EXS最新文献_第5页

Integrated data analysis for genome-wide research. 全基因组研究的综合数据分析。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_13

Matthias Steinfath, Dirk Repsilber, Matthias Scholz, Dirk Walther, Joachim Selbig

引用次数: 30

Case studies for transcriptional profiling. 转录分析的案例研究。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_4

Lars Hennig, Claudia Köhler

引用次数: 0

Regulatory small RNAs in plants. 植物中的调节小rna。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_5

Cameron Johnson, Venkatesan Sundaresan

{"title":"Regulatory small RNAs in plants.","authors":"Cameron Johnson, Venkatesan Sundaresan","doi":"10.1007/978-3-7643-7439-6_5","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_5","url":null,"abstract":"The discovery of microRNAs in the last decade altered the paradigm that protein coding genes are the only significant components for the regulation of gene networks. Within a short period of time small RNA systems within regulatory networks of eukaryotic cells have been uncovered that will ultimately change the way we infer gene regulation networks from transcriptional profiling data. Small RNAs are involved in the regulation of global activities of genic regions via chromatin states, as inhibitors of 'selfish' sequences (transposons, retroviruses), in establishment or maintenance of tissue/organ identity, and as modulators of the activity of transcription factor as well as 'house keeping' genes. With this chapter we provide an overview of the central aspects of small RNA function in plants and the features that distinguish the different small RNAs. We furthermore highlight the use of computational prediction methods for identification of plant miRNAs/precursors and their targets and provide examples for the experimental validation of small RNA candidates that could represent trans-regulators of downstream genes. Lastly, the emerging concepts of small RNAs as modulators of gene expression constituting systems networks within different cells in a multicellular organism are discussed.","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"99-113"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664721","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: 9

Methods, applications and concepts of metabolite profiling: primary metabolism. 代谢物谱分析的方法、应用和概念:初级代谢。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_8

Dirk Steinhauser, Joachim Kopka

{"title":"Methods, applications and concepts of metabolite profiling: primary metabolism.","authors":"Dirk Steinhauser, Joachim Kopka","doi":"10.1007/978-3-7643-7439-6_8","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_8","url":null,"abstract":"In the 1990s the concept of a comprehensive analysis of the metabolic complement in biological systems, termed metabolomics or alternately metabonomics, was established as the last of four cornerstones for phenotypic studies in the post-genomic era. With genomic, transcriptomic, and proteomic technologies in place and metabolomic phenotyping under rapid development all necessary tools appear to be available today for a fully functional assessment of biological phenomena at all major system levels of life. This chapter attempts to describe and discuss crucial steps of establishing and maintaining a gas chromatography/electron impact ionization/ mass spectrometry (GC-EI-MS)-based metabolite profiling platform. GC-EI-MS can be perceived as the first and exemplary profiling technology aimed at simultaneous and non-biased analysis of primary metabolites from biological samples. The potential and constraints of this profiling technology are among the best understood. Most problems are solved as well as pitfalls identified. Thus GC-EI-MS serves as an ideal example for students and scientists who intend to enter the field of metabolomics. This chapter will be biased towards GC-EI-MS analyses but aims at discussing general topics, such as experimental design, metabolite identification, quantification and data mining.","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"171-94"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-7643-7439-6_8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664610","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

Introduction to systems biology. 系统生物学导论。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_1

Frank J Bruggeman, Jorrit J Hornberg, Fred C Boogerd, Hans V Westerhoff

{"title":"Introduction to systems biology.","authors":"Frank J Bruggeman, Jorrit J Hornberg, Fred C Boogerd, Hans V Westerhoff","doi":"10.1007/978-3-7643-7439-6_1","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_1","url":null,"abstract":"The developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experimental data. Many different types of modeling approaches are useful depending on the amount and quality of the molecular data available and the purpose of the model. Analysis of such models and the structure of molecular networks have led to the discovery of principles of cell functioning overarching single species. Two main approaches of systems biology can be distinguished. Top-down systems biology is a method to characterize cells using system-wide data originating from the Omics in combination with modeling. Those models are often phenomenological but serve to discover new insights into the molecular network under study. Bottom-up systems biology does not start with data but with a detailed model of a molecular network on the basis of its molecular properties. In this approach, molecular networks can be quantitatively studied leading to predictive models that can be applied in drug design and optimization of product formation in bioengineering. In this chapter we introduce analysis of molecular network by use of models, the two approaches to systems biology, and we shall discuss a number of examples of recent successes in systems biology.","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"1-19"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-7643-7439-6_1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664717","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: 294

Natural and artificially induced genetic variability in crop and model plant species for plant systems biology. 植物系统生物学中作物和模式植物物种的自然和人工诱导遗传变异。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_2

Christophe Rothan, Mathilde Causse

引用次数: 13

Differential display and protein quantification. 差异显示和蛋白质定量。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_6

Erich Brunner, Bertran Gerrits, Mike Scott, Bernd Roschitzki

引用次数: 2

Network visualization and network analysis. 网络可视化和网络分析。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_11

Victoria J Nikiforova, Lothar Willmitzer

{"title":"Network visualization and network analysis.","authors":"Victoria J Nikiforova, Lothar Willmitzer","doi":"10.1007/978-3-7643-7439-6_11","DOIUrl":"https://doi.org/10.1007/978-3-7643-7439-6_11","url":null,"abstract":"Network analysis of living systems is an essential component of contemporary systems biology. It is targeted at assemblance of mutual dependences between interacting systems elements into an integrated view of whole-system functioning. In the following chapter we describe the existing classification of what is referred to as biological networks and show how complex interdependencies in biological systems can be represented in a simpler form of network graphs. Further structural analysis of the assembled biological network allows getting knowledge on the functioning of the entire biological system. Such aspects of network structure as connectivity of network elements and connectivity degree distribution, degree of node centralities, clustering coefficient, network diameter and average path length are touched. Networks are analyzed as static entities, or the dynamical behavior of underlying biological systems may be considered. The description of mathematical and computational approaches for determining the dynamics of regulatory networks is provided. Causality as another characteristic feature of a dynamically functioning biosystem can be also accessed in the reconstruction of biological networks; we give the examples of how this integration is accomplished. Further questions about network dynamics and evolution can be approached by means of network comparison. Network analysis gives rise to new global hypotheses on systems functionality and reductionist findings of novel molecular interactions, based on the reliability of network reconstructions, which has to be tested in the subsequent experiments. We provide a collection of useful links to be used for the analysis of biological networks.","PeriodicalId":77125,"journal":{"name":"EXS","volume":"97 ","pages":"245-75"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-7643-7439-6_11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26664613","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: 26

Transcriptional profiling approaches to understanding how plants regulate growth and defence: a case study illustrated by analysis of the role of vitamin C. 了解植物如何调节生长和防御的转录分析方法:通过分析维生素C的作用说明的案例研究。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_3

Christine H Foyer, Guy Kiddle, Paul Verrier

引用次数: 12

Protein identification using mass spectrometry: a method overview. 用质谱法鉴定蛋白质:方法概述。

EXS Pub Date : 2007-01-01 DOI: 10.1007/978-3-7643-7439-6_7

Sven Schuchardt, Albert Sickmann

引用次数: 25