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Author: Matthias Dehmer Publisher: John Wiley & Sons ISBN: 9783527318223 Category : Medical Languages : en Pages : 448
Book Description
This book is the first to focus on the application of mathematical networks for analyzing microarray data. This method goes well beyond the standard clustering methods traditionally used. From the contents: * Understanding and Preprocessing Microarray Data * Clustering of Microarray Data * Reconstruction of the Yeast Cell Cycle by Partial Correlations of Higher Order * Bilayer Verification Algorithm * Probabilistic Boolean Networks as Models for Gene Regulation * Estimating Transcriptional Regulatory Networks by a Bayesian Network * Analysis of Therapeutic Compound Effects * Statistical Methods for Inference of Genetic Networks and Regulatory Modules * Identification of Genetic Networks by Structural Equations * Predicting Functional Modules Using Microarray and Protein Interaction Data * Integrating Results from Literature Mining and Microarray Experiments to Infer Gene Networks The book is for both, scientists using the technique as well as those developing new analysis techniques.
Author: Matthias Dehmer Publisher: John Wiley & Sons ISBN: 9783527318223 Category : Medical Languages : en Pages : 448
Book Description
This book is the first to focus on the application of mathematical networks for analyzing microarray data. This method goes well beyond the standard clustering methods traditionally used. From the contents: * Understanding and Preprocessing Microarray Data * Clustering of Microarray Data * Reconstruction of the Yeast Cell Cycle by Partial Correlations of Higher Order * Bilayer Verification Algorithm * Probabilistic Boolean Networks as Models for Gene Regulation * Estimating Transcriptional Regulatory Networks by a Bayesian Network * Analysis of Therapeutic Compound Effects * Statistical Methods for Inference of Genetic Networks and Regulatory Modules * Identification of Genetic Networks by Structural Equations * Predicting Functional Modules Using Microarray and Protein Interaction Data * Integrating Results from Literature Mining and Microarray Experiments to Infer Gene Networks The book is for both, scientists using the technique as well as those developing new analysis techniques.
Author: M. Francis Shannon Publisher: CRC Press ISBN: 1498713734 Category : Science Languages : en Pages : 149
Book Description
While every cell of an organism has an identical genomic content, extremely complex networks exist to tailor the genomic output to the needs of that cell. This program of gene expression is different for every cell type and stage of development. In addition, the cell can respond to its environment by modulating its gene expression program in a fairly dramatic manner. For many decades gene transcription has been investigated in systems from bacteria to mammalian cells and along the way many landmark findings have set new paradigms that often apply across wide evolutionary distances. Studying individual genes, however, especially in mammalian systems has been a painstaking business and although we know the transcription activators and other complexes that control specific genes in minute detail, generalizing these findings has often proven to be difficult. It has become clear that transcription factors do not operate alone but form complex networks in the cell. If one component of this complexity is disturbed then there are repercussions across the entire network, but it has been impossible to study these networks until very recently. The advent of microarray technology within the last decade has revolutionized how we study gene transcription. There are several types of array technology that essentially screen for relative mRNA levels for many thousands of genes at once. We do not focus here on the technology as this has become routine and is available to many researchers. Microarray technology has given us the ability to measure the entire gene expression program of a cell in a single experiment and compare it to other cells thus allowing a global view of cell behaviour at the level of gene transcription. Expression profiling, as this endeavour has become known, is now a relatively simple undertaking and hundreds, probably thousands of papers have been published demonstrating the power of this technology. Expression profiling has been applied to many diverse biological problems and is also being developed as a method for disease diagnosis especially in the cancer classification field. There are constant improvements or modified uses of the technology that are allowing more and more high throughput experiments to be carried out.
Author: Michael A. Savageau Publisher: CreateSpace ISBN: 9781449590765 Category : Biological control systems Languages : en Pages : 400
Book Description
The reductionist approach of molecular biology has given us detailed descriptions for many biochemical constituents of complex biological systems. For some of the simpler systems nearly the entire "parts catalog" has been assembled. These developments have set the stage for a new generation of questions -- questions of integration that deal with the relation between behavior of intact systems and their underlying molecular determinants, questions of unifying design principles that will give meaning to the bewildering diversity of alternative molecular designs, questions of higher-level theory and quantitative prediction, which currently are not available in most of biology. The motivation to develop this new perspective comes from the study of complex biochemical pathways, intricate circuits of gene regulation, network interactions within the immune system, plasticity of neural networks, and pattern formation by cellular networks. All these networks consist of more elemental constituents that find their meaning within the context of the intact system. The integrative perspective requires a new language and methodology. The objective of this text is to systematically develop these and to apply them to specific classes of metabolic networks and gene circuitry. The applications demonstrate the power of this approach to formulate and answer fundamental questions concerning network function, design and evolution that currently cannot be addressed by other methods. The text was first published in 1976 and is being reissued to commemorate the 40th anniversary of the author's first paper published on Biochemical Systems Analysis.
Author: Leif E. Peterson Publisher: John Wiley & Sons ISBN: 0470170816 Category : Computers Languages : en Pages : 752
Book Description
Wiley Series in Bioinformatics: Computational Techniques and Engineering Yi Pan and Albert Y. Zomaya, Series Editors Wide coverage of traditional unsupervised and supervised methods and newer contemporary approaches that help researchers handle the rapid growth of classification methods in DNA microarray studies Proliferating classification methods in DNA microarray studies have resulted in a body of information scattered throughout literature, conference proceedings, and elsewhere. This book unites many of these classification methods in a single volume. In addition to traditional statistical methods, it covers newer machine-learning approaches such as fuzzy methods, artificial neural networks, evolutionary-based genetic algorithms, support vector machines, swarm intelligence involving particle swarm optimization, and more. Classification Analysis of DNA Microarrays provides highly detailed pseudo-code and rich, graphical programming features, plus ready-to-run source code. Along with primary methods that include traditional and contemporary classification, it offers supplementary tools and data preparation routines for standardization and fuzzification; dimensional reduction via crisp and fuzzy c-means, PCA, and non-linear manifold learning; and computational linguistics via text analytics and n-gram analysis, recursive feature extraction during ANN, kernel-based methods, ensemble classifier fusion. This powerful new resource: Provides information on the use of classification analysis for DNA microarrays used for large-scale high-throughput transcriptional studies Serves as a historical repository of general use supervised classification methods as well as newer contemporary methods Brings the reader quickly up to speed on the various classification methods by implementing the programming pseudo-code and source code provided in the book Describes implementation methods that help shorten discovery times Classification Analysis of DNA Microarrays is useful for professionals and graduate students in computer science, bioinformatics, biostatistics, systems biology, and many related fields.
Author: Verónica Bolón-Canedo Publisher: Humana ISBN: 9781493994410 Category : Science Languages : en Pages : 299
Book Description
This book provides a comprehensive, interdisciplinary collection of the main, up-to-date methods, tools, and techniques for microarray data analysis, covering the necessary steps for the acquisition of the data, its preprocessing, and its posterior analysis. Featuring perspectives from biology, computer science, and statistics, the volume explores machine learning methods such as clustering, feature selection, classification, data normalization, and missing value imputation, as well as the statistical analysis of the data and the most popular computer tools to analyze microarray data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will aid researchers in getting successful results. Cutting-edge and authoritative, Microarray Bioinformatics serves as an ideal guide for researchers and graduate students in bioinformatics, with basic knowledge in biology and computer science, and with a view to work with microarray datasets.
Author: Uwe R. Müller Publisher: Springer Science & Business Media ISBN: 3540265783 Category : Medical Languages : en Pages : 388
Book Description
Ithasbeenstatedthatourknowledgedoublesevery20years,butthatmaybe an understatement when considering the Life Sciences. A series of discoveries and inventions have propelled our knowledge from the recognition that DNA isthegeneticmaterialtoabasicmolecularunderstandingofourselvesandthe living world around us in less than 50 years. Crucial to this rapid progress was thediscoveryofthedouble-helicalstructureofDNA,whichlaidthefoundation forallhybridizationbasedtechnologies. Thediscoveriesofrestrictionenzymes, ligases, polymerases, combined with key innovations in DNA synthesis and sequencing ushered in the era of biotechnologyas a new science with profound sociological and economic implications that are likely to have a dominating in?uence on the development of our society during this century. Given the process by which science builds on prior knowledge, it is perhaps unfair to single out a few inventions and credit them with having contributed most to thisavalancheofknowledge. Yet,therearesurelysomethatwillberecognized as having had a more profound impact than others, not just in the furthering of our scienti?c knowledge, but by leveraging commercial applications that provide a tangible return to our society. The now famous Polymerase Chain Reaction, or PCR, is surely one of those, as it has uniquely catalyzed molecular biology during the past 20 years, and continues to have a signi?cant impact on all areas that involve nucleic acids, ranging from molecular pathology to forensics. Ten years ago micro- ray technology emerged as a new and powerful tool to study nucleic acid - quences in a highly multiplexed manner, and has since found equally exciting and useful applications in the study of proteins, metabolites, toxins, viruses, whole cells and even tissues.
Author: Bor-Sen Chen Publisher: Academic Press ISBN: 0128173351 Category : Science Languages : en Pages : 673
Book Description
Systems Immunology and Infection Microbiology provides a large amount of biological system models, diagrams and flowcharts to illustrate development procedures and help users understand the results of systems immunology and infection microbiology. Chapters discuss systems immunology, systems infection microbiology, systematic inflammation and immune responses in restoration and regeneration process, systems' innate and adaptive immunity in infection process, systematic genetic and epigenetic pathogenic/defensive mechanism during bacterial infection on human cells is introduced, and the systematic genetic and epigenetic pathogenic/defensive mechanisms during viral infection on human cells. This book provides new big data-driven and systems-driven systems immunology and infection microbiology to researchers applying systems biology and bioinformatics in their work. It is also invaluable to several members of biomedical field who are interested in learning more about those approaches. - Encompasses one applicable example in every chapter to illustrate the solution procedure from big data mining, network modeling, host/pathogen cross-talk detection, drug target identification and systems drug design - Presents flowcharts to represent the development procedure of systematic immunology and infection in a very clear format - Contains 100 color diagrams to help readers understand the related biological networks, their corresponding mechanisms, and significant network biomarkers for therapeutic drug design
Author: Timothy D. Veenstra Publisher: John Wiley & Sons ISBN: 0470007737 Category : Science Languages : en Pages : 361
Book Description
Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.
Author: Timothy R. Hughes Publisher: Springer Science & Business Media ISBN: 904819069X Category : Medical Languages : en Pages : 310
Book Description
Transcription factors are the molecules that the cell uses to interpret the genome: they possess sequence-specific DNA-binding activity, and either directly or indirectly influence the transcription of genes. In aggregate, transcription factors control gene expression and genome organization, and play a pivotal role in many aspects of physiology and evolution. This book provides a reference for major aspects of transcription factor function, encompassing a general catalogue of known transcription factor classes, origins and evolution of specific transcription factor types, methods for studying transcription factor binding sites in vitro, in vivo, and in silico, and mechanisms of interaction with chromatin and RNA polymerase.
Author: Matthias Dehmer
Author: Matthias Dehmer
Author: M. Francis Shannon
Author: Michael A. Savageau
Author: Bernhard Schölkopf
Author: Leif E. Peterson
Author: Verónica Bolón-Canedo
Author: Uwe R. Müller
Author: Bor-Sen Chen
Author: Timothy D. Veenstra
Author: Timothy R. Hughes