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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271-280 订阅

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Surface approximation based image simplification and applications

Surface approximation based image simplification and applica...

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ieee International conference on systems, Man and Cybernetics

作者： Mingen Lin Jinhui Xu S. Bhattacharya R. Berezney Department of Computer Science and Engineering State University of New York University at Buffalo Buffalo NY USA Department of Computer Science and Engineering University of Buffallo Buffalo NY USA Department of Biological Sciences State University of New York University at Buffalo Buffalo NY USA

In this paper, we consider the problems of simplifying microscopic images of cell nucleus and segmenting genomic structures (such as DNA replication/transcription sites or foci and chromatin domains) from such images. DNA foci often have small sizes, and could be hidden by diffuse signals or quasi-foci (fanned by the overlapping of some neighboring foci), making the simplification and segmentation tasks extremely challenging. Existing simplification algorithms often yield large-sized images and take unreasonably long execution time. Available segmentation algorithms either fail reporting all DNA foci or generate incorrect boundaries. Based on an interesting observation on the intensity of microscopic images of cell nucleus, we present in this paper a novel approach for simplifying microscopic images by approximating the intensity surface of images by a set of normal distribution functions. Our technique yields much smaller-sized simplified images and runs in near linear time. With this technique, we further develop an efficient algorithm for segmenting DNA foci. Comparing with existing segmentation algorithms (such as watershed method), our algorithm detects all possible foci and generates much more accurate boundary of the detected foci. Our techniques are readily extendable to other types of images.

关键词： DNA Image segmentation Pixel Genomics bioinformatics Computer vision Application software computational geometry Optical microscopy Partitioning algorithms

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computational inference of transcription regulation and response networks in Synechococcus sp. WH8102

Computational inference of transcription regulation and resp...

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ieee Symposium on bioinformatics and Bioengineering (BIBE)

作者： Zhengchang Su PhuongAn Dam V. Olman Ying Xu Department of Biochemistry and Molecular Biology University of Georgia Athens USA Oak Ridge National Laboratory Institute of Computational Biology Oak Ridge TN USA

We have recently developed a computational capability for (a) inference of individual response networks and (b) global transcription regulation networks in Synechococcus sp. WH8102. The overall framework for inference of response networks can be summarized as follows. The framework employs a template-based network inference strategy. Under this framework, we first identify organisms that are known to have similar response systems to Synechococcus sp for a particular stimulus, and that have a large quantity of experimental data available, particularly microarray gene expression data. For each such "template" organism, we first build network models, and then map these template network models to Synechococcus sp. Through literature search and database search, we build a conceptual framework first for a specific response network in each template organism. The detailed network models will be then built through a series of predictions of gene functions, operon and regulon structures, transcription regulatory binding sites, protein-protein interactions and protein-DNA interactions, and incorporate these prediction results into the conceptual model. After the template network models are built, we map these models to Synechococcus sp through a constrained orthologous gene mapping scheme. The basic idea is to map genes of a network model to their predicted homologous genes under the constraints that these genes should belong to a group of co-regulated operons, which is predicted based on operon structure prediction and prediction of transcriptional regulatory binding sites. The mapped network models will then be refined and expanded through application of a genome-scale protein-protein interaction network, which is predicted through a series of computational prediction tools. We have applied this capability to derive a number of response networks in Synechococcus sp, such as phosphorus assimilation pathway, carbon fixation pathway, nitrogen assimilation pathway. Experiments a

关键词： Computer networks Predictive models Organisms Proteins Genomics bioinformatics Regulators Gene expression Databases Nitrogen

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proceedings of the 2003 ieee bioinformatics conference, csb 2003

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB ...

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2nd International ieee Computer Society computational systems bioinformatics conference, csb 2003

ISBN: (纸本)0769520006

The proceedings contain 134 papers. The topics discussed include: stepping up the pace of discovery: the genomes to life program;the role of algorithmic research in computational genomics;high performance computational biology - past progress and future promise;bridging paradigm gaps between biology and engineering;microbial functional genomics: pulling together a variety of approaches and concepts;the sea urchin endomesoderm gene regulatory network, an encoded logic map for early development;epitope prediction algorithms for peptide-based vaccine design;eulerian path methods for multiple sequence alignment;integrating bioinformatics advances into disease management systems to improve quality of care;motifs and modules in cellular signal processing: applications to microbial stress response pathways;and analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter.

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The role and efficacy of non-linear models in decision making and prognostication

The role and efficacy of non-linear models in decision makin...

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Annual International conference of the ieee Engineering in Medicine and Biology Society (EMBC)

作者： A.F.G. Taktak A.C. Fisher A.S. Jones B.E. Damato Department of Clinical Engineering Royal Liverpool University Hospital Liverpool UK Head and Neck Oncology Group University Hospital Aintree Liverpool UK Department of Ophthalmology Royal Liverpool University Hospital Liverpool UK

In few types of cancer, genomic abnormalities have been linked to the phenotype and carcinogenesis with a degree of precision. For most cancers, however, this is not the case and the literature provides no clear indication of any logical process. The main difficulties are the great redundancy within the genome and proteome, the vast number of interconnections and the vast number of feedback loops. Such complicated systems can be modelled, but will require highly sophisticated analysis using computational mathematics techniques. Neural networks have been in common use in medical research for the past 20 years. They have been used for classification and for prediction of hazard or failure but are still not widely used for explanation. The binary output can be modified by, for example, adding a Bayesian function to the output stage so that survival probabilities can be given. We looked at the application of probabilistic neural networks in providing prognosis in two types of cancer; laryngeal carcinoma which has a relatively short hazard time and a medium survival rate and ocular melanoma with longer hazard time and higher survival rate. We compared their performance with the more traditional methods and studied their limitations and boundaries.

关键词： Decision making Cancer Hazards Genomics bioinformatics Neural networks Feedback loop Mathematical model Mathematics Bayesian methods

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computational systems bioinformatics. csb2003. proceedings of the 2003 ieee bioinformatics conference. csb2003

Computational Systems Bioinformatics. CSB2003. Proceedings o...

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ieee conference on bioinformatics

The following topics are dealt with: genomes to life; microarray data analysis; pathways, networks, and systems biology; biomedical research and visualization; data mining; pattern recognition; sequence alignment; data integration; functional genomics; genomic annotation; genotyping and SNPs; molecular simulation; phylogeny and evolution; predictive methods; sequence comparison; strings, graphs, and algorithms; structural biology; text mining and ontologies; and systems biology.

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Pathway bioinformatics 2

Pathway bioinformatics

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2nd International computational systems bioinformatics conference

作者： Karp, P SRI Int Bioinformat Res Grp Menlo Pk CA 94025 USA

ISBN: (纸本)0769520006

Pathway bioinformatics is a subfield of bioinformatics that is concerned with pathway algorithms, ontologies, visualizations, and databases [4]. This talk will provide an overview of the pathway databases and software under development in the bioinformatics research group at SRI International, and will then discuss three pathway algorithms in detail. © 2003 ieee.

关键词： bioinformatics

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PTC: An interactive tool for phylogenetic tree construction 2

PTC: An interactive tool for phylogenetic tree construction

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2nd International computational systems bioinformatics conference

作者： Yang, C Khuri, S San Jose State Univ Dept Comp Sci San Jose CA 95192 USA

ISBN: (纸本)0769520006

A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, Phylogenetic Tree Construction package. The package supports four well-known algorithms, Unweighted Pair Group Method using Arithmetic average, Neighbor Joining, Fitch Margoliash, and Maximum Parsimony.

关键词： bioinformatics

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Development and assessment of bioinformatics tools for species conservation and habitat management 2

Development and assessment of bioinformatics tools for speci...

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2nd International computational systems bioinformatics conference

作者： Sutton, MA Deneke, L Eme, J Bennett, W Wray, F Univ W Florida Dept Biol Pensacola FL 32514 USA

ISBN: (纸本)0769520006

This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.

关键词： Data visualization

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Using easel for modeling and simulating the interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors 2

Using easel for modeling and simulating the interactions of ...

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2nd International computational systems bioinformatics conference

作者： Stojkovic, V Steele, G Lupton, W MSU Baltimore MD USA

ISBN: (纸本)0769520006

Modeling, simulation, visualization, and animation play a significant role in the study of bioinformatics. Research in this area is generally multidisciplinary in nature and collaboratively conducted by researchers with expertise in biology, bioinformatics, computer science, artificial intelligence, mathematics, and statistics. Easel programming language is used for modeling, simulation, visualization, and animation of interactions of cells in order to better understand the basics of biological processes and to predict their likely behaviors. This paper presents a computer science - modeling, simulation, visualization, and animation approach to such research. The paper provides a brief overview of the basic ideas in the "Message Passing" Easel program to demonstrate the transmission of signals between cells based on their physical proximity.

关键词： bioinformatics

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Pathway bioinformatics

Pathway bioinformatics

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ieee conference on bioinformatics

作者： P. Karp Bioinformatics Research Group SRI International Inc. USA

关键词： bioinformatics

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