检索结果-内蒙古大学图书馆

亚洲晶体学联合大会

作者： Yu-Yuan Hsiao Lyudmila G.Doudeva Hanna S.Yuan Institute of Molecular Biology Academia Sinica Institute of Bioinformatics and Structural Biology National Tsing Hua University Graduate Institute of Biochemistry and Molecular Biology National Taiwan University Taiwan Institute of Chemical Biology and Molecular Biophysics Taiwan International Graduate ProgramAcademia Sinica

Rrp46 is one of the RNase PH family proteins, first identified as a component protein of the eukaryotic exosome, a protein complex involved in RNA turnover, surveillance and processing. The Rrp46 homolog, CRN-5, was s... 详细信息

关键词： DNase Dual functions of an exosome component protein Rrp46/CRN-5 in RNA degradation and DNA fragmentation DNA exosome RNA

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

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

引用

Standards in genomic sciences 2010年第3期3卷 259-66页

作者： Carsten Kettner Dawn Field Susanna-Assunta Sansone Chris Taylor Jan Aerts Nigel Binns Andrew Blake Cedrik M Britten Ario de Marco Jennifer Fostel Pascale Gaudet Alejandra González-Beltrán Nigel Hardy Jan Hellemans Henning Hermjakob Nick Juty Jim Leebens-Mack Eamonn Maguire Steffen Neumann Sandra Orchard Helen Parkinson William Piel Shoba Ranganathan Philippe Rocca-Serra Annapaola Santarsiero David Shotton Peter Sterk Andreas Untergasser Patricia L Whetzel Beilstein-Institut Frankfurt am Main Germany Centre for Ecology & Hydrology UK Oxford e-Research Centre University of Oxford UK The European Bioinformatics Institute (EBI) UK Faculty of Engineering - ESAT/SCD Leuven University Leuven-Heverlee Belgium Division of Pathway Medicine University of Edinburgh Medical School Edinburgh UK MRC Harwell UK Medical Department University Medical Center Johannes Gutenberg University-Mainz Mainz Germany Consortium for Genomic Technology Milano Italy University of Nova Gorica Nova Gorica Slovenia NIEHS NIH US National Toxicology Program USA Swiss Institute of Bioinformatics Geneva Switzerland Computational and Systems Medicine and Department of Computer Science University College London London UK Department of Computer Science Aberystwyth University Aberystwyth UK Center for Medical Genetics Ghent University Ghent Belgium Department of Plant Biology University of Georgia Athens USA Department of Stress- and Developmental Biology Institute for Plant Biochemistry Halle Germany Peabody Museum of Natural History Yale University New Haven USA Macquarie University Sydney Australia National University of Singapore Singapore Cancer Pharmacology The Mario Negri Institute for Pharmacological Research Milan Italy Image Bioinformatics Research Group Department of Zoology University of Oxford Oxford UK Wellcome Trust Sanger Institute UK Zentrum für Molekulare Biologie der Universität Heidelberg Heidelberg Germany The National Center for Biomedical Ontology / Stanford Center for Biomedical Informatics Research Stanford University Stanford USA

This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://***/.

关键词： Minimum Information European bioinformatics Institute Biomedical Ontology Stable Link Breakout Group

来源：评论

学校读者我要写书评

暂无评论

Erratum to: An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

引用

BMC Research Notes 2009年第1期2卷 1-2页

作者： Rajkumar Sasidharan Ashish Agarwal Joel Rozowsky Mark Gerstein Molecular Biophysics and Biochemistry Department Yale University New Haven CT 06520 USA Department of Plant Biology Carnegie Institution for Science Stanford California 94305 USA Interdepartmental Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA Department of Computer Science Yale University New Haven CT 06520 USA

We are correcting the abstract of our published article ([1]). The sentence that starts "We observe that 4.5% of MPSS tags...." was not scientifically complete in the original abstract, having only two of the four numbers required to describe a comparison of two technologies in two different organisms. The abstract below more accurately describes our findings, as documented in Figure 1 of the manuscript.

关键词：

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

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: The anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity

引用

BMC Genomics 2009年第1期10卷 480-480页

作者： Liu, Yuen-Jong Zheng, Deyou Balasubramanian, Suganthi Carriero, Nicholas Khurana, Ekta Robilotto, Rebecca Gerstein, Mark B. Department of Surgery Beth Israel Deaconess Medical Center Harvard Medical School Boston MA 110 Francis Street United States Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 P.O. Box 208114 United States Albert Einstein College of Medicine of Yeshiva University Department of Neurology Rose F. Kennedy Center Bronx NY 10461 1410 Pelham Parkway South United States Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 United States Department of Computer Science Yale University New Haven CT 06520 Bass 432 266 Whitney Avenue United States

Background: Pseudogenes provide a record of the molecular evolution of genes. As glycolysis is such a highly conserved and fundamental metabolic pathway, the pseudogenes of glycolytic enzymes comprise a standardized genomic measuring stick and an ideal platform for studying molecular evolution. One of the glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has already been noted to have one of the largest numbers of associated pseudogenes, among all proteins. Results: We assembled the first comprehensive catalog of the processed and duplicated pseudogenes of glycolytic enzymes in many vertebrate model-organism genomes, including human, chimpanzee, mouse, rat, chicken, zebrafish, pufferfish, fruitfly, and worm (available at http://***/glycolysis/). We found that glycolytic pseudogenes are predominantly processed, i.e. retrotransposed from the mRNA of their parent genes. Although each glycolytic enzyme plays a unique role, GAPDH has by far the most pseudogenes, perhaps reflecting its large number of non-glycolytic functions or its possession of a particularly retrotranspositionally active sub-sequence. Furthermore, the number of GAPDH pseudogenes varies significantly among the genomes we studied: none in zebrafish, pufferfish, fruitfly, and worm, 1 in chicken, 50 in chimpanzee, 62 in human, 331 in mouse, and 364 in rat. Next, we developed a simple method of identifying conserved syntenic blocks (consistently applicable to the wide range of organisms in the study) by using orthologous genes as anchors delimiting a conserved block between a pair of genomes. This approach showed that few glycolytic pseudogenes are shared between primate and rodent lineages. Finally, by estimating pseudogene ages using Kimura's two-parameter model of nucleotide substitution, we found evidence for bursts of retrotranspositional activity approximately 42, 36, and 26 million years ago in the human, mouse, and rat lineages, respectively. Conclusion: Overall, we pe

关键词： Glycolytic Enzyme Segmental Duplication Chimpanzee Genome Assembly Version ENSEMBL Release

来源：评论

学校读者我要写书评

暂无评论

On codeword design in metric DNA spaces

引用

Natural Computing 2008年第3期8卷 571-588页

作者： Vinhthuy Phan Max H. Garzon Department of Computer Science and the Bioinformatics Program University of Memphis Memphis USA

Finding a large set of single DNA strands that do not crosshybridize to themselves and/or to their complements is an important problem in DNA computing, self-assembly, and DNA memories. We describe a theoretical framework to analyze this problem, gauge its computational difficulty, and provide nearly optimal solutions. In this framework, codeword design is reduced to finding large sets of strands maximaly separated in a DNA space and the size of such sets depends on the geometry of these metric spaces. We show that codeword design is NP-complete using any single reasonable measure that approximates the Gibbs energy, thus practically excluding the possibility of finding any procedure to find maximal sets efficiently. Second, we extend a technique known as shuffling to provide a construction that yields provably nearly-maximal codes. Third, we propose a filtering process that removes strands creating pairs with low Gibbs energies, as approximated by the nearest-neighbor model. These two steps produce large codes of thermodynamic high quality. The proposed framework can be used to gain an understanding of the Gibbs energy landscapes for DNA strands on which much of DNA computing and self-assembly are based.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Glycans on influenza hemagglutinin affect receptor binding and immune response

引用

Proceedings of the National Academy of Sciences of the United States of America 2009年第43期106卷 18137-18142页

作者： Wang, Cheng-Chi Chen, Juine-Ruey Tseng, Yung-Chieh Hsu, Che-Hsiung Hung, Yu-Fu Chen, Shih-Wei Chen, Chin-Mei Khoo, Kay-Hooi Cheng, Ting-Jen Cheng, Yih-Shyun E. Jan, Jia-Tsrong Wu, Chung-Yi Ma, Che Wong, Chi-Huey Genomics Research Center Taipei 115 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 106 Taiwan Institute of Biochemistry and Molecular Biology National Yang-Ming University Taipei 112 Taiwan Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Taipei 115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu 300 Taiwan Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan

Recent cases of avian influenza H5N1 and the swine-origin 2009 H1N1 have caused a great concern that a global disaster like the 1918 influenza pandemic may occur again. Viral transmission begins with a critical interaction between hemagglutinin (HA) glycoprotein, which is on the viral coat of influenza, and sialic acid (SA) containing glycans, which are on the host cell surface. To elucidate the role of HA glycosylation in this important interaction, various defined HA glycoforms were prepared, and their binding affinity and specificity were studied by using a synthetic SA microarray. Truncation of the N-glycan structures on HA increased SA binding affinities while decreasing specificity toward disparate SA ligands. The contribution of each monosaccharide and sulfate group within SA ligand structures to HA binding energy was quantitatively dissected. It was found that the sulfate group adds nearly 100-fold (2.04 kcal/mol) in binding energy to fully glycosylated HA, and so does the biantennary glycan to the monoglycosylated HA glycoform. Antibodies raised against HA protein bearing only a single N-linked GlcNAc at each glycosylation site showed better binding affinity and neutralization activity against influenza subtypes than the fully glycosylated HAs elicited. Thus, removal of structurally nonessential glycans on viral surface glycoproteins may be a very effective and general approach for vaccine design against influenza and other human viruses.

关键词： Flu vaccine Glycan binding Glycosylation

来源：评论

学校读者我要写书评

暂无评论

Microfluidic assembly blocks

Microfluidic assembly blocks

引用

12th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2008

作者： Rhee, Minsoung Burns, Mark A. Department of Chemical Engineering University of Michigan United States Bioinformatics Program University of Michigan United States Department of Biomedical Engineering University of Michigan United States

The use of microfluidic systems in the life sciences is still limited due to the high-level fabrication expertise required for construction. A novel assembly approach for microdevice construction is presented. This approach involves prefabrication of in-dividual "microfluidic assembly blocks" in PDMS that can be readily assembled on plain glass slides to form microfluidic systems in minutes by non-expert users. We describe the prefabrication of various blocks and the hermetic assembly of microflui-dic devices using the MAB methodology. Finally, we demonstrate common micro-fluidic applications including laminar flow development, valve control, and cell cul-ture. © 2008 CBMS.

关键词： Fabrication

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：