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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91-100 订阅

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Gene length and alternative transcription in fruit fly

Gene length and alternative transcription in fruit fly

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： B. Budagyan A. Loraine University of Alabama Birmingham UK

Alternative transcription, in which a single gene may give rise to multiple variant mRNA forms, is widely recognized as an important source of protein diversity in complex, eukaryotic genomes. Here we show that in the Drosophila genome, larger genes with greater numbers of exons tend to be alternatively transcribed to a greater degree than smaller genes with fewer exons. In addition, we show that a log-normal distribution provides a good approximation for gene length distributions in Drosophila and that an exponential function relates the number of variants produced per gene with average exon count.

关键词： bioinformatics Genomics Testing Proteins Statistical distributions Data mining Data processing Computer languages Log-normal distribution Shape

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A knowledge base for computational pathway reconstruction

A knowledge base for computational pathway reconstruction

引用

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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BioSPRINT: classification of intron and exon sequences using the SPRINT algorithm

BioSPRINT: classification of intron and exon sequences using...

引用

proceedings of the ieee computational systems bioinformatics conference, csb

作者： K. Crosby P. Gabbert Furman University USA

An important problem for computer scientists as well as geneticists involves classifying particular items into common groups. This paper focuses on classifying sequences of DNA as either an intron or an exon. Insights from this classification can reduce the time needed for laboratory work to distinguish between introns and exons. Using a classification tree based on the SPRINT algorithm, sequences from the Drosophila melanogaster and the Caenorhabditis elegans genomes were used for training and testing. A large test sample error rate of 15% was shown for the Drosophila melanogaster, whereas the Caenorhabditis elegans was only 1.6%.

关键词： Sequences Classification tree analysis DNA bioinformatics Genomics Testing Decision trees Feature extraction Data mining Classification algorithms

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Labeling and enhancing life sciences links

Labeling and enhancing life sciences links

引用

proceedings of the ieee computational systems bioinformatics conference, csb

作者： S. Heymann F. Naumann L. Raschid P. Rieger Humboldt-Universitaet zu Berlin Germany University of Maryland USA

Life sciences data sources contain data about scientific objects such as genes and sequences that are richly interconnected, i.e., a gene object may have links to sequences, proteins, SNPs, citations, etc. Scientific knowledge is enhanced by exploration of relationships between scientific objects, requiring traversal of both links and paths (informally concatenations of links). There are significant limitations and challenges of such exploration, because the links are inherently poor with respect to syntactic representation and semantic knowledge. The links are syntactically poor because the source

关键词： Labeling Proteins Diseases Data models Database languages HTML bioinformatics Performance analysis Algorithm design and analysis Humans

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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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Locating all tandem repeat families in a sequence

Locating all tandem repeat families in a sequence

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： D. Adjeroh Jianan Feng Lane Department of Computer Science and Electrical Engineering Virginia University Morgantown WV USA

We present a new data structure called the BSCP (block sorted common prefix), and its tree representation, called the BSCP tree. We also introduce the notion of PTR family - a biologically motivated description and representation of the tandem repetitions hi a sequence. The PTR family implicitly encodes each distinct primitive tandem repeat in the sequence as its part. Based on the BSCP tree, we describe a method to locate all the primitive tandem repeat families in an input sequence T. The proposed method requires average space and time complexity in O(u), where u = |T|.

关键词： Diseases Genomics bioinformatics Data structures Vocabulary Biological information theory Genetics Computer science US Department of Energy Engineering profession

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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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Probabilistic consistency analysis for gene selection

Probabilistic consistency analysis for gene selection

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： S. Mukherjee S.J. Roberts Department of Engineering Science University of Oxford Oxford UK

A great deal of recent research has focused on the problem of selecting differentially expressed genes from microarray data ('gene selection'). Recent theoretical work has shown that the effectiveness of a gene selection algorithm can be captured as a probability called 'selection accuracy'. Unfortunately, in practice, there tends to be relatively little known about the very features upon which selection accuracy depends, making it difficult to choose a suitable method. In this paper we present a 'consistency analysis' which allows the inference of posterior distributions over selection accuracy from data. The utility of our approach lies in the fact that it can be used to assess gene selection algorithms in a practical but principled manner, and thus choose an appropriate method for given experimental data.

关键词： Inference algorithms bioinformatics Biological systems Data engineering Graphical models Statistics

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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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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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