检索结果-内蒙古大学图书馆

Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Chi-Huang Chen Sheau-Ling Hsieh Yung-Ching Weng Wen-Yung Chang Feipei Lai Department of Electrical Engineering National Taiwan University Taipei Taiwan EECS International Graduate Program Institute IT Center National Chiao Tung University Hsinchu Taiwan Department of Computer Science and Engineering National Taiwan University Taiwan Institute of Computer Science and Engineering College of Computer Science National Chiao Tung University Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan

Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

关键词： Semantics Biomedical measurements Correlation Kernel Training Medical services Support vector machine classification

来源：评论

学校读者我要写书评

暂无评论

Erratum to: Genetic analysis of Down syndrome-associated heart defects in mice

引用

Human Genetics 2011年第5期130卷 633-633页

作者： Liu, Chunhong Morishima, Masae Yu, Tao Matsui, Sei-Ichi Zhang, Li Fu, Dawei Pao, Annie Costa, Alberto C. Gardiner, Katheleen J. Cowell, John K. Nowak, Norma J. Parmacek, Michael S. Liang, Ping Baldini, Antonio Yu, Y. Eugene Children’s Guild Foundation Down Syndrome Research Program Department of Cancer Genetics Roswell Park Cancer Institute Buffalo USA Department of Anatomy and Developmental Biology Department of Pediatric Cardiology Tokyo Women’s Medical University Tokyo Japan Division of Clinical Pharmacology and Toxicology Department of Medicine University of Colorado School of Medicine Aurora USA Department of Pediatrics Intellectual and Developmental Disability Research Center Human Medical Genetics and Neuroscience Programs University of Colorado Denver Aurora USA MCG Cancer Center School of Medicine Medical College of Georgia Augusta USA New York State Center of Excellence in Bioinformatics and Life Sciences Buffalo USA Department of Cellular and Molecular Biology Roswell Park Division of Graduate School State University of New York at Buffalo Buffalo USA University of Pennsylvania Cardiovascular Institute Philadelphia USA Department of Biological Sciences Brock University St. Catharines Canada Institute of Biosciences and Technologies Texas A&M University Houston USA Institute of Genetics and Biophysics National Research Council Naples Italy

来源：评论

学校读者我要写书评

暂无评论

Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains

引用

Immunome Research 2009年第1期5卷 1-8页

作者： Volpe, Joseph M Kepler, Thomas B Center for Computational Immunology Duke University Durham NC United States Departments of Biostatistics and Bioinformatics and Immunology Duke University Medical Center Durham NC United States Computational Biology and Bioinformatics Graduate Program Institute for Genome Sciences and Policy Duke University Durham NC United States

Background. Immature bone marrow B cells are known to have longer CDR3 than mature peripheral B cells, and this genetic characteristic has been shown to correlate with autoreactivity in these early cells. B-cell Central tolerance eliminates these cells, but it is known that autoreactive B cells nevertheless appear commonly in healthy human blood. We examined over 7,300 Ig genes from Genbank, including those annotated by their discoverers as associated with autoreactivity, to determine the genetic correlates of autoreactivity in mature B cells. Results. We find differential biases in gene segment usage and higher mutation frequency in autoreactivity-associated Ig genes, but the CDR3 lengths do not differ between autoreactive and non-autoreactive Ig genes. The most striking genetic signature of autoreactivity is an increase in the proportion of N-nucleotides relative to germline-encoded nucleotides in CDR3 from autoreactive genes. Conclusion. We hypothesize that peripheral autoreactivity results primarily from somatic mutation, and that the genetic correlates of autoreactivity in mature B-cells are not the same as those for autoreactivity in immature B cells. What is seen in mature autoreactive B cells are the correlates of autoreactive potential, not of autoreactivity per se. The autoreactive potential is higher for V(D)J rearrangements encoded to a large extent by N-nucleotides rather than by the gene segments that, we posit, have been selected in germline evolution for their suppression of autoreactive potential.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Predicting helix-helix interactions from residue contacts in membrane proteins

引用

bioinformatics 2009年第8期25卷 996-1003页

作者： Lo, Allan Chiu, Yi-Yuan Rødland, Einar Andreas Lyu, Ping-Chiang Sung, Ting-Yi Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Institute of Bioinformatics and Structural Biology Department of Life Sciences National Tsing Hua University Hsinchu Taiwan Bioinformatics Laboratory Institute of Information Science Academia Sinica Taipei Taiwan Centre for Cancer Biomedicine University of Oslo NO-0027 Oslo Norway SAMBA Norwegian Computing Center Blindern NO-0314 Oslo P.O. Box 114 Norway

Motivation: Helix-helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or more residue contacts. Although previous studies focused on helix-packing patterns and sequence motifs, few of them developed methods specifically for contact prediction. Results: We present a new hierarchical framework for contact prediction, with an application in membrane proteins. The hierarchical scheme consists of two levels: in the first level, contact residues are predicted from the sequence and their pairing relationships are further predicted in the second level. Statistical analyses on contact propensities are combined with other sequence and structural information for training the support vector machine classifiers. Evaluated on 52 protein chains using leave-one-out cross validation (LOOCV) and an independent test set of 14 protein chains, the two-level approach consistently improves the conventional direct approach in prediction accuracy, with 80% reduction of input for prediction. Furthermore, the predicted contacts are then used to infer interactions between pairs of helices. When at least three predicted contacts are required for an inferred interaction, the accuracy, sensitivity and specificity are 56%, 40% and 89%, respectively. Our results demonstrate that a hierarchical framework can be applied to eliminate false positives (FP) while reducing computational complexity in predicting contacts. Together with the estimated contact propensities, this method can be used to gain insights into helix-packing in membrane proteins. © 2009 The Author(s).

关键词：

来源：评论

学校读者我要写书评

暂无评论

Impact of DNA-binding position variants on yeast gene expression

引用

Nucleic Acids Research 2009年第21期37卷 6991-7001页

作者： Swamy, Krishna B.S. Cho, Chung-Yi Chiang, Sufeng Tsai, Zing Tsung-Yeh Tsai, Huai-Kuang Institute of Information Science National Yang-Ming University Taiwan Bioinformatics Program Taiwan International Graduate Program National Yang-Ming University Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Research Center for Information Technology Innovation Academia Sinica Taipei 115 Taiwan

Transcription factors (TFs) regulate gene expression by binding to specific binding sites (TFBSs) in gene promoters. TFBS motifs may contain one or more variable positions. Although the prevailing assumption is that nucleotide variants at such positions are functionally equivalent, there is increasing evidence that such variants play a role in regulation of gene expression. In this article, we propose a method for studying the relationship between the expression of target genes and nucleotide variants in TFBS motifs at a genome-wide scale in Saccharomyces cerevisiae, especially the combinatorial effects of variants at two positions. Our analysis shows that nucleotide variations in more than one-third of variable positions and in 20% of dependent position pairs are highly correlated to gene expression. We define such positions as 'functional'. However, some positions are only functional as dependent pairs, but not individually. In addition, a significant proportion of the functional positions have been well conserved across all yeast-related species studied. We also find that some positions require the presence of co-occurring TFs, while others maintain their functionality in the absence of a co-occurring TF. Our analysis supports the importance of nucleotide variants at variable positions of TFBSs in gene regulation. © The Author(s) 2009. Published by Oxford University Press.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Identification of microRNA in the protist Trichomonas vaginalis

引用

Genomics 2009年第5期93卷 487-493页

作者： Lin, Wei-Chen Li, Sung-Chou Lin, Wen-Chang Shin, Jyh-Wei Hu, Song-Nian Yu, Xiao-Min Huang, Ting-Yun Chen, Shih-Chieh Chen, Hua-Chien Chen, Shu-Jen Huang, Po-Jung Ruei-Chi Gan, Richie Chiu, Cheng-Hsun Tang, Petrus Molecular Regulation and Bioinformatics Laboratory Chang Gung University Taoyuan 333 Taiwan Division of Microbiology Graduate Institute of Biomedical Sciences Chang Gung University Taoyuan 333 Taiwan Institute of Biomedical Informatics National Yang-Ming University Taipei 112 Taiwan Taiwan International Graduate Program in Bioinformatics Academia Sinica Taipei 115 Taiwan Institute of Biomedical Sciences Academia Sinica Taipei 115 Taiwan Department of Parasitology National Cheng Kung University Tainan 701 Taiwan Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing China Graduate University Chinese Academy of Sciences Beijing China Department of Life Sciences Chang Gung University Taoyuan 333 Taiwan Molecular Medicine Research Center Chang Gung University Taoyuan 333 Taiwan Bioinformatics Center Chang Gung University Tao-Yuan 333 Taiwan Chang Gung Molecular Infectious Diseases Research Center Chang Gung Memorial Hospital Taoyuan 333 Taiwan

MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. However, miRNA has never been identified experimentally in protist. Direct cloning of 438 expressed miRNA tags by microRNA serial analysis of gene expression from the parasitic protist Trichomonas vaginalis identified nine candidate miRNAs. bioinformatics analysis of the corresponding genomic region revealed that these miRNA candidates contain a classical stem-loop-stem structure of pre-microRNAs. Analysis of the 20 nt long mature tva-miR-001 showed that it is an intergenic miRNA located at the scaffold DS113596. Tva-miR-001 was differentially expressed in the trophozoite, pseudocyst and amoeboid stages. Based on the experimental results of the present study, we provided solid evidence that protist possesses a miRNA regulating network comparable with multicellular organisms for the first time. © 2009 Elsevier Inc. All rights reserved.

关键词： MicroRNA Protist Trichomonas vaginalis

来源：评论

学校读者我要写书评

暂无评论

Classification of Multiple Time-Series via Boosting

Classification of Multiple Time-Series via Boosting

引用

IEEE Digital Signal Processing Workshop

作者： Patrick L. Harrington Arvind Rao Alfred O., Hero Bioinformatics Graduate Program University of Michigan Ann Arbor MI USA Lane Center of Computational Biology Carnegie Mellon University Pittsburgh PA USA Department of Statistics University of Michigan Ann Arbor MI USA

Much of modern machine learning and statistics research consists of extracting information from high-dimensional patterns. Often times, the large number of features that comprise this high-dimensional pattern are themselves vector valued, corresponding to sampled values in a time-series. Here, we present a classification methodology to accommodate multiple time-series using boosting. This method constructs an additive model by adaptively selecting basis functions consisting of a discriminating feature's full time-series. We present the necessary modifications to fisher linear discriminant analysis and least-squares, as base learners, to accommodate the weighted data in the proposed boosting procedure. We conclude by presenting the performance of our proposed method against a synthetic stochastic differential equation data set and a real world data set involving prediction of cancer patient susceptibility for a particular chemoradiotherapy.

关键词： Boosting Statistics Vectors Linear discriminant analysis Gene expression bioinformatics Computational biology Machine learning Data mining Stochastic processes

来源：评论

学校读者我要写书评

暂无评论

Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis

引用

BMC Genomics 2009年第SUPPL. 3期10卷 1-10页

作者： Rhee, Je-Keun Joung, Je-Gun Chang, Jeong-Ho Fei, Zhangjun Zhang, Byoung-Tak Graduate Program in Bioinformatics Seoul National University Seoul 151-744 South Korea Center for Biointelligence Technology (CBIT) Seoul National University Seoul 151-744 South Korea Boyce Thompson Institute for Plant Research Cornell University Ithaca NY 14853 United States Konan Technology Inc Seoul 135-080 South Korea USDA Robert W. Holley Center for Agriculture and Health Ithaca NY 14853 United States School of Computer Science and Engineering Seoul National University Seoul 151-744 South Korea

Background: Gene regulation is a key mechanism in higher eukaryotic cellular processes. One of the major challenges in gene regulation studies is to identify regulators affecting the expression of their target genes in specific biological processes. Despite their importance, regulators involved in diverse biological processes still remain largely unrevealed. In the present study, we propose a kernel-based approach to efficiently identify core regulatory elements involved in specific biological processes using gene expression profiles. Results: We developed a framework that can detect correlations between gene expression profiles and the upstream sequences on the basis of the kernel canonical correlation analysis (kernel CCA). Using a yeast cell cycle dataset, we demonstrated that upstream sequence patterns were closely related to gene expression profiles based on the canonical correlation scores obtained by measuring the correlation between them. Our results showed that the cell cycle-specific regulatory motifs could be found successfully based on the motif weights derived through kernel CCA. Furthermore, we identified co-regulatory motif pairs using the same framework. Conclusion: Given expression profiles, our method was able to identify regulatory motifs involved in specific biological processes. The method could be applied to the elucidation of the unknown regulatory mechanisms associated with complex gene regulatory processes. © 2009 Rhee et al;licensee BioMed Central Ltd.

关键词： Canonical Correlation Analysis Regulatory Motif Upstream Sequence Gene Expression Dataset Yeast Cell Cycle

来源：评论

学校读者我要写书评

暂无评论

Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis

Identification of cell cycle-related regulatory motifs using...

引用

8th International Conference on bioinformatics: Computational Biology, InCoB 2009

作者： Rhee, Je-Keun Joung, Je-Gun Chang, Jeong-Ho Fei, Zhangjun Zhang, Byoung-Tak Graduate Program in Bioinformatics Seoul National University Seoul 151-744 Korea Republic of Seoul National University Seoul 151-744 Korea Republic of Boyce Thompson Institute for Plant Research Cornell University Ithaca NY 14853 United States Konan Technology Inc. Seoul 135-080 Korea Republic of USDA Robert W. Holley Center for Agriculture and Health Ithaca NY 14853 United States School of Computer Science and Engineering Seoul National University Seoul 151-744 Korea Republic of

关键词： Gene expression

来源：评论

学校读者我要写书评

暂无评论

Evolution of olfactory receptor genes in East Asian loaches

引用

Zoological Studies 2009年第2期48卷 223-237页

作者： Wang, Daryi Wang, Tzi-Yuan Weng, Li-Chuan Emori, Yasufumi Tzeng, Chyng-Shyan Li, Wen-Hsiung Biodiversity Research Center Academia Sinica Taipei 115 Taiwan Genomics Research Center Academia Sinica Taipei 115 Taiwan Department of Biophysics and Biochemistry Graduate School of Science University of Tokyo Bunkyo Tokyo 113-0033 7-3-1 Hongo Japan Undergraduate Program for Bioinformatics and System Biology University of Tokyo Bunkyo Tokyo 113-0033 7-3-1 Hongo Japan Institute of Bioinformatics and Structural Biology Department of Life Sciences National Tsing Hua University Hsinchu 300 Taiwan

Daryi Wang, Tzi-Yuan Wang, Li-Chuan Weng, Yasufumi Emori, Chyng-Shyan Tzeng, and Wen-Hsiung Li (2009) Evolution of olfactory receptor genes in East Asian loaches. Zoological Studies 48(2): 223-237. It is well known that fish have fewer olfactory receptor (OR) genes than mammals do. In order to investigate the divergence of and evolutionary changes in OR genes in fish, 2 loach OR gene families (D1/3 and D32) from Taiwanese and Chinese populations of 2 species (Misgurnus anguillicaudatus and Paramisgurnus dabryanus) were analyzed. We found duplications in both D1/3 and D32 that had accumulated after the separation of the island of Taiwan from the Asian mainland ~5 million yrs ago. The accumulation of duplicate copies in a relatively short time suggests that gaining extra copies of OR genes may have been selectively advantageous for adapting to local environments. On the other hand, the loss of some OR genes in the 2 species in Taiwan may reflect loss of selective constraints on some OR genes. Moreover, unlike the situation in mammals in which pseudogenes are found in each family, pseudogenes are clustered in an expanding gene family in P. dabryanus in Taiwan. The presence of pseudogenes and the limited number of functional OR genes in fish suggest that fish do not need a large number of OR genes. Finally, the dynamic changes in OR gene number and the possible explanation for a lower OR gene number in fish are discussed. http://***/Journals/48.2/***.

关键词： Adaptation Misgurnus anguillicaudatus Multigene family Olfaction Paramisgurnus dabryanus

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：