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21st International Parallel and Distributed Processing Symposium, IPDPS 2007

作者： Taufer, M. Leung, M.-Y. Johnson, K.L. Licon, A. Dept. of Computer Science University of Texas El Paso Dept. of Mathematical Sciences University of Texas El Paso Dept. of Biological Sciences University of Texas El Paso Bioinformatics Program University of Texas El Paso

ISBN: (纸本)1424409101

Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. An RNA molecule is a linear polymer which folds back on itself to form a three dimensional (3D) functional structure. While experimental determination of precise 3D RNA structures is a time consuming and costly process, useful insight into the molecule can be gained from knowing its secondary structure. Structural elements in RNA secondary structures can be separated into two large categories: stem-loops and pseudoknots. The development of mathematical models and computational prediction algorithms for simple stem-loop structures started early in the 1980's. However, building systems that provide the tremendous computer time and memory needed for RNA analysis of both stem-loops and pseudoknots remains a challenge even today. The recently developed grid computing technology can offer a possible solution to this challenge. In this paper we briefly address mathematical problems associated with the grid computing approach to RNA structure prediction. In particular, we introduce models to partition a large RNA molecule into smaller segments to be assigned to different computers on the grid. Based on these models, we formulate a sampling strategy to select RNA segments for computational prediction to maximize prediction consistency. This strategy is under construction as part of RNAVLab, our unified environment for computational RNA structure analysis, i.e., prediction, alignment, comparison, and classification, A first prototype of RNAVLab is presented and used to investigate the possible association of secondary structure types with RNA functions by analyzing secondary structures for a family of nodavirus genomes. © 2007 IEEE.

关键词： Grid computing

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Correcting base-assignment errors in repeat regions of shotgun assembly

Correcting base-assignment errors in repeat regions of shotg...

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作者： Zhi, Degui Keich, Uri Pevzner, Pavel Heber, Steffen Tang, Haixu Bioinformatics Program University of California San Diego San Diego CA 92093 Department of Computer Science 4130 Upson Hall Cornell University Ithaca NY 14853 Department of Computer Science and Engineering University of California San Diego San Diego CA 92093 North Carolina State University Raleigh NC 27695-7566 School of Informatics Center for Genomics and Bioinformatics Indiana University Bloomington IN 47408

Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers may place these reads arbitrarily. As a result, the base-assignment error rate in repeats is likely to be much higher than that in the rest of the genome. We developed an iterative algorithm, EULER-AIR, that is able to correct base-assignment errors in finished genome sequences in public databases. The Wolbachia genome is among the best finished genomes. Using this genome project as an example, we demonstrated that EULER-AIR can 1) discover and correct base-assignment errors, 2) provide accurate read assignments, 3) utilize finishing reads for accurate base-assignment and 4) provide guidance for designing finishing experiments. In the genome of Wolbachia, EULER-AIR found 16 positions with ambiguous base-assignment and two positions with erroneous bases. Besides Wolbachia, many other genome sequencing projects have significantly fewer finishing reads and, hence, are likely to contain more base-assignment errors in repeats. We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project. © 2007 IEEE.

关键词： Error analysis

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The role of heritability in mapping expression quantitative trait loci

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BMC proceedings 2007年第1期1 Suppl 1卷 S86页

作者： Song Huang David Ballard Hongyu Zhao Program of Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA. song.huang@yale.edu

Gene expression, as a heritable complex trait, has recently been used in many genome-wide linkage studies. The estimated overall heritability of each trait may be considered as evidence of a genetic contribution to the total phenotypic variation, which implies the possibility of mapping genome regions responsible for the gene expression variation via linkage analysis. However, heritability has been found to be an inconsistent predictor of significant linkage signals. To investigate this issue in human studies, we performed genome-wide linkage analysis on the 3554 gene expression traits of 194 Centre d'Etude du Polymorphisme Humain individuals provided by Genetic Analysis Workshop 15. Out of the 422 expression traits with significant linkage signals identified (LOD > 5.3), 89 traits have low estimated heritability (h2 < 10%), among which 23 traits have an estimated heritability equal to 0. The linkage analysis on individual pedigree shows that the overall LOD scores may result from a few pedigrees with strong linkage signals. Screening gene expressions before linkage analysis using a relatively low heritability (h2 < 20%) may result in a loss of significant linkage signals, especially for trans-acting expression quantitative trait loci (49%).

关键词： Linkage Analysis Heritability Estimate Expression Trait Genetic Analysis Workshop Select Gene Expression

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Structural characterization of RNA-binding sites of proteins: Preliminary results

Structural characterization of RNA-binding sites of proteins...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Fadi Towfic David C. Gemperline Cornelia Caragea Feihong Wu Drena Dobbs Vasant Honavar Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA Department of Biology Department of Chemistry Carthage College Kenosha WI USA Department of Computer Science Iowa State University Ames IA USA Department of Genetics Development and Cell Biology Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA Department of Computer Science Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA

We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc), using a non-redundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis sug gests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.

关键词： RNA Protein engineering Biology computing Amino acids bioinformatics Computer interfaces Rough surfaces Surface roughness Solids Machine learning

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Study of equilibrium sense improvement displaying visual information

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Key Engineering Materials 2008年 381-382卷 369-372页

作者： Kim, G.B. Jeong, S.H. Chong, W.S. Kang, H.S. Kim, S.J. Kim, M.H. Hwang, J.W. Hong, C.U. Education Program for 21st Century Chonbuk National University Research Institute of Clinical Medicine Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Computer Engineering Graduate School Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Biomedical Engineering Graduate School Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Pharmacology College of Veterinary Medicine Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Bio and Applied Chemistry Iksan National College Ma-Dong Iksan Chonbuk 570-752 Korea Republic of Department of Thoracic and Cardiovascular Surgery Chonbuk National University Medical Schools Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Division of Bionics and Bioinformatics Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of

The effectiveness of the visual feedback to improve ability with the sense and muscular strength of human in our bicycle system was quantitatively verified in our study. Experiments were performed to find the factors related to the training of equilibrium sense. The subjects consisted of young and the aged and the group of young people was compared against the group of the aged. We investigated three different training modes, non-visual feedback (NVF), visual feedback of the weight (VFW), and visual feedback of the center of pressure (VFC) and measured the riding time and speed, the weight shift, and the center of pressure (COP) for twenties and seventies. The results showed that the running capability of the young and the aged became much better after repeated training. In addition, it was found out that the ability to control postural balance and the capability of equilibrium sense were improved with the presentation of the visual feedback information. These results will be effective in the diagnosis of equilibrium sense and vestibular function with the aged.

关键词： Feedback

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Study on the intravenous lung assist device (ILAD) using PZT actuators and PVDF sensors

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Key Engineering Materials 2008年 381-382卷 353-356页

作者： Kim, G.B. Kim, S.J. Lee, Y.C. Hong, C.U. Kang, H.S. Kim, J.S. Kim, S.Z. Yoon, S.J. Kim, M.H. Education Program for 21st Century Chonbuk National University Research Institute of Clinical Medicine Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of Department of Bio and Applied Chemistry Iksan National Collage Ma-Dong Iksan Jeonbuk 570-752 Korea Republic of Department of Internal Chonbuk National University Medical Schools Duckjin-Dong Jeonju Jeonbuk 561-752 Korea Republic of Division of Bionics and Bioinformatics Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of Department of Pharmacology Collage of Veterinary Medicine Chonbuk National University Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of Department of Physiology Center for Healthcare Technology Development Chonbuk National University Medical Schools Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of Division of Mechanics and Aerospace Engineering Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Jeonbuk Korea Republic of Department of Thoracic and Cardiovascular Surgery Chonbuk National University Medical Schools Duckjin-Dong Jeonju Jeonbuk 561-756 Korea Republic of

The purpose of this study was to investigate the effect of vibration device in gas transfer rate for usage as intravenous lung assist device. Specific attention was focused on the effect of membrane vibration. Quantitative experimental measurements were performed to evaluate the performance of the device, and to identify membrane vibration dependence on hemolysis. Scaling analysis was then used to infer the dimensionless groups that correlate the performance of a vibrated hollow tube membrane oxygenator. The experimental design and procedure are then given for a device for assessing the effectiveness of membrane vibrations. This ILAD is used to provide some insight into how wall vibrations might enhance the performance of an intravascular lung assist device. The time and the frequency response of PVDF sensor were investigated through various frequencies in the ILAD. In these devices, the flow of blood and the source of oxygen were separated by a semipermeable membrane allows oxygen to diffuse into and out of the fluid, respectively. The results of experiments have shown vibrating ILAD performs effectively.

关键词： Oxygen

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Simulation of developmental changes in action potentials with ventricular cell models

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Systems and Synthetic Biology 2007年第1期1卷 11-23页

作者： Itoh, Hitomi Naito, Yasuhiro Tomita, Masaru Institute for Advanced Biosciences Keio University Fujisawa Kanagawa 252-8520 Japan Bioinformatics Program Graduate School of Media and Governance Keio University Fujisawa Kanagawa 252-8520 Japan Japan Society for the Promotion of Science (DC1) Tokyo Japan Department of Environmental Information Keio University Fujisawa Kanagawa 252-8520 Japan

During cardiomyocyte development, early embryonic ventricular cells show spontaneous activity that disappears at a later stage. Dramatic changes in action potential are mediated by developmental changes in individual ionic currents. Hence, reconstruction of the individual ionic currents into an integrated mathematical model would lead to a better understanding of cardiomyocyte development. To simulate the action potential of the rodent ventricular cell at three representative developmental stages, quantitative changes in the ionic currents, pumps, exchangers, and sarcoplasmic reticulum (SR) Ca²⁺ kinetics were represented as relative activities, which were multiplied by conductance or conversion factors for individual ionic systems. The simulated action potential of the early embryonic ventricular cell model exhibited spontaneous activity, which ceased in the simulated action potential of the late embryonic and neonatal ventricular cell models. The simulations with our models were able to reproduce action potentials that were consistent with the reported characteristics of the cells in vitro. The action potential of rodent ventricular cells at different developmental stages can be reproduced with common sets of mathematical equations by multiplying conductance or conversion factors for ionic currents, pumps, exchangers, and SR Ca ²⁺ kinetics by relative activities. © Springer Science + Business Media B.V. 2007.

关键词： Cardiac ventricular cell Computer modeling Development Electrophysiology Ion channels Spontaneous electrical activity

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Identification of expression quantitative trait loci by the interaction analysis using genetic algorithm

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BMC proceedings 2007年第1期1 Suppl 1卷 S69页

作者： Junghyun Namkung Jin-Wu Nam Taesung Park Bioinformatics Program at College of Natural Science Seoul National University San 56-1 Sillim-dong Gwanak-gu Seoul 151-747 Korea. jh.namkung@***

Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient and robust algorithm is needed. The genetic algorithm (GA) is useful in searching for the optimal solution from a very large searchable space. In this study, we show that genome-wide interaction analysis using GA and a statistical interaction model can provide a practical method to detect biologically interacting loci. We focus our search on transcriptional regulators by analyzing gene x gene interactions for cancer-related genes. The expression values of three cancer-related genes were selected from the expression data of the Genetic Analysis Workshop 15 Problem 1 data set. We implemented a GA to identify the expression quantitative trait loci that are significantly associated with expression levels of the cancer-related genes. The time complexity of the GA was compared with that of an exhaustive search algorithm. As a result, our GA, which included heuristic methods, such as archive, elitism, and local search, has greatly reduced computational time in a genome-wide search for gene x gene interactions. In general, the GA took one-fifth the computation time of an exhaustive search for the most significant pair of single-nucleotide polymorphisms.

关键词： Genetic Algorithm Local Search Acute Lymphocytic Leukemia Exhaustive Search Linkage Disequilibrium Block

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Tag clouds for summarizing web search results 07

Tag clouds for summarizing web search results

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16th International World Wide Web Conference, WWW2007

作者： Kuo, Byron Y.-L. Hentrich, Thomas Good, Benjamin M . Wilkinson, Mark D. ICAPTURE Centre for Cardiovascular and Pulmonary Research University of British Columbia St. Paul.s Hospital Vancouver BC V6Z 1Y6 Canada Computing Science Simon Fraser University Burnaby BC Canada Bioinformatics Graduate Program University of British Columbia Vancouver BC Canada

ISBN: (纸本)1595936548

In this paper, we describe an application, PubCloud that uses tagclouds for the summarization of results from queries over thePubMed database of biomedical literature. PubCloud responds toqueries of this database with tag clouds generated from wordsextracted from the abstracts returned by the query. The results ofa user study comparing the PubCloud tag-cloud summarization ofquery results with the standard result list provided by PubMedindicated that the tag cloud interface is advantageous in presenting descriptive information and in reducing user frustrationbut that it is less effective at the task of enabling users to discoverrelations between concepts.

关键词： Online searching

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Decision fusion of circulating markers for breast cancer detection in premenopausal women

Decision fusion of circulating markers for breast cancer det...

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7th IEEE International Conference on bioinformatics and Bioengineering, BIBE

作者： Jesneck, Jonathan L. Mukherjee, Sayan Nolte, Loren W. Lokshin, Anna E. Marks, Jeffrey R. Lo, Joseph Department of Biomedical Engineering Department of Statistical Science Computational Biology and Bioinformatics Program Duke Advanced Imaging Labs. Institute for Genome Sciences and Policy Department of Computer Science Duke University Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine University of Pittsburgh Cancer Institute Pittsburgh PA 15213 United States Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC 27708 United States

ISBN: (纸本)1424415098

Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions. ©2007 IEEE.

关键词： Tissue

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