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Annual International Conference of the ieee Engineering in Medicine and biology Society (EMBC)

作者： Athos Antoniades Ioanna Kalvari Constantinos Pattichis Neil Jones Paul M. Matthews Enrico Domenici Pierandrea Muglia Department of Computer Science University of Cyprus Nicosia Cyprus Department of Computer Science University of Cyprus 75 Kallipoleos Str P.O. Box 20537 Nicosia 1678 Cyprus Discovery Technology Group Molecular Discovery Research Glaxo SmithKline India Glaxo Smith Kline Clinical Imaging Center Imperial College London Hammersmith Hospital London UK Translational Medicine Mood and Anxiety Disorders Neurosciences Centre of Excellence in Drug Discovery GlaxoSmithKline Research and Development Medicine Research Centre Verona Italy Discovery Medicine Neurosciences Centre of Excellence in Drug Discovery GlaxoSmithKline Research and Development Medicine Research Centre Verona Italy

Genetic differences have been shown to contribute to gene expression variability. A complete evaluation of the associations between a whole genome scan with 550 k Single Nucleotide Polymorphisms (SNPs) and 54 k detectable expression levels (probesets) was performed on 176 human peripheral blood samples. The results are presented along with visualizations that reveal cis and trans gene expression regulatory effects. The algorithmic approach followed utilized a distributed computational system. The analysis was performed using a linear regression adjusting for all relevant covariates. Permutation testing on a random subset of the top results provided an indication of the significance levels adjusted for multiple testing and the non independence of SNPs due to linkage disequilibrium. The database of the produced results can be used as a resource to assess the functional impact of genetic polymorphisms to gene expression regulation. This resource is applicable across all disease areas.

关键词： Genetics Gene expression Genomics bioinformatics Testing Performance evaluation Humans Blood Visualization computational intelligence Society

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RiboSW – A Web Server for Identifying RNA Riboswitches

RiboSW – A Web Server for Identifying RNA Riboswitches

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： Tzu-Hao Chang Li-Ching Wu Chi-Ta Yeh Cheng-Wei Chang Baw-Jhiune Liu Hsien-Da Huang Jorng-Tzong Horng Department of Computer Science and Information Engineering National Central University Jhongli Taiwan Department of Computer Science and Engineering Yuan-Ze University Jhongli Taiwan Institute of Systems Biology and Bioinformatics National Central University Jhongli Taiwan Department of Biological Science and Technology Institute of Bioinformatics National Chiao Tung University Hsinchu Taiwan Department of Information Management Hsing Wu College LinKou Taiwan Department of Computer Science and Engineering Yuan Ze University Jhongli Taiwan Department of Bioinformatics Asia University Wufeng Taiwan Department of Biological Science and Technology National Chiao-Tung University Hsinchu Taiwan Department of Computer Science and Information Engineering Asia University Wufeng Taiwan

Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://***/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence.

关键词： Web server RNA bioinformatics Computer science Genetic engineering Sequences Genetic mutations Collision mitigation Switches Biomedical engineering

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Asymptotics of Canonical RNA Secondary Structures

Asymptotics of Canonical RNA Secondary Structures

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： Peter Clote Evangelos Kranakis Danny Krizanc Biology Department Boston College Graduate School Chestnut Hill MA USA School of Computer Science Carleton University Ottawa ONT Canada Department of Mathematics Wesleyan University Middletown CT USA

It is a classical result of Stein and Waterman that the asymptotic number S(n) of RNA secondary structures is 1.104366 ldr n -3/2 ldr 2.618034 n , where the combinatorial model of RNA concerns a length n homopolymer, such that any base can pair with any other base, subject to the usual convention that hairpin loops must contain at least thetas = 1 unpaired bases. The result of Stein and Waterman is proved by developing recursions,using generating functions and applying Bender's theorem. These recursions form the basis to compute the minimum free energy secondary structure for a given RNA sequence, with respect to the Nussinov energy model, later extended by Zuker to substantially more complicated resursions for the Turner nearest neighbor energy model. In this paper, we study combinatorial asymptotic for two special subclasses of RNA secondary structures - canonical and saturated structures. Canonical secondary structures are defined to have no lonely (isolated) base pairs. This class of secondary structures was introduced b y Bompfuenewerer et al., who noted that the runtime of Vienna RNA Package is substantially decreased when restricting computations to canonical structures. Here we provide an explanation for the speed-up, by proving that the asymptotic number of canonical RNA secondary structures is 2.1614 ldr n -3/2 ldr 1.96798 n . Saturated secondary structures have the property that no base pairs can be added without violating the definition of secondary structure (i.e. introducing a pseudoknotor base triple). In the Nussinov energy model,where the energy for a base pair is -1, saturated structures correspond to kinetic traps.n prior work, we showed that the asymptotic number of saturated structures of a length n homopolymer is 1.07427 ldr n -3/2 ldr 2.35467 n . In this paper, we show that the expected number of base pairs of random saturated structures, generated by a natural stochastic procedure, is (z thetas+1 )/((1-z) 2 ) (-z-Sigma i=0 thetas (z 2 )/(

关键词： RNA Amino acids USA Councils bioinformatics Biomedical engineering Mathematics Computer science computational biology Educational institutions Mathematical model

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Life science application support in an interoperable e-science environment

Life science application support in an interoperable e-scien...

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Annual ieee symposium on Computer-Based Medical Systems

作者： Sonja Holl Morris Riedel Bastian Demuth Mathilde Romberg Achim Streit Vinod Kasam Forschungszentrum Juelich Juelich Supercomputing Center Juelich Germany Schloss Birlinghoven Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

In the last decade, life science applications have become more and more integrated into e-Science environments, hence they are typically very demanding, both in terms of computational capabilities and data capacities. Especially the access to life science applications, embedded in such environments via Grid clients still constitutes a major hurdle for scientists that do not have an IT background. Life science applications often comprise a whole set of small programs instead of a single executable. Many of the graphical Grid clients are not perfectly suited for these types of applications, as they often assume that Grid jobs will run a single executable instead of a set of chained executions (i.e. sequences). This means that in order to execute a sequence of multiple programs on a single Grid resource, piping data from one program to the next, the user would have to run a hand-written shell script. Otherwise each program is independently scheduled as a Grid job, which causes unnecessary file transfers between the jobs, even if they are scheduled on the same resource. We present a generic solution to this problem and provide a reference implementation, which seamlessly integrates with the Grid middleware UNICORE. Our approach focuses on a comfortable user interface for the creation of such program sequences, validated in UNICORE-driven HPC-based Grids. Thus, we applied our approach in order to provide support for the usage of the AMBER package (a widely-used collection of programs for molecular dynamics simulations) within Grid workflows. We finally provide a scientific use case of our approach leveraging the interoperability of two different scientific infrastructures that represents an instance of the infrastructure interoperability reference model.

关键词： Middleware biology computing Sequences Biological system modeling bioinformatics Scientific computing User interfaces Packaging Collaborative work Chemistry

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Discovering Novel Cancer Therapies: A computational Modeling and Search Approach

Discovering Novel Cancer Therapies: A Computational Modeling...

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ieee symposium on computational intelligence in bioinformatics and computational biology

作者： Mahoney, Arthur W. Smith, Brian G. Flann, Nicholas S. Podgorski, Gregory J. Utah State Univ Dept Comp Sci Logan UT 84322 USA Utah State Univ Ctr Integrated Bio Syst Dept Biol Logan UT 84322 USA

ISBN: (纸本)9781424417780

Solid tumors must recruit new blood vessels for growth and maintenance. Discovering drugs that block this tumor-induced development of new blood vessels (angiogenesis) is an important approach in cancer treatment. However, the complexity of angiogenesis and the difficulty in implementing and evaluating rationally-designed treatments prevent the discovery of effective new therapies. This paper presents a massively parallel computational search-based approach for the discovery of novel potential cancer treatments using a high fidelity simulation of angiogenesis. Discovering new therapies is viewed as multi-objective combinatorial optimization over two competing objectives: minimizing the cost of developing the intervention while minimizing the oxygen provided to the cancer tumor by angiogenesis. Results show the effectiveness of the search process in finding interventions that are currently in use and more interestingly, discovering some new approaches that are counter intuitive yet effective.

关键词： cancer therapy Exploration Angiogenesis Search process Solid Tumor high fidelity computational modeling

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A wrapper feature selection method based on simulated annealing algorithm for prostate protein mass spectrometry data

A wrapper feature selection method based on simulated anneal...

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2008 ieee symposium on computational intelligence in bioinformatics and computational biology, CIBCB '08

作者： Li, Yifeng Liu, Yihui Institute of Intelligence Information Processing School of Information Science and Technology Shandong Institute of Light Industry Jinan Shandong 250353 China

ISBN: (纸本)9781424417780

Protein mass spectrometry is an integration of mass spectrometry and biological chip techniques, and it shows great potential for exploration of biomarkers and diagnosis of diseases. But the curse of dimensionality inherently from mass spectrometry data makes the dimensionality reduction a necessary phase of proteomic pattern recognition before classification. This paper presents a simulated annealing algorithm to select discriminant feature subsets. Experiments indicate that this wrapper feature selection method performs well and outperforms the other reported methods. © 2008 ieee.

关键词： Simulated annealing

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Special section on machine intelligence approaches systems biology

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ieee TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS 2008年第1期38卷 2-4页

作者： Fogel, Gary B. Bullinger, Eric Su, Shun-Feng Azuaje, Francisco Nat Select Inc San Diego CA 92130 USA Univ Strathclyde Dept Elect & Elect Engn Glasgow G1 1XW Lanark Scotland Natl Taiwan Univ Sci & Technol Dept Elect Engn Taipei 10617 Taiwan Univ Ulster Jordanstown BT37 0QB North Ireland

The three papers in this special section focus on machine intelligence approaches to systems biology.

关键词： Special issues and sections Machine intelligence Systems biology bioinformatics Proteins computational intelligence Biological system modeling Electrical engineering Biological systems biology computing

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Distributed Peer-to-Peer Cooperative Partitional-Divisive Clustering for Gene Expression Datasets

Distributed Peer-to-Peer Cooperative Partitional-Divisive Cl...

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ieee symposium on computational intelligence in bioinformatics and computational biology

作者： Kashef, R. Kamel, M. S. Univ Waterloo Dept Elect & Comp Engn Pattern Anal & Machine Intelligence Lab Waterloo ON N2L 3G1 Canada

ISBN: (纸本)9781424417780

Clustering techniques are helpful In understanding gene regulation, cellular processes, and subtypes of cells. A major thrust of gene expression analysis over the last twenty years has been the acquisition of enormous amount of various distributed sources of gene expression datasets. Thus, it Is becoming increasingly important to perform clustering of distributed data In-place, without the need to pool it first into a central node. The general goal of distributed clustering is achieving a level of speedup than the centralized approaches. A recent study shows that centralized cooperative clustering outperforms the non-cooperative centralized clustering approaches. In this paper a novel distributed Cooperative Partitional-Divisive Clustering in a Peer-to-Peer network is presented. The distributed CPDC approach is based on intermediate cooperation between the Partitional k-means and the Divisive bisecting k-means in a distributed Peer-to-Peer network to produce better global solutions. computational experiments were conducted to test the performance of the distributed CPDC approach using different gene expression datasets. Undertaken experimental results show that the performance of the distributed CPDC method is better than that of the non-cooperative distributed k-means and distributed bisecting k-means. Thus a new cooperative technique for distributed gene expression repositories is efficiently presented to discover regularities and genes that may span multiple nodes.

关键词： Distribute Cluster Analysis Genes Dataset Gene regulation Peer-to-peer network Speeding

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The Research of Plant Simulation Based On Genetic Algorithm

The Research of Plant Simulation Based On Genetic Algorithm

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1st International symposium on computational intelligence and Design

作者： Li Xiang Zhu Li Li Xuguang China Univ Geosci Sch Comp Wuhan 430074 Peoples R China

ISBN: (纸本)9780769533117

Plants simulation is a challenging research domain. Under the condition that external environment affect trees, the paper proposes that adopting illumination model as plants-growing simulation mechanism, optimizing and adjusting external-environment parameters with genetic algorithm, and simulating the plant-growing process well. Experiments results show that using phototropism of plants and influence among them, forest-environment model established by GA can avoid cross and overcast among trees as far as possible, reflect tree-growing space characteristic well, and reproduce the forest-growing process factually.

关键词： Genetic algorithms Biological system modeling computational modeling Lighting Algorithm design and analysis Computer simulation Shape control Evolution (biology) Automatic control computational intelligence

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Design of an Immune-inspired Danger Theory Model Based on Fuzzy Set

Design of an Immune-inspired Danger Theory Model Based on Fu...

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1st International symposium on computational intelligence and Design

作者： Fu Hai-Dong Li Gui-Feng Wuhan Univ Sci & Technol Coll Comp Sci & Technol Wuhan 430065 Hubei Peoples R China

ISBN: (纸本)9780769533117

An immune-inspired danger theory model based on fuzzy set was proposed in this article. In the model the concept of fuzzy set and degree of membership are presented in the foundation of the "danger" definition in artificial immune system. By carrying on the computation to the degree of danger, it makes the organism to apperceive the danger and simultaneously to make a strategy efficiently. It improves the organism to recognize the "danger" effectively, and then enhances the rate of intrusion detection based on the artificial immune model, and reduces the false alarm.

关键词： Fuzzy set theory Immune system Organisms Biological system modeling Cells (biology) computational intelligence Educational institutions Computer science Fuzzy sets Fuzzy systems

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