greenblatt Department of Computer Science University of Vermont USA

To aid researchers in obtaining, organizing and managing biological data, we have developed a sophisticated digital library system that utilizes advanced data mining techniques. Our digital library system is centralized with Web links to publicly accessible data repositories. Our digital library is based on a framework used for conventional libraries and an object-oriented paradigm, and will provide personalized user-centered services based on the user's areas of interests and preferences. To make personalized service possible, a "user profile" that represents the preferences of an individual user is constructed based upon the user's past activities, goals indicated by the user, and options. Utilizing these user profiles, our system will make relevant information available to the user in an appropriate form, amount, and level of detail with minimal user effort.

关键词： Intelligent systems Software libraries Data mining Databases Dictionaries Computer science bioinformatics Organizing computational biology Cloning

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Subspace clustering for microarray data analysis:multiple criteria and significance assessment

Subspace clustering for microarray data analysis:multiple cr...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Hui Fang Chengxiang Zhai Lei Liu Jiong Yang Department of Computer Science University of Illinois Urbana-Champaign USA W. M. Keck Center for Comparative and Functional Genomics University of Illinois Urbana-Champaign USA

As one of the latest breakthroughs in experimental molecular biology, microarray technology provides a powerful tool for monitoring the expression patterns of thousands of genes simultaneously, producing huge amounts of valuable gene expression data. Gene expression data are organized as matrices --- tables where rows represent genes, columns represent various samples such as tissues or experimental conditions, and a cell number indicates the expression level of a particular gene in a particular sample.

关键词： Data analysis Subspace constraints Gene expression Fluctuations Clustering algorithms Clustering methods bioinformatics Inspection Biology computing Computer science

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An algorithm for reconstruction of Markov blankets in Bayesian networks of gene expression datasets

An algorithm for reconstruction of Markov blankets in Bayesi...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： C. Barbacioru D.J. Cowden J. Saltz Department of Biomedical Informatics Ohio State Uinversity Columbus OH USA

This work presents an efficient algorithm, of polynomial complexity for learning Bayesian belief networks over a dataset of gene expression levels. Given a dataset that is large enough, the algorithm generates a belief network close to the underlying model by recovering the Markov blanket of every node. The time complexity is dependent on the connectivity of the generating graph and not on the size of it, and therefore yields to exponential savings in computational time relative to some previously known algorithms. We use bootstrap and permutation techniques in order to measure confidence in our finding. To evaluate this algorithm, we present experimental results on *** cell-cycle measurements of Spettman et al. (1998).

关键词： Intelligent networks Bayesian methods Gene expression Character generation Probability distribution Biomedical informatics Polynomials Biomedical measurements Greedy algorithms bioinformatics

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An efficient algorithm for unique signature discovery on whole-genome EST databases

An efficient algorithm for unique signature discovery on who...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Hsiao Ping Lee Tzu Fang Sheu Yin Te Tsai Ching Hua Shih Chuan Yi Tang Department of Computer Science National Tsing Hua University Taiwan Institute of Communication Engineering National Tsing Hua University Taiwan Department of Computer Science and Information Management Providence University Taiwan Department of Life Science National Tsing Hua University Taiwan

ISBN: (纸本)0769521940

ESTs can be used to accelerate the various research activities for the discovery of new genes. Unique oligonucleotides are signatures that distinguish an EST from all the others. An important application of those short signatures is to be used in PCR primer design and microarray experiments. In this research, we propose an efficient approach to enhance our previous work on unique signature discovery to handle the dataset of whole-genome scale. The performances of our method are evaluated by the experiments on human chromosome EST databases.

关键词： Databases Humans Biological cells Computer science Performance evaluation bioinformatics Sequences Statistics Hamming distance Acceleration

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Synchronized oscillations and chaos in coupled genetic repressilators

Synchronized oscillations and chaos in coupled genetic repre...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Jianbo Gao J. Bridgewater V.P. Roychowdhury Department of Electrical and Computer Engineering University of Florida Gainesville FL USA Electrical Engineering Department UCLA Los Angeles USA

Living organisms are complex, and are typically composed of many interacting subsystems. In order to understand the complex genetic networks present in the whole cell, it is of crucial importance to first understand the dynamic behavior of modular genetic circuits. Recently a few subsystems on the genetic level, namely, genetic repressilators or oscillators, and bi-stable gene circuits, have been constructed and manipulated. In the former case, while mathematical model predicts simple oscillations, it has been observed that period varies from one oscillation to another considerably. Realizing that laboratory biochemical experiments take place in space in a distributed way, we study coupled repressilators. Let the repressilator of Elowitz and Leibler [1] be described by the following set of 6 ordinary differential equations:

关键词： Chaos Genetics Oscillators Circuits Equations bioinformatics Bifurcation Organisms Mathematical model Laboratories

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Protein classification into domains of life using Markov chain models

Protein classification into domains of life using Markov cha...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： F. Zanoguera M. de Francesco Serono Pharmaceutical Research Institute Switzerland

It has recently been shown that oligopeptide composition allows clustering proteomes of different organisms into the main domains of life. In this paper, we go a step further by showing that, given a single protein, it is possible to predict whether it has a bacterial or eukaryotic origin with 85% accuracy, and we obtain this result after ensuring that no important homologies exist between the sequences in the test set and the sequences in the training set. To do this, we model the sequence as a Markov chain. A bacterial and an eukaryote model are produced using the training sets. Each input sequence is then classified by calculating the log-odds ratio of the sequence probability for each model. By analyzing the models obtained we extract a set of most discriminant oligopeptides, many of which are part of known functional motifs.

关键词： Proteins Microorganisms Archaea Testing Amino acids bioinformatics Sequences Peptides Databases Performance analysis

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Association tests and estimation of haplotype frequencies and of penetrance-related parameters in a case-control study

Association tests and estimation of haplotype frequencies an...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： S. Furihata T. Ito N. Kamatani Japan Biological Information Research Center Japan Biological Informatics Consortium Koto Tokyo Japan Mitsubishi Research Institute INC. Chiyoda Tokyo Japan Division of Genomic Medicine Department of Advanced Biomedical Engineering and Science and Institute of Rheumatology Tokyo Womens Medical University Shinjuku Tokyo Japan

This study shows the applicability of our algorithm which tests haplotype and qualitative phenotype association, in a case-control study. Although our algorithm named PENHAPLO is originally developed for analysis of a cohort study, it is shown that PENHAPLO is a useful tool for analysis of case-control studies as well. Simulations confirms that type I errors under null hypothesis are accurately estimated. The statistical power for alternative hypothesis calculated using the algorithm is comparable to those analyzed using known-phase data.

关键词： Frequency estimation Testing Algorithm design and analysis bioinformatics Data analysis Diseases Biomedical informatics Indium tin oxide Genomics Biomedical engineering

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A mixed factors model for dimension reduction and extraction of a group structure in gene expression data

A mixed factors model for dimension reduction and extraction...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： R. Yoshida T. Higuchi S. Imoto Graduate University of Advanced Studies (SOKENDAI) Minato Tokyo Japan Institute for Statistical Mathematics Minato Tokyo Japan Human Genome Center Institute of Medical Science University of Tokyo Minato Tokyo Japan

When we cluster tissue samples on the basis of genes, the number of observations to be grouped is much smaller than the dimension of feature vector. In such a case, the applicability of conventional model-based clustering is limited since the high dimensionality of feature vector leads to overfilling during the density estimation process. To overcome such difficulty, we attempt a methodological extension of the factor analysis. Our approach enables us not only to prevent from the occurrence of overfilling, but also to handle the issues of clustering, data compression and extracting a set of genes to be relevant to explain the group structure. The potential usefulness are demonstrated with the application to the leukemia dataset.

关键词： Data mining Gene expression Principal component analysis bioinformatics Mathematics Humans Genomics Data compression Diseases Eigenvalues and eigenfunctions

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Recognition of exon/intron boundaries using dynamic ensembles

Recognition of exon/intron boundaries using dynamic ensemble...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Xuanfu Wu Zhengxin Chen Department of Computer Science University of Nebraska Omaha Omaha NE USA

ISBN: (纸本)0769521940

Many studies have been carried out in recognition of exon/intron boundaries. For example, PROCRUSTES uses similarity-based approach to gene recognition. Other examples include GRAIL (Gene Recognition and Assembly Internet Link) http://***/Grail-1.3/help/(1996) and Glimmer (Gene Locator and Interpolated Markov Modeler). Since the problem of recognition of exon/intron boundaries can be cast as a classification task, ensemble learning can be applied. An ensemble consists of a set of organized individual trained classifiers whose individual decisions are combined in a certain way for classification purpose. However, existing studies typically take static approaches which hampered flexibility for improved accuracy. To overcome this problem we have proposed the concept of dynamic ensemble and developed a new algorithm, BAGA, which combines bagging and genetic algorithm techniques.

关键词： Voting Genetic algorithms Biological cells Bagging Genetic mutations Computer science Assembly Internet Skeleton bioinformatics

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