2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering最新文献_第3页

Inferring Causal Relations from Multivariate Time Series: A Fast Method for Large-Scale Gene Expression Data 从多元时间序列推断因果关系:大规模基因表达数据的一种快速方法

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.8

Yinyin Yuan, Chang-Tsun Li

{"title":"Inferring Causal Relations from Multivariate Time Series: A Fast Method for Large-Scale Gene Expression Data","authors":"Yinyin Yuan, Chang-Tsun Li","doi":"10.1109/BIBE.2009.8","DOIUrl":"https://doi.org/10.1109/BIBE.2009.8","url":null,"abstract":"Various multivariate time series analysis techniques have been developed with the aim of inferring causal relations between time series. Previously, these techniques have proved their effectiveness on economic and neurophysiological data,which normally consist of hundreds of samples. However, in their applications to gene regulatory inference, the small sample size of gene expression time series poses an obstacle. In this paper, we describe some of the most commonly used multivariate inference techniques and show the potential challenge related to gene expression analysis. In response, we propose a directed partial correlation (DPC) algorithm as an ef¿cient and effective solution to causal/regulatory relations inference on small sample gene expression data. Comparative evaluations on the existing techniques and the proposed method are presented. To draw reliable conclusions, a comprehensive benchmarking on data sets of various setups is essential. Three experiments are designed to assess these methods in a coherent manner. Detailed analysis of experimental results not only reveals good accuracy of the proposed DPC method in large-scale prediction, but also gives much insight into all methods under evaluation.","PeriodicalId":162768,"journal":{"name":"2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering","volume":"133 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117180693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The MAPK Signal Pathway Research and New Drug Discovery MAPK信号通路研究与新药发现

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.80

Po-Yuan Chen, Mien-De Jhuo, W. Hsu, T. Shih, Tzu-Hurng Cheng

引用次数: 1

Efficiency Enhancement of Protein Folding for Complete Molecular Simulation via Hardware Computing 基于硬件计算的蛋白质折叠全分子模拟效率的提高

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.46

Wen-Tsai Sung

引用次数: 2

Phylogenetic Analysis Using Nuclear-Encoded Mitochondrial Proteins 核编码线粒体蛋白的系统发育分析

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.66

Alan Chen, H. Hsiao, J. Tsai

引用次数: 3

Wedjat: A Mobile Phone Based Medicine In-take Reminder and Monitor 一种基于手机的服药提醒和监测系统

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.60

Mei-Ying Wang, P. Tsai, J. W. Liu, J. Zao

{"title":"Wedjat: A Mobile Phone Based Medicine In-take Reminder and Monitor","authors":"Mei-Ying Wang, P. Tsai, J. W. Liu, J. Zao","doi":"10.1109/BIBE.2009.60","DOIUrl":"https://doi.org/10.1109/BIBE.2009.60","url":null,"abstract":"Out-patient medication administration has been identified as the most error-prone procedure in modern health¬care. Under or over doses due to erratic in-takes, drug-drug or drug-food interactions caused by un-reconciled prescriptions and the absence of in-take enforcement and monitoring mechanisms have caused medication errors to become the common cases of all medical errors. Most medication administration errors were made when patients bought different prescribed and over-the-counter medicines from several drug stores and use them at home without little or no guidance. Elderly or chronically ill patients are particularly susceptible to these mistakes. In this paper, we introduce Wedjat, a smart phone application designed to help patients avoiding these mistakes. Wedjat can remind its users to take the correct medicines on time and record the in-take schedules for later review by healthcare professionals. Wedjat has two distinguished features: (1) it can alert the patients about potential drug-drug/drug-food interactions and plan a proper in-take schedule to avoid these interactions; (2) it can revise the in-take schedule automatically when a dose was missed. In both cases, the software always tries to produce the simplest schedule with least number of in-takes. Wedjat is equipped with user friendly interfaces to help its users to recognize the proper medicines and obtain the correct instructions of taking these drugs. It can maintain the medicine in-take records on board, synchronize them with a data¬base on a host machine or upload them onto a Personal Heath Record (PHR) system. A proof-of-concept prototype of Wedjat has been implemented on Window Mobile platform and will be migrated onto Android for Google Phones. This paper introduces the system concept and design principles of Wedjat with emphasis on its medication scheduling algorithms and the modular implementation of mobile computing application.","PeriodicalId":162768,"journal":{"name":"2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116721968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 57

A Data Mining Approach to Predicting Phylum for Microbial Organisms Using Genome-Wide Sequence Data 利用全基因组序列数据预测微生物门的数据挖掘方法

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.14

Rao M. Kotamarti, Douglas W. Raiford, M. Raymer, M. Dunham

{"title":"A Data Mining Approach to Predicting Phylum for Microbial Organisms Using Genome-Wide Sequence Data","authors":"Rao M. Kotamarti, Douglas W. Raiford, M. Raymer, M. Dunham","doi":"10.1109/BIBE.2009.14","DOIUrl":"https://doi.org/10.1109/BIBE.2009.14","url":null,"abstract":"Genomic sequencing projects are generating vast stores of data that provide opportunities and challenges in data analysis. Investigations of trends in codon usage have proven to be a rich area of study in this field. There are a number of methods for isolating codon usage bias in microbial organisms, each designed to capture a specific aspect of the bias. We posit that each species has evolved under the influence of a unique set of environmental constraints that has governed the shaping of the organism's codon usage. Analysis of codon usage data should, therefore, provide insights into the selection process at work influencing genomic composition. To this end, we describe the large-scale mining of genome-level data from several codon usage bias isolation techniques to determine whether this information can be used to predict the phylum and class to which each organism belongs. Successful prediction is an indication that the forces molding the codon usage of a given phylum/class are indeed distinctive, and that it would be of use in understanding the evolutionary forces involved. Additionally, it supports using this method to aid in, and validate existing taxonomic classification techniques.","PeriodicalId":162768,"journal":{"name":"2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering","volume":"121 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117115848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Beamformer-Based Spatiotemporal Imaging of Correlated Brain Activities 基于波束形成的相关脑活动时空成像

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.67

I. Chen, Yong-Sheng Chen, Li-Fen Chen

引用次数: 3

The Optimization of Monascus Fermentation Process for Pigments Increment and Citrinin Reduction 红曲发酵过程中色素增加和柑桔素还原的优化

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.33

C. Chung, Tzou-Chi Huang, Ho‐Hsien Chen

{"title":"The Optimization of Monascus Fermentation Process for Pigments Increment and Citrinin Reduction","authors":"C. Chung, Tzou-Chi Huang, Ho‐Hsien Chen","doi":"10.1109/BIBE.2009.33","DOIUrl":"https://doi.org/10.1109/BIBE.2009.33","url":null,"abstract":"The species of the fungus (Monascus purpureus, NPUST, Taiwan) used to produce the high pigment was isolated from rice waste. Its genomic DNA was confirmed by examining the NCBI database to check this species is M. purpureus strain ATCC 36114 (Identity 100%, Gap 0%). In this study, Taguchi Method was applied to find the optimal conditions of medium composition to enhance the production of pigments synthesis, and to reduce the yield of citrinin, metabolites in the M. purpureus fermentation process. In the production of the yellow pigment (OD400) and the red pigment (OD500), the result showed that their optimal conditions were A2B3C3D4E4 (1% Japonica-type rice, 1% peptone, 0.01% glycerol, 0.01% potassium phosphate and pH 9). In the production of the orange pigment (OD460), the result showed that the optimal conditions were A2B3C3D1E4 (1% Japonica-type rice, 1% peptone, 0.01% glycerol, 0.01% magnesium sulfate and pH 9). Under the optimal conditions for the best yield of pigment synthesis, the result showed that yellow pigment was 4.132 ppm, red pigment was 8.480 ppm and the orange pigment was 4.573 ppm. In the reduction of the citrinin yield, the result showed that A4B1C1D3E1 (1% whole wheat flour, 1% gelatin, 0.01% olive oil, 0.01% sodium choride and pH 3) were optimal conditions inhibit citrinin metabolism. Citrinin was reduced to 0.055 ppb. The optimal combination obtained from this study could be a reference for production line Monascus fermentation processing.","PeriodicalId":162768,"journal":{"name":"2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133083700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Integration of Heterogeneous Medical Decision Support Systems Based on Web Services 基于Web服务的异构医疗决策支持系统集成

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.59

Chung C. Chang, Hsueh-Ming Lu

{"title":"Integration of Heterogeneous Medical Decision Support Systems Based on Web Services","authors":"Chung C. Chang, Hsueh-Ming Lu","doi":"10.1109/BIBE.2009.59","DOIUrl":"https://doi.org/10.1109/BIBE.2009.59","url":null,"abstract":"This study employs the framework of web services in conjunction with Bayesian theorem and decision trees to construct a web-services-based decision support system for medical diagnosis and treatment. The purpose is to help users (physicians) with issues pertinent to medical diagnosis and treatment decisions. Users through the system key in available prior probability and through computation based on Bayesian theorem obtain the diagnosis. The process helps users enhance the quality and efficiency of medical decisions, and the diagnosis can be transmitted to a decision-tree-based treatment decision support service component via XML to generate recommendation and analysis for treatment decisions. On the other hand, features of web services enable this medical decision support system to offer more service platforms than conventional one. Users will have access to the system whether they use Windows, Macintosh, Linux or any other platforms that connect with the Internet via HTTP. More important is the fact that after the system is completed all Internet service providers will be able to access the system as a software unit freely and quickly. This way, the goal of this study to provide medical decision support tools and speedily integrate heterogeneous medical decision support systems can be effectively attained.","PeriodicalId":162768,"journal":{"name":"2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering","volume":"186 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114966026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

The Energy Distribution Data Bank: Collecting Energy Features of Protein Molecular Structures 能量分布数据库:收集蛋白质分子结构的能量特征

2009 Ninth IEEE International Conference on Bioinformatics and BioEngineering Pub Date : 2009-06-22 DOI: 10.1109/BIBE.2009.40

Dariusz Mrozek, Bożena Małysiak-Mrozek, S. Kozielski, A. Świerniak

引用次数: 11