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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121-130 订阅

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Automatic prediction of functional site regions in low-resolution protein structures

Automatic prediction of functional site regions in low-resol...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Jaspreet Singh Sodhi L.J. McGuffin K. Bryson J.J. Ward L. Wernisch D.T. Jones Department of Computer Science University College London London UK

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

关键词： Proteins bioinformatics Genomics Sequences Predictive models Biological system modeling Design methodology Robustness Biological information theory DNA

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Minimum entropy clustering and applications to gene expression analysis

Minimum entropy clustering and applications to gene expressi...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Haifeng Li Keshu Zhang Tao Jiang University of California Riverside CA USA Rensselaer Polytechnic Institute Troy NY USA

Clustering is a common methodology for analyzing the gene expression data. We present a new clustering algorithm from an information-theoretic point of view. First, we propose the minimum entropy (measured on a posteriori probabilities) criterion, which is the conditional entropy of clusters given the observations. Pane's inequality indicates that it could be a good criterion for clustering. We generalize the criterion by replacing Shannon's entropy with Havrda-Charvat's structural /spl alpha/-entropy. Interestingly, the minimum entropy criterion based on structural /spl alpha/-entropy is equal to the probability error of the nearest neighbor method when /spl alpha/ = 2. This is another evidence that the proposed criterion is good for clustering. With a nonparametric approach for estimating a posteriori probabilities, an efficient iterative algorithm is then established to minimize the entropy. The experimental results show that the clustering algorithm performs significantly better than k-means/medians, hierarchical clustering, SOM, and EM in terms of adjusted Rand index. Particularly, our algorithm performs very well even when the correct number of clusters is unknown. In addition, most clustering algorithms produce poor partitions in presence of outliers while our method can correctly reveal the structure of data and effectively identify outliers simultaneously.

关键词： Entropy Gene expression Clustering algorithms Iterative algorithms Partitioning algorithms Data analysis Biological processes bioinformatics Nearest neighbor searches Cells (biology)

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Recurrence time statistics: versatile tools for genomic DNA sequence analysis

Recurrence time statistics: versatile tools for genomic DNA ...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Yinhe Cao Wen-wen Tung Jian-Bo Gao Department of Electrical and Computer Engineering University of Florida Gainesville FL USA National Center for Atmospheric Research Boulder CO USA

With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or noncoding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

关键词： Statistical analysis Genomics bioinformatics Sequences Humans Organisms DNA computing Feature extraction Proteins Statistics

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Mapping of microbial pathways through constrained mapping of orthologous genes

Mapping of microbial pathways through constrained mapping of...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： V. Olman Hanchuan Peng Zhengchang Su Ying Xu Computational Systems Biology Laboratory Biochemistry and Molecular Biology Department University of Georgia USA Computational Biology Institute Oak Ridge National Laboratory USA

We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a target genome that is most consistent with (a) predicted orthologous gene relationship, (b) predicted operon structures, and (c) predicted co-regulation relationship of operons. Mathematically, we have formulated this problem as a constrained minimum spanning tree problem (called a Steiner network problem), and demonstrated that this formulation has the desired property through applications. We have solved this mapping problem using a combinatorial optimization algorithm, with guaranteed global optimality. We have implemented this algorithm as a computer program, called P-MAP. Our test results on pathway mapping are highly encouraging - we have mapped a number of pathways of H. influenzae, B. subtilis, H. pylori, and M. tuberculosis to E. coli using P-MAP, whose homologous pathways in E coli. are known and hence the mapping accuracy could be checked. We have then mapped known E. coli pathways in the EcoCyc database to the newly sequenced organism Synechococcus sp WHS 102, and predicted 158 Synechococcus pathways. Detailed analyses on the predicted pathways indicate that P-MAP's mapping results are consistent with our general knowledge about (local) pathways. We believe that P-MAP will be a useful tool for microbial genome annotation projects and inference of individual microbial pathways.

关键词： bioinformatics Genomics Organisms computational systems biology Biology computing Biological information theory Biochemistry computational biology Steiner trees Application software

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proceedings of the 2004 ieee International conference on computational Intelligence for Homeland Security and Personal Safety, CIHSPS 2004

Proceedings of the 2004 IEEE International Conference on Com...

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proceedings of the 2004 ieee International conference on computational Intelligence for Homeland Security and Personal Safety, CIHSPS 2004

ISBN: (纸本)0780383818

The proceedings contain 18 papers from the proceedings of the 2004 ieee International conference on computational & Intelligence for Homeland Security and Personal Safety, CIHSPS 2004. The topics discussed include: a novel measure of estimating color purity of image regions;image segmentation optimisation for X-ray images of airline luggage;video-based human posture recognition;an attention monitoring system for high demanding operational tasks;database-editing metrics for pattern matching;collaboration and modeling tools for counter-terrorism analysis;supporting anti-terrorist analyst teams using agents with shared RPD process;and using evolutionary computation for seismic signal detection: a homeland security application.

关键词： Security systems

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Abstracts of the Controlling Complexity Workshop

Abstracts of the Controlling Complexity Workshop

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proceedings of the ieee computational systems bioinformatics conference, csb

Summary form only given. Presents a series of abstracts from the conference proceedings.

关键词： bioinformatics Biology computing computational modeling Biological system modeling Distributed computing Computer vision

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An algorithm for detecting homologues of known structured RNAs in genomes

An algorithm for detecting homologues of known structured RN...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Shu-Yun Le J.V.Jr. Maizel Kaizhong Zhang Laboratory of Experimental and Computational Biology NCI Center for Cancer Research National Cancer Institute Frederick MD USA Department of Computer Science University of Western Ontario London ONT Canada School of Computing Science Simon Fraser University Burnaby BC Canada

Distinct RNA structures are frequently involved in a wide-range of functions in various biological mechanisms. The three dimensional RNA structures solved by X-ray crystallography and various well-established RNA phylogenetic structures indicate that functional RNAs have characteristic RNA structural motifs represented by specific combinations of base pairings and conserved nucleotides in the loop region. Discovery of well-ordered RNA structures and their homologues in genome-wide searches will enhance our ability to detect the RNA structural motifs and help us to highlight their association with functional and regulatory RNA elements. We present here a novel computer algorithm, HomoStRscan, that takes a single RNA sequence with its secondary structure to search for homologous RNAs in complete genomes. This novel algorithm completely differs from other currently used search algorithms of homologous structures or structural motifs. For an arbitrary segment (or window) given in the target sequence, that has similar size to the query sequence, HomoStRscan finds the most similar structure to the input query structure and computes the maximal similarity score (MSS) between the two structures. The homologous RNA structures are then statistically inferred from the MSS distribution computed in the target genome. The method provides a flexible, robust and fine search tool for any homologous structural RNAs.

关键词： RNA Genomics bioinformatics Sequences Laboratories computational biology Databases Cancer detection Jacobian matrices Computer science

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Are we there yet? Genomic profiling and mechanism in cancer research

Are we there yet? Genomic profiling and mechanism in cancer ...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： P. Meltzer S. Davis K. Baird Yidong Chen Cancer Genetics Branch National Human Genome Research Institute USA

The advent of the human genome sequence and genomic profiling technologies has impacted all of biomedical research. The effect has been particularly great on cancer research because cancer is a disease uniformly characterized by disturbed genome function. Studies which take a whole genome view of cancer are transforming the classification of tumors, enhancing understanding of tumorigenesis and promising to affect patient care. However, the development of large sets of genomic data has challenged cancer biologists who as a rule have never encountered data on this scale. Implementation of conventional statistical techniques has brought a level of order to the biologist's desktop, but significant problems remain to be solved. The challenge remains to extract the maximum useful information from genomic data. This requires both new algorithmic approaches which can accommodate the complexity of the underlying rules of genome function and effective strategies for linking different types of genomic data to each other and to external sources of gene and genome annotation. Progress in this arena will be necessary to fully realize the potential of genomics to impact on our ability to intervene in the clinical arena. Of particular importance will be approaches which help identify critical genes and pathways which are essential to tumor growth and survival. Examples will be presented which illustrate the boundaries of conventional analyses based on studies of tumor profiling at the expression and gene copy number level as well as experimental models designed to explore the function of specific pathways.

关键词： Genomics bioinformatics Cancer Neoplasms Humans Genetics Diseases Data mining Joining processes

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Segmental duplications containing tandem repeated genes encoding putative deubiquitinating enzymes

Segmental duplications containing tandem repeated genes enco...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Hong Liu Li Li A. Zilberstein C.S. Hahn Aventis Pharmaceuticals Inc. Bridgewater NJ USA

Both inter- and intra-chromosomal segmental duplications are known to occur in human genome during evolution. Few cases of such segments involving functional genes have been reported. While searching for the human orthologs of murine hematopoietic deubiquitinating enzymes (DUBs), we identified four clusters of DUB-like genes on chromosome 4p15 and chromosome 8p22-23 that are over 90% identical to each other at the DNA level. These genes are expressed in a cell type- and activation-specific manner, with different clusters possessing potentially distinct expression profiles. Examining the surrounding sequences of these gene duplication events, we have identified previously unreported conserved sequence elements that are as large as 35 to 74 kb encircling the gene clusters. Traces of these elements are also found on chromosome 12p13 and chromosome 11q13. The coding and immediate upstream sequences for DUB - like genes as well as the surrounding conserved elements, are present in the chimpanzee trace database, but not in rodent genome. We hypothesize that the segments containing these DUB clusters and surrounding elements arose relatively recently in evolution through inter- and intra-chromosomal duplicative transpositions, following the divergence of primates and rodents. Genome wide systematical search of the segmental duplication containing duplicated gene cluster has been performed.

关键词： Encoding Biochemistry Biological cells Genomics bioinformatics Sequences Humans Rodents DNA Databases

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Gene recovery of two genome-filtration sequencing techniques when applied to the maize genome

Gene recovery of two genome-filtration sequencing techniques...

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proceedings of the ieee computational systems bioinformatics conference, csb

作者： Xiequn Xu W.B. Barbazuk Yucheng Feng K. Schubert A.P. Chan G. Pertea Li Zheng Foo Cheung Yuandan Lee Donald Danforth Plant Science Center Saint Louis USA Donald Danforth Plant Science Center The Institute of Genomics Research Rockville USA

The large size of the maize genome and the expectation that most of the genome is represented by repetitive elements is a challenge to standard genome sequencing techniques. Genome-filtration sequencing techniques may target gene-rich regions in the genome. Two such approaches, methylation filtration and high Cot selection, may provide rapid and cost-effective alternative to sequencing the maize genome. Approximately 450k sequence reads have been obtained from both methylation filtration (MF) and high Cot (HC) libraries, and these sequences have been clustered and assembled. An analysis was undertaken to examine whether MF and MC enrich for maize genes and target non-identical sequence space. Simple sequence repeat analysis and mapped marker coverage provide gauges to examine whether MF and HC sample identical sequence space. Marker hits also provide evidence that MF and HC enrich for unique genic portions of the genome. Finally, the identification of maize and other protein sequences in the MF and HC sequence sets can indicate the expected fraction and coverage of the maize gene space by MF and HC.

关键词： Genomics bioinformatics Assembly Libraries Filtration Proteins Cloning Kinetic theory Helium

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