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

共 372 条记录，以下是291-300 订阅

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

Development and assessment of bioinformatics tools for speci...

引用

ieee conference on bioinformatics

作者： M.A. Sutton L. Deneke J. Eme W. Bennett F. Wray Departments of Biology and Computer Science University of West Florida USA Departments of Biology University of West Florida USA

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： bioinformatics Biology computing Biological systems Mice Marine animals Data mining computational intelligence Deductive databases Spatial databases Visual databases

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A semantic mediation approach for problems in computational molecular biology

A semantic mediation approach for problems in computational ...

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ieee conference on bioinformatics

作者： M. Chagoyen M.E. Kurul P.A. De-Alarcon S. Santini B. Ludascher J.M. Carazo A. Gupta Biocomputing Unit Centro Nacional de Biotecnologia Madrid Spain San Diego Supercomputer Center University of California San Diego San Diego CA USA Integromics S. L. Madrid Spain University of California San Diego San Diego CA USA

As great amount of data are being produced and accumulated in life sciences, information access and consequent integration in analytical and computational methods become critical issues in order to conduct research. In this work we describe how the synergic combination of a high-level programmable planner engine and formal semantics are suitable to resolve many information integration problems in molecular biology.

关键词： Mediation Biology computing computational biology Proteins XML Engines bioinformatics Web pages Relational databases Information filtering

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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

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

引用

ieee conference on bioinformatics

作者： V. Stojkovic G. Steele W. Lupton M. S. U. Baltimore MD USA

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： Biological system modeling Predictive models Cells (biology) Biological processes computational modeling Visualization Animation bioinformatics Computer science Collaboration

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Computing for the DOE genomes to life program

Computing for the DOE genomes to life program

引用

ieee conference on bioinformatics

作者： E. Uberbacher D. Thomassen A. Patrinos G. Johnson C.E. Oliver M. Frazier Office of Science Office of Biological and Environmental Research Office of Science Office of Advanced Scientific Computing Research Oak Ridge National Laboratory USA

A key goal of the DOE office of science's systems biology program, genomes to life (GTL), is to achieve, over the next 10 to 20 years, a basic understanding of thousands of environmental microbes and microbial systems in their native environments. This goal demands that we develop new models for scientific discovery that integrate methods and systems which tightly couple advanced computing, mathematics, algorithms, and data-management technologies with large-scale experimental data generation.

关键词： US Department of Energy Genomics bioinformatics Biology computing Biological system modeling Computer networks Concurrent computing Distributed computing Biological systems Image analysis

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Implementing parallel hmm-pfam on the EARTH multithreaded architecture

Implementing parallel hmm-pfam on the EARTH multithreaded ar...

引用

ieee conference on bioinformatics

作者： W. Zhu Y. Niu J. Lu G.R. Gao Department of Electrical & Computer Engineering University of Delaware USA

Hmmpfam is a widely used computation-intensive bioinformatics software for sequence classification. This poster describes a new parallel implementation of hmmpfam on EARTH, which is an event-driven fine-grain multithreaded programming execution model. The comparison results of the original PVM implementation and our implementation shows notable improvements on absolute speedup and scalability. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes.

关键词： Hidden Markov models Earth Master-slave Load management bioinformatics Databases Scalability Testing Concurrent computing Programming profession

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Eulerian path methods for multiple sequence alignment

Eulerian path methods for multiple sequence alignment

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ieee conference on bioinformatics

作者： M.S. Waterman Y. Zhang Department of Biological Science University of Southern California Los Angeles CA USA Department of Mathematics University of Southern California Los Angeles CA USA

With the rapid increase in the size of genome sequence databases, the multiple sequence alignment problem is increasingly important and often requires the alignment of a large number of sequences. Beginning in 1975, many heuristic algorithms have been created to improve the speed of computation and the quality of alignment. We introduce a novel approach that is fundamentally distinct from all currently available methods. Our motivation comes from the Eulerian method for fragment assembly in DNA sequence determination, that transforms all the DNA sequencing fragments into a de Bruijn graph and then reduces sequence assembly to a Eulerian path problem.

关键词： Sequences DNA bioinformatics Assembly Biology Mathematics Genomics Databases Heuristic algorithms computational modeling

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A statistical model of proteolytic digestion

A statistical model of proteolytic digestion

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ieee conference on bioinformatics

作者： I.-J. Wang C.P. Diehl F.J. Pineda Research & Technology Development Center Johns Hopkins University-Applied Physics Laboratory USA Department of Molecular Microbiology & Immunology Johns Hopkins Bloomberg School of Public Health USA

We present a stochastic model of proteolytic digestion of a proteome, assuming the distribution of parent protein lengths in the proteome, the relative abundances of the 20 amino acids in the proteome, and the digestion "rules" of the enzyme used in the digestion. We derived a closed form expression for the fragment mass distribution for a large class of enzymes including the widely used trypsin. The expression uses the distribution of lengths in a mixture of proteins taken from a proteome, as well as the relative abundances of the 20 amino acids in the proteome. The agreement between theory and the in silica digest is excellent.

关键词： bioinformatics

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The SCP and compressed domain analysis of biological sequences

The SCP and compressed domain analysis of biological sequenc...

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ieee conference on bioinformatics

作者： D. Adjeroh J. Feng Lane Department of Compiter Science and Electrical Engineering West Virginia University Morgantown WV USA

We introduce the SCP - the sorted common prefix, and study some of its properties. Based on the internal representations used by a class of new compression schemes, we show how the SCP table can be constructed using an O(u+| /spl Sigma/ |K/sub max/) number of comparisons on average, and O(u | /spl Sigma/ |) worst case, where u is the size of the sequence, | /spl Sigma/ | is the number of symbols, and K/sub max/ is the maximum SCP value. We describe one application of the SCP to the problem of anchor points in multiple sequence alignment.

关键词： Sequences Genomics bioinformatics Data structures Compression algorithms Pattern analysis DNA Diseases Humans Biological system modeling

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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

Analysis of the genetic potential and gene expression of mic...

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ieee conference on bioinformatics

作者： D. Lovley Department of Microbiology University of Massachusetts Amherst USA

The goal of this genomes-to-life project is to develop models that can describe the functioning of the microbial communities involved in the in situ bioremediation of uranium-contaminated groundwater and harvesting electricity from waste organic matter. Previous studies have demonstrated that the microbial communities involved in uranium bioremediation and energy harvesting are both dominated by microorganisms in the family Geobacteraceae and that these Geobacteraceae are responsible for the uranium bioremediation and electron transfer to electrodes. The research plan is diagrammed below. Examples of how both pure culture and environmental genomic studies have dramatically changed the concepts of how Geobacteraceae-dominated subsurface communities function will be presented.

关键词： Genetics Gene expression bioinformatics Genomics Biochemical analysis Microorganisms Electrons Electrodes DNA Proteomics

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Minimum redundancy feature selection from microarray gene expression data

Minimum redundancy feature selection from microarray gene ex...

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ieee conference on bioinformatics

作者： C. Ding H. Peng NERSC Division Lawrence Berkeley National Laboratory University of California Berkeley CA USA

Selecting a small subset of genes out of the thousands of genes in microarray data is important for accurate classification of phenotypes. Widely used methods typically rank genes according to their differential expressions among phenotypes and pick the top-ranked genes. We observe that feature sets so obtained have certain redundancy and study methods to minimize it. Feature sets obtained through the minimum redundancy - maximum relevance framework represent broader spectrum of characteristics of phenotypes than those obtained through standard ranking methods; they are more robust, generalize well to unseen data, and lead to significantly improved classifications in extensive experiments on 5 gene expressions data sets.

关键词： Gene expression Filters Learning systems Cancer Diseases Testing Laboratories Robustness bioinformatics Proteins

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