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检索条件"任意字段=IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology"

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Prediction of protein-protein interactions using support vector machines

Prediction of protein-protein interactions using support vec...

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： S. Dohkan A. Koike T. Takagi Department of Computational Biology Graduate School of Frontier Sciences University of Tokyo Kashiwa Chiba Japan Central Research Laboratory Hitachi and Limited Tokyo Japan

Protein-protein interactions play a crucial role in the cellular process. Although recent studies have elucidated a huge amount of protein-protein interactions within Saccharomyces cerevisiae, many still remain to be identified. This paper presents a new interaction prediction method that associates domains and other protein features by using support vector machines (SVMs), and it reports the results of investigating the effect of those protein features on the prediction accuracy. Cross-validation tests revealed that the highest F-measure of 79%, was obtained by combining the features "domain, " "amino acid composition, " and "subcellular localization. " These prediction results were more accurate than the predictions reported previously. Furthermore, predicting the interaction of unknown protein pairs revealed that high-scoring protein pairs tend to share similar GO annotations in the biological process hierarchy. This method can be applied across species.

关键词： Support vector machines Prediction methods Protein engineering Support vector machine classification Fungi computational biology Laboratories Cities and towns Accuracy Testing

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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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Designing synthetic biological systems by multiple time scale networks

Designing synthetic biological systems by multiple time scal...

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Proceedings of the ieee computational Systems bioinformatics Conference, CSB

作者： Ruiqi Wang J. Nakai Mitsuyasu Seo Luonan Chen Osaka Sangyo University Osaka Japan

Rhythmic phenomena exist in living organisms at all levels with periods ranging from less than a second to years [1]. From both theoretical and experiment viewpoints, it is a great challenging problem in biological science to model, analyze and further predict the periodic behaviors of biosystems. This paper aims to develop a new methodology to analyze and design biological oscillating networks with time delays, by using multiple time-scale networks (MTN) which are composed of a cyclic feedback network (CFN) and multiple positive feedback networks (PFN). We show that a MTN with certain conditions has no stable equilibria but stable periodic oscillations, depending on the total time delay of the CFN, although it has a complicated network structure including both positive and negative feedback loops. As an implementation example, a biologically plausible two-gene synthetic model with genes lac and cI is designed to demonstrate the theoretical result. The detail theoretical and numerical results are described in [1].

关键词： Biological systems Biological system modeling Delay effects Feedback Artificial intelligence Bismuth Organisms biology Predictive models Periodic structures

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Analysis of signaling pathways in human T-cells using Bayesian network modeling of single cell data

Analysis of signaling pathways in human T-cells using Bayesi...

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Proceedings of the ieee computational Systems bioinformatics Conference, CSB

作者： K. Sachs O.D. Perez D. Pe'er C.P. Nolan D.K. Gifford T.S. Jaakkola D.A. Lauffenburger Biological Engineering Division Massachusetts Institute of Technology Cambridge MA USA Department of Microbiology and Immunology The Baxter Laboratory of Genetic Pharmacology Department of Molecular Pharmacology Stanford University School of Medicine Stanford CA USA Department of Genetics Harvard Medical School Boston MA USA MIT Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA Biological Engineering Division Department of Chemical Engineering Department of Biology Massachusetts Institute of Technology Cambridge MA USA

We perform network inference ('reverse-engineering') on phospho-specific multi-dimensional flow cytometry measurements of signaling molecules in human T cells using Bayesian networks. Inferred networks are fou... 详细信息

关键词： Signal analysis Intelligent networks Humans Bayesian methods Biological system modeling Fluid flow measurement Chemical technology Molecular biophysics Laboratories Genetics

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The effect of part-of-speech tagging on ir performance for Turkish

The effect of part-of-speech tagging on ir performance for T...

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19th International symposium on Computer and Information Sciences, ISCIS 2004

作者： Dinçer, B. Taner Karaoğlan, Bahar Ege Üniversitesi Uluslararası Bilgisayar Enstitüsü Bornovaİzmir35100 Turkey

ISBN: (纸本)3540235264

In this paper, we experimentally evaluate the effect of the Part-of- Speech (POS) tagging on Information Retrieval performance for Turkish. We used four term-weighting schemas to index SABANCI-METU Turkish Treebank corpus. The term weighting schemas are "tf", "tf x idf", "***", and "Okapi". Each weighting scheme is factored over three POS tagging cases that are namely "No POS tagging", "POS tag with no history (i.e. 1-gram)", and "POS tag with one step history (i.e. 2-gram)". The Meta-scoring function is used to analyze the effect of these nine factors on IR performance. Results show that weighting schema are significantly different from each other with a p-value of 0.04 (Friedman Non-parametric Test), but there is not enough evidence in the corpus to reject the null hypothesis that the three weighting schemas, on the average, show equal performance over the three cases of POS tagging with a p-value of 0.36. © Springer-Verlag Berlin Heidelberg 2004.

关键词： computational linguistics

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Nonlinear methods for biopattern analysis: role and challenges

Nonlinear methods for biopattern analysis: role and challeng...

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

作者： E.C. Ifeachor N.J. Outram G.T. Henderson H.S.K. Wimalaratna N. Hudson R. Sneyd C. Dong C. Bigan University of Plymouth UK Radcliff Infirmary Oxford UK Derriford Hospital Plymouth UK Peninsula Medical School Plymouth UK Ecological University of Bucharest Romania

An important trend in medical technology is towards support for personalised healthcare, fuelled by developments in genomic-based medicine. New computational intelligent techniques for biodata analysis will be needed to fully exploit the vast amounts of data that are being generated. Non-linear signal processing methods will form an important part of such computational intelligent techniques. This paper introduces some non-linear methods which are likely to play a role in the emerging area of biopattern and bioprofile analysis that will underpin personalized healthcare. We highlight their application to clinical problems involving EEG and fetal ECG and heart rate analysis, and issues that arise when they are applied to real world problems. The clinical problems include dementia assessment, drug administration and fetal monitoring. The potential role and challenges in the application of non-linear signal analysis of biopattern and bioprofile are highlighted within the context of a major EU project, BIOPATTERN.

关键词： Medical services computational intelligence Competitive intelligence Genomics bioinformatics Biomedical signal processing Electroencephalography Electrocardiography Heart rate Dementia

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An effective approach for constructing the phylogenetic tree on a grid-based architecture

An effective approach for constructing the phylogenetic tree...

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： D.S.-M. Liu Che-Hao Wu Department of Computer Science and Information Engineering National Chung Engineering University Chiayi Taiwan

In biological research, scientists often need to use the information of the species to infer the evolutionary relationship among them. The evolutionary relationships are generally represented by a labeled binary tree, called the evolutionary tree (or phylogenetic tree). Reconstructing evolutionary tree is a major research problem in biology, and this problem is often known as phylogeny problem. The difficulty of such problem is that the number of possible evolutionary trees is very large. As the number of species increases, exhaustive enumeration of all possible relationships is not feasible. The quantitative nature of species relationships therefore requires the development of more rigorous methods for tree construction. The phylogeny problem is computationally intensive, thus it is suitable for distributed computing environment. Grid computing (or computational grid) is a new concept to integrate the CPU power, the storage and other resources via Internet in order to get overall computing power. Nowadays, many bioinformaticists are developing the BioGrid technology in order to solve the challenges that need intensive computing in biology. In this paper, we design and develop a grid-based system, and propose an efficient method based on the concept of quartet for solving the phylogeny problem on this architecture.

关键词： Phylogeny biology computing Grid computing bioinformatics Evolution (biology) Computer architecture Distributed computing Internet Computer science Binary trees

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An improved algorithm for the maximum agreement subtree problem

An improved algorithm for the maximum agreement subtree prob...

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： Chuan-Min Lee Ling-Ju Hung Maw-Shang Chang Chuan-Yi Tang Department of Computer Science & Information Engineering National Chung Engineering University Chiayi Taiwan Department of Computer Science National Tsing Hua University Hsinchu Taiwan

ISBN: (纸本)0769521738

In this paper, we solve the maximum agreement subtree problem for a set T of k rooted, leaf-labelled evolutionary trees on n leaves where T contains a binary tree. We show that the O(kn/sup 3/)-time dynamic programming algorithm proposed by Farach et al. and Bryant can be implemented in O(n/sup 2/log/sup k-1/n) and O(k/spl middot/n/sup 3-(1/k-1)/) using the k-dimensional binary search tree and the k-dimensional range search tree, respectively.

关键词： Computer science Binary trees Binary search trees History Vegetation mapping Dynamic programming Heuristic algorithms Pediatrics computational biology Electrical capacitance tomography

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A mutation-sensitive approach for locating conserved gene pairs between related species

A mutation-sensitive approach for locating conserved gene pa...

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： H.L. Chan T.W. Lam W.K. Sung P.W.H. Wong S.M. Yiu Department of Computer Science University of Hong Kong Hong Kong China Department of Computer Science National University of Singapore Singapore

This paper proposes a new approach for solving the whole genome alignment problem. Our approach is based on a new structural optimization problem (called the MUM selection problem) related to mutations via reversals and transpositions. We have devised a practical algorithm for this optimization problem and have evaluated the algorithm using 15 pairs of human and mouse chromosomes. The results show that our algorithm is both effective and efficient. More specifically, our algorithm can reveal 91% of the conserved gene pairs that have been reported in the literature. When compared to existing software MUMmer and MaxMinCluster , our algorithm uncovers 15% and 7% more genes on average, respectively. The sensitivity of our algorithm is also slightly higher. The paper concludes with a remark on the computational hardness of the MUM selection problem.

关键词： Genomics bioinformatics Genetic mutations Computer science Samarium Humans Mice Biological cells Software algorithms Evolution (biology)

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Phylogenetic reconstruction from arbitrary gene-order data

Phylogenetic reconstruction from arbitrary gene-order data

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ieee symposium on bioinformatics and Bioengineering (BIBE)

作者： Jijun Tang B.M.E. Moret Liying Cui C.W. dePamphilis Department of Computer Science University of New Mexico Albuquerque NM USA Department of Biology and Institute of Molecular Evolutionary Genetics Pennsylvania State University University Park PA USA

Phylogenetic reconstruction from gene-order data has attracted attention from both biologists and computer scientists over the last few years. So far, our software suite GRAPPA is the most accurate approach, but it requires that all genomes have identical gene content, with each gene appearing exactly once in each genome. Some progress has been made in handling genomes with unequal gene content, both in terms of computing pair-wise genomic distances and in terms of reconstruction. In this paper, we present a new approach for computing the median of three arbitrary genomes and apply it to the reconstruction of phylogenies from arbitrary gene-order data. We implemented these methods within GRAPPA and tested them on simulated datasets under various conditions as well as on a real dataset of chloroplast genomes; we report the results of our simulations and our analysis of the real dataset and compare them to reconstructions made by using neighbor-joining and using the original GRAPPA on the same genomes with equalized gene contents. Our new approach is remarkably accurate both in simulations and on the real dataset, in contrast to the distance-based approaches and to reconstructions using the original GRAPPA applied to equalized gene contents.

关键词： Phylogeny bioinformatics Genomics computational modeling Analytical models DNA Sequences biology Biological cells Computer science

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