检索结果-内蒙古大学图书馆

IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Sunwon Lee Jaewoo Kang Junho Oh Department of Graduate Program in Bioinformatics Korea University Seoul South Korea Department of Computer Science and Engineering Korea University Seoul South Korea

The recent advance in SNP genotyping has made a significant contribution to reduction of the costs for large-scale genotyping. The development also has dramatically increased the size of the SNP genotype data. The increase of the volume of the data, however, has posed a huge obstacle to the conventional analysis techniques that are typically vulnerable to the high-dimensionality problem. To address the issue, we propose a method that exploits two well-tested models: the document-term model and the transaction analysis model. The proposed method consists of two phases. In the first phase, we reduce the dimensions of the SNP genotype data by extracting significant SNPs through transformation of the data in lieu of the document-term model. In the second phase, we discover the association rules that signify the relations between the SNPs and the traits, through the application of the transactional analysis in the reduced-dimension genotype data. We validated the discovered rules through the literature survey. Experiments were also carried out using the HGDP panel data provided by the Foundation Jean Dausset-CEPH, which prove the validity of our new method for identifying appropriate dimensional reduction and associations of multiple SNPs and traits.

关键词： Association rules Data models Analytical models Diseases Asia Context

来源：评论

学校读者我要写书评

暂无评论

FISH: Finding of identical spectra set for Homogenous peptide using two-stage clustering algorithm

FISH: Finding of identical spectra set for Homogenous peptid...

引用

IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Seungmook Lee Min-Seok Kwon Hyoung-Joo Lee Young-Ki Paik Jae K. Lee Taesung Park Department of Statistics and Interdisciplinary program in Bioinformatics Seoul National University South Korea Interdisciplinary program in Bioinformatics Seoul National University South Korea Department of Biochemistry Yonsei Proteome Research Center and Biomedical Proteome Research Center Yonsei University South Korea Department of Public Health Sciences Division of Biostatistics University of Virginia School of Medicine USA

MS/MS experiments generate hundreds to tens of thousands of fragment ion spectra during the experiment. In the peptide identification, MS/MS spectra are often identified by database searching algorithms such as SEQUEST and Mascot. Most database searching algorithms calculate score functions to compare the experimental MS/MS spectra with theoretical MS/MS spectra of certain peptides derived from protein sequence databases. However, these indirect methods are vulnerable to potential errors. Thus, some spectra may not be assigned to peptides. To overcome these limitations, we propose a novel algorithm called Finding Identical Spectra for Homogenous peptide (FISH) by using two-stage clustering algorithm. Our proposed FISH algorithm can cluster spectra from the same peptide as a group based on the direct comparison. That is, through all possible pair-wise comparisons, our FISH method provides a set of spectra from the same peptide. To investigate the efficiency of our proposed method, we performed Nano-LC-MS/MS experiment for human tissue samples. Also, we conducted the simulation study to compare the performance of our proposed method with other database searching methods. Our simulation study showed that FISH yielded higher sensitivity than the other methods.

关键词： Peptides Databases Marine animals Proteomics Ions Proteins Correlation

来源：评论

学校读者我要写书评

暂无评论

Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context

Dynamic and static analysis of transcriptional regulatory ne...

引用

IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Nitin Bhardwaj Mark Gerstein Program in Computational Biology and Bioinformatics Yale University New Heaven CT USA Department of Computer Science Yale University New Heaven CT USA

Gene regulatory networks have been shown to share some common aspects with commonplace social governance structures such as hierarchies. Thus, we can get some intuition into their organization by arranging them into well-known hierarchical layouts. Here we study a wide range of regulatory networks (transcriptional, modification and phosphorylation) in a hierarchical context for five evolutionarily diverse species. We specify three levels of regulators - top, middle and bottom - which collectively regulate the non-regulator targets lying in the lowest fourth level, and we define quantities for nodes, levels and entire networks that measure their degree of collaboration and autocratic or democratic character. Overall we show that in all the networks studied, the middle level has the highest collaborative propensity and that co-regulatory partnerships occur most frequently amongst mid-level regulators, an observation that has parallels in efficient corporate settings where middle managers need to interact most to ensure organizational effectiveness. Then to study dynamic effects, superimpose the phenotypic effects of tampering with nodes and edges directly onto the hierarchies. We reconstruct modified hierarchies reflecting changes in the level of regulators within the hierarchy upon deletions or insertions of nodes or edges. Overall, we find that rewiring events that affect upper levels have a more dramatic effect on cell proliferation rate and survival than do those involving lower levels. We also investigate other features connected to the importance of upper-level regulators: expression divergence, back-up copies and expression level.

关键词： Regulators Collaboration Context bioinformatics Biochemistry Molecular biophysics Performance analysis

来源：评论

学校读者我要写书评

暂无评论

Geometric order in proliferating epithelia: Impact of rearrangements and cleavage plane orientation

Geometric order in proliferating epithelia: Impact of rearra...

引用

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

作者： Hammad Naveed Yinzi Li Sema Kachalo Jie Liang Bioinformatics Program Department of Bio-Engineering University of Illinois Chicago Chicago IL USA Department of Biomedical Engineering Shanghai Jiaotong University Shanghai China

Regulation of proliferation is required for normal development of tissues and prevention of cancer formation. Continuous control of proliferation leads to regular shaped cells forming characteristic tissue patterns. Epithelial tissues serve as a model system for studying tissue morphogenesis. Several groups have studied epithelial morphogenesis using topological or geometric models, with various assumptions. In this study, we have developed a method to simulate the dynamic process of proliferating epithelia using an off-lattice cellular model. Our method realistically models the shape, size, geometry, lineage, cleavage plane orientation as well as topological properties of individual cells. We find that cellular rearrangements and cleavage plane orientation are critical in the formation of the observed cellular pattern of epithelia, including a high percentage of hexagons in proliferating epithelial cells. It is likely that the rearrangements and orientation of the cleavage plane reduces the overall stress on the cell. We show that a high percentage of hexagons in proliferating epithelia can be obtained using uniform growth rates, which was considered unlikely in previous studies. Our off-lattice cellular model provides an improvement over existing topological for studying the dynamics of proliferating epithelium.

关键词： Shape Stress Force USA Councils Epidermis bioinformatics Geometry

来源：评论

学校读者我要写书评

暂无评论

The keyword-based and semantic-driven data matching approach for assisting structuralizing the textual clinical documents

The keyword-based and semantic-driven data matching approach...

引用

International Conference on Biomedical Engineering and Informatics

作者： Chen, Chi-Huang Ping, Xiao-Ou Wang, Zi-Jun Hsieh, Sheau-Ling Chen, Li-Chin Tseng, Yi-Ju Hsu, Ching-Wei Lai, Feipei Department of Electrical Engineering National Taiwan University Taipei Taiwan Graduate Institute of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronic and Bioinformatics National Taiwan University Taipei Taiwan EECS International Graduate Program Institute/IT Center National Chiao Tung University Hsinchu Taiwan

ISBN: (纸本)9781424464968

The clinical data stored in the health information system can be categorized as two types including structuralized data and non-structuralized ones. In the paper, a data extraction system is developed to assist data retrieval from the non-structuralized textual clinical documents such as radiology reports, pathology reports, etc. The system provides keyword-based and semantic-driven data matching methodology to extract the specific information from the textual clinical documents. The matching methodology provides the capabilities to recognize the selected keywords and the related semantics in the documents. Through the extraction verification interface, clinicians can extract and verify the matched information semi-automatically. The extracted data can be filled into predefined case-oriented templates. The structuralized data can be stored back into the clinical data warehouse for further analyzing. Moreover, the case-oriented templates can support collecting corresponding extracted data for various researches. ©2010 IEEE.

关键词： Semantics

来源：评论

学校读者我要写书评

暂无评论

PS2-108. Infection with Hepatitis C down-regulates the expression of cytokine genes in peripheral blood

引用

Cytokine 2011年第1期56卷 94-94页

作者： Milton W. Taylor Christopher R. Bolen Steven H. Kleinstein Leonid Brodsky Department of Biology Indiana University Bloomington IN 47401 USA 1Interdepartmental Program in Computational Biology and Bioinformatics Yale University 300 George St. Suite 501 New Haven CT 06511 USA Department of Pathology Yale University School of Medicine New Haven CT USA Institute of Evolution University of Haifa Mount Carmel Haifa 31905 Israel

来源：评论

学校读者我要写书评

暂无评论

KAREBrowser: SNP database of Korea Association REsource project

KAREBrowser: SNP database of Korea Association REsource proj...

引用

IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Chang Bum Hong Young Jin Kim Sanghoon Moon Young-Ah Shin Yoon Shin Cho Jong-Young Lee Division of Structural and functional Genomics Center for Genome Science National Institute of Health Seoul South Korea Interdisciplinary Program in bioinformatics Seoul National University Seoul South Korea

International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information for the public. However, these kinds of information available from HapMap and HGDP are limited mainly due to the small size of samples in both databases. Recently we conducted genome-wide association study (GWAS) with 8,842 Korean subjects (Cho et al., Nature Genetics 2009). In an effort to build a publicly available browsing system for genome data resulted from our large scale GWAS, we developed the browser, namely Korea Association REsource (KARE) browser. This browser provides users with a large scale of single nucleotide polymorphisms (SNP) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse) that is a web-based application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://***/karebrowser/.

关键词： bioinformatics Genomics Databases Browsers Couplings Humans

来源：评论

学校读者我要写书评

暂无评论

Erratum to: triple-negative, basal-like, and quintuple-negative breast cancers: better prediction model for survival

引用

BMC Cancer 2011年第1期11卷 1-2页

作者： Yoon-La Choi Eun Yoon Cho Ensel Oh Kyug Song Young Kee Shin Sarah Park Yeonju Kim Yeon-Hee Park Young-Hyuck Lim Yun-Chul Hong Jong Sun Choi Jeong Eon Lee Jung Han Kim Seok Jin Nam Jung-Hyun Yang Laboratory of Cancer Genomics and Molecular Pathology South Korea Department of Pathology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul South Korea Research Institute of Pharmaceutical Science South Korea Interdiciplinary Program of Bioinformatics Department of Pharmacy Seoul National University College of Pharmacy Seoul South Korea Division of Medical Oncology Department of Internal Medicine Seoul St. Mary's hospital Catholic University Seoul South Korea Cancer Early Detection Branch National Cancer Control Research Institute National Cancer Center Goyang South Korea Department of Internal Medicine Samsung Medical Center Sungkyunkwan University School of Medicine Seoul South Korea Department of Preventive Medicine Seoul National University College of Medicine Seoul South Korea Department of Pathology Dongguk University Ilsan Hospital Dongguk University College of Medicine Goyang South Korea Department of Surgery Samsung Medical Center Sungkyunkwan University School of Medicine Seoul South Korea

来源：评论

学校读者我要写书评

暂无评论

BioSMACK: A linux Live CD for analysis of genome-wide association

BioSMACK: A linux Live CD for analysis of genome-wide associ...

引用

IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Chang Bum Hong Young Jin Kim Sanghoon Moon Young-Ah Shin Min Jin Go Jong-Young Lee Yoon Shin Cho Division of Structural and functional Genomics Center for Genome Science National Institute of Health Seoul South Korea Interdisciplinary Program in bioinformatics Seoul National University Seoul South Korea

Recent advancement of high-throughput genotyping technologies has enabled us to carry out a genome-wide association study (GWAS) in a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNP) is still a troublesome task for researchers to encounter in conducting GWAS. Several difficulties in using analysis tools are one of the major challenges for researchers such as compatibility and dependencies during installation process of softwares. This is a huge obstacle to research institute without computing facilities and specialists. Thus proper research environment is an urgent demand for researchers working on GWAS. We developed BioSMACK to provide research environment for GWAS with no configuration and easy usage. BioSMACK is based on Ubuntu Live CD that offers complete linux-based operating system environment without installation. Moreover, we provide users with GWAS manual that is consist of series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://***/biosmack.

关键词： bioinformatics Genomics Linux Metals Operating systems Manuals

来源：评论

学校读者我要写书评

暂无评论

cuGWAM: Genome-wide association multifactor dimensionality reduction using CUDA-enabled high-performance graphics processing unit

cuGWAM: Genome-wide association multifactor dimensionality r...

引用

IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Min-Seok Kwon Kyunga Kim Sungyoung Lee Taesung Park Interdisciplinary program in Bioinformatics Seoul National University South Korea Department of Statistics Seoul National University South Korea Department of statistics Seoul National University South Korea

Multifactor dimensionality reduction (MDR) method has been widely applied to detect gene-gene interactions that are well recognized as playing an important role in understanding complex traits, such as disease susceptibility. However, because of an exhaustive analysis of MDR, the current MDR software has some limitations to be extended to the genome-wide association studies (GWAS) with a large number of genetic markers up to ~1 million. To overcome this computational problem, we developed CUDA based genome-wide association MDR (cuGWAM) software using efficient hardware accelerators. Not only cuGWAM has better performance than CPU-based MDR methods (original MDR and parallel MDR) and GPU-based other methods (MDRGPU), but also initial construction cost is also less expensive. Furthermore, cuGWAM provides various performance measures to evaluate MDR classifiers, including tau-b, likelihood ratio, normalized mutual information as well as balanced accuracy. Also, cuGWAM provided three methods for handling missing genotypes: complete, available and missing category. Executable cuGWAM are freely available at http://***/cugwam for system with CUDA-enabled GPU devices.

关键词： Graphics processing unit bioinformatics Genomics Performance evaluation Classification algorithms Graphics Instruction sets

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：