Statistical genomics is a rapidly developing field, with more and more people involved in this area. However, a lack of synthetic reference books and textbooks in statistical genomics has become a major hurdle on the development of the field. Although many books have been published recently in bioinformatics, most of them emphasize DNA sequence analysis under a deterministic approach. Principles of Statistical Genomics synthesizes the state-of-the-art statistical methodologies (stochastic approaches) applied to genome study. It facilitates understanding of the statistical models and methods behind the major bioinformatics software packages, which will help researchers choose the optimal algorithm to analyze their data and better interpret the results of their analyses. Understanding existing statistical models and algorithms assists researchers to develop improved statistical methods to extract maximum information from their data. Resourceful and easy to use, Principles of Statistical Genomics is a comprehensive reference for researchers and graduate students studying statistical genomics.

Transcriptome Analysis, by Frank Stahl, Bernd Hitzmann, Kai Mutz, Daniel Landgrebe, Miriam Lubbecke, Cornelia Kasper, Johanna Walter und Thomas Scheper Transcriptome Data Analysis for Cell Culture Processes, by Marlene Castro-Melchor, Huong Le und Wei-Shou Hu Modeling Metabolic Networks for Mammalian Cell Systems: General Considerations, Modeling Strategies, and Available Tools, by Ziomara P. Gerdtzen Metabolic Flux Analysis in Systems Biology of Mammalian Cells, by Jens Niklas und Elmar Heinzle Advancing Biopharmaceutical Process Development by System-Level Data Analysis and Integration of Omics Data, by Jochen Schaub, Christoph Clemens, Hitto Kaufmann und Torsten W. Schulz Protein Glycosylation and Its Impact on Biotechnology, by Markus Berger, Matthias Kaup und Veronique Blanchard Protein Glycosylation Control in Mammalian Cell Culture: Past Precedents and Contemporary Prospects, by Patrick Hossler Modeling of Intracellular Transport and Compartmentation, by Uwe Jandt und An-Ping Zeng Genetic Aspects of Cell Line Development from a Synthetic Biology Perspective, by L. Botezatu, S. Sievers, L. Gama-Norton, R. Schucht, H. Hauser und D. Wirth."

This book describes how genomics has revolutionized our scientific understanding of agriculturally important plant-associated bacteria. Each chapter focuses on the genomics of particular bacteria: the first described plant pathogen, "Erwinia amylovora"; phytoplasmas lacking cell walls; fastidious, phloem-restricted liberibacters; "Pseudomonas syringae," which is a genetically tractable model system; "Xanthomonas citri," which causes a disease that can devastate citrus crops and "Pseudomonas fluorescens," which can protect plants from diseases.

Topics considered in this volume include the importance of horizontal gene transfer in originating new bacterial strains and species and advances in transcriptomics that allow us to describe the complex regulatory networks critical to plant-microbe interactions. The availability of the "Xanthomonas oryzae" genome has led to new technologies in genome editing, which will revolutionize approaches to genetic engineering, even in eukaryotes. The contributions show how genomics has greatly accelerated progress toward understanding the biology of these bacteria and how that understanding can be translated into novel crop protection methods.

Innate DNA and RNA Recognition: Method and Protocols presents validated experimental strategies to dissect nucleic acid sensing in-vitro and in-vivo sources. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Innate DNA and RNA Recognition: Method and Protocols provides a resource for immunologists, molecular biologists, virologists, microbiologists, and researchers studying how the innate immune system handles nucleic acids from endogenous or foreign sources.

In this timely new 2-volume treatise, experts from around the world have banded together to produce a first-of-its-kind synopsis of the exciting and fast moving field of plant evolutionary genomics. In Volume I of Plant Genome Diversity, an update is provided on what we have learned from plant genome sequencing projects. This is followed by more focused chapters on the various genomic "residents" of plant genomes, including transposable elements, centromeres, small RNAs, and the evolutionary dynamics of genes and non-coding sequences. Attention is drawn to advances in our understanding of plant mitochondrial and plastid genomes, as well as the significance of duplication in genic evolution and the non-independent evolution among sequences in plant genomes. Finally, Volume I provides an introduction to the vibrant new frontier of plant epigenomics, describing the current state of our knowledge and the evolutionary implications of the epigenomic landscape.

In 2001, first reports of the human draft genome were published. Since then, genomes of many other organisms have been sequenced, including several primate species: the chimpanzee, rhesus macaque, gorilla, orangutan, gibbon, baboon, marmoset, tarsier, galago, lemur, and more recently Neanderthals. In a new era of "post-genome biology", scientists now have the vast amount of information revealed by genome research to confront one of the most challenging, fundamental questions in primatology and anthropology: What makes us human? This volume comprises a collection of articles on a variety of topics relevant to primate genomes, including evolution, human origins, genome structure, chromosome genomics, and bioinformatics. The book covers the cutting-edge research in molecular primatology and provides great insights into the functional diversity of primates. This valuable collection will benefit researchers and students, including primatologists, anthropologists, molecular biologists, evolutionary biologists, and animal behaviorists.

Structural Genomics and Drug Discovery: Methods and Protocols focuses on high throughput structure determination methods and how they can be applied to lay the groundwork for structure aided drug discovery. The methods and protocols that are described can be applied in any laboratory interested in using detailed structural information to advance the initial stages of drug discovery. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Structural Genomics and Drug Discovery: Methods and Protocols seeks to aid scientists in the further study into structural genomics approach as an efficient initial step toward drug discovery and the methods described will be useful to anyone interested in moving in this direction.

In DNA Cloning and Assembly Methods, expert researchers in the field detail many of the methods which are now commonly used for DNA cloning and make cloning procedures faster, more reliable and also suitable for high-throughput handling. These include methods and protocols that are based on several mechanisms including type II and IIS restriction enzymes, single stranded annealing, sequence overlap, and recombination. With additional chapters on software programs that are suitable for primer design, a feature crucial for the functionality of the described methods. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, DNA Cloning and Assembly Methods seeks to provide scientist with a valuable and useful resource for wet lab researchers within life sciences.

The application of modern genomic approaches to research on halophilic Archaea and Bacteria and their viruses in recent years has yielded fascinating insights into the adaptations and evolution of these unique organisms. This book highlights current genetics and genomics research to provide a timely overview.

This book provides a broad introduction to all major aspects of quantum dot properties including fluorescence, electrochemical, photochemical and electroluminescence. Such properties have been produced for applications in biosensing, cell tracking, in vivo animal imaging and so on. It focuses on their special applications in DNA biosensing and provides readers with detailed information on the preparation and functionalization of quantum dots and the fabrication of DNA biosensors, using examples to show how these properties can be used in DNA biosensor design and the advantages of quantum dots in DNA biosensing. Further new emerging quantum dots such as metal nanoclusters and graphene dots and their applications in DNA biosensing have also been included.

While there has been an increasing number of books on various aspects of epigenetics, there has been a gap over the years in books that provide a comprehensive understanding of the fundamentals of chromatin. Chromatin is the combination of DNA and proteins that make up the genetic material of chromosomes. Its primary function is to package DNA to fit into the cell, to strengthen the DNA to prevent damage, to allow mitosis and meiosis, and to control the expression of genes and DNA replication. The audience for this book is mainly newly established scientists and graduate students. Rather than going into the more specific areas of recent research on chromatin the chapters in this book give a strong, updated groundwork about the topic. Some the fundamentals that this book will cover include the structure of chromatin and biochemistry and the enzyme complexes that manage it.

In the past four years, many genetic loci have been implicated for BMI from the outcomes of genome-wide association studies (GWAS), primarily in adults. Insulin-induced gene 2 (INSIG2) was the first locus to be reported by this method to have a role in obesity but replication attempts have yielded inconsistent outcomes. The identification of the second locus, the fat mass- and obesity-associated gene (FTO), h has been more robustly observed by others. Studies from both FTO knock out and FTO overexpression mouse model support the fact that FTO is directly involved in the regulation of energy intake and metabolism in mice, where the lack of FTO expression leads to leanness while enhanced expression of FTO leads to obesity. Along with numerous other studies, a number of genetic variants have been established robustly in the context of obesity, giving us fresh insights into the pathogenesis of the disease. This book will give a comprehensive overview of efforts aimed at uncovering genetic variants associated with obesity, which have been particularly successful in the past 5 years with the advent of genome-wide association studies (GWAS). This book will cover this state of the art technology and its application to obesity in great detail. Topics covered will include genetics of childhood obesity, genetics of syndromic obesity, copy number variants and extreme obesity, co-morbidities of obesity genetics, and functional follow-up of genetic variants. "

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."

Burkholderia are a multi-faceted group of bacteria with considerable genetic and metabolic diversity and very versatile lifestyles. In this book leading international investigators review key advances in Burkholderia research to provide timely overview. The topics covered include: genomic taxonomy and biodiversity, comparative genomics, molecular epidemiology, transcriptomics, proteomics, molecular pathogenesis of virulence in B. mallei/B. pseudomallei and the Burkholderia cepacia complex. The theme underpinning each chapter is the use of DNA/protein sequence data and post-genomic technologies to understand Burkholderia biology.

Fingerprints have provided a valuable method of personal identification in forensic science and criminal investigations for over 100 years. Fingerprints left at crime scenes generally are latent prints -- unintentional reproductions of the arrangement of ridges on the skin made by the transfer of materials (such as amino acids, proteins, polypeptides, and salts) to a surface. Palms and the soles of feet also have friction ridge skin that can leave latent prints. The examination of a latent print consists of a series of steps involving a comparison of the latent print to a known (or exemplar) print. Courts have accepted latent print evidence for the past century. However, several high-profile cases in the United States and abroad have highlighted the fact that human errors can occur, and litigation and expressions of concern over the evidentiary reliability of latent print examinations and other forensic identification procedures has increased in the last decade. This book discusses latent print examinations in detail, and provides methods to improving the practice through a systems approach.

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Featuring current resources used to discover new legume family genes and to understand genes and their interactions, Legume Genomics: Methods and Protocols provides techniques from expert researchers to study these plants that are so vitally important for food, feed, human nutrition, bioenergy, and industrial purposes. This detailed volume covers genome characterization and analysis, transcriptome analysis and miRNA identification/analysis, forward and reverse genetics, molecular markers, as well as transformation strategies used to investigate gene function and many other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and useful, Legume Genomics: Methods and Protocols aims to serve plant molecular biologists, molecular breeders, plant physiologists and biochemists, developmental biologists, and those interested in plant-microbe interactions.

Quantitative Real-Time PCR: Methods and Protocols focuses on different applications of qPCR ranging from microbiological detections (both viral and bacterial) to pathological applications. Several chapters deal with quality issues which regard the quality of starting material, the knowledge of the minimal information required to both perform an assay and to set the experimental plan, while the others focus on translational medicine applications that are ordered following an approximate logical order of their medical application. The last part of the book gives you an idea of an emerging digital PCR technique that is a unique qPCR approach for measuring nucleic acid, particularly suited for low level detection and to develop non-invasive diagnosis. Written for the Methods in Molecular Biology series, most chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, Quantitative Real-Time PCR: Methods and Protocols aims to aid researchers seeking to devise new qPCR-based approaches related to his or her area of investigation.

In Tiling Arrays: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study tiling microarrays in genomic discovery . These include methods and applications for transcriptional regulation, expression, genetic and epigenetic regulation, as well as techniques and skills on tiling microarray data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Tiling Arrays: Methods and Protocols seeks to provide scientists with a comprehensive and down to earth approach to maximize results.

As imaging technologies and approaches have evolved, the scope of certain imaging techniques has moved far beyond the production of purely illustrative images or appealing time-lapse movies to providing the scientist with a rich range of ways to measure and quantify the biological process and outcome of gene expression. In Imaging Gene Expression: Methods and Protocols, expert authors offer up-to-date approaches and protocols that scientists in the field have developed, which would benefit the broader scientific community. Divided in three convenient parts, this detailed book covers the output of a gene, namely the RNA molecules that are transcribed from the gene and the way by which these molecules can be tracked or quantified in fixed or living cells, protocols that focus on the gene, DNA, or chromatin, as well as a variety of ways by which nuclear processes intertwined with gene expression can be followed and quantified in living cells as well as approaches for studying several sub-nuclear structures found in eukaryotic cells. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Imaging Gene Expression: Methods and Protocols will serve researchers working toward imaging in the context of complete organisms.

This volume provides an overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research.

This text explores the most recent advances in NGS instrumentation and data anlysis. It begins with a comprehensive description of current NSG platforms, their sequencing chemistries, instrument specifications, and general workflows and procedures. A separate chapter is dedicated to low-quanitity, single molecule sequencing technology. Further chapters explore the application of NSG technologies in various fields.

Transposable elements have played a major role in shaping plant genome structure and gene expression. Transposons not only drive sequence expansion, induce mutations and generate chromosome rearrangements, they also help to shape the epigenetic topology of the eukaryotic genome. In Plant Transposable Elements: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study transposons. These methods include computational approaches to study the ancient transposon remnants that comprise the bulk of plant genomes, as well as laboratory techniques to identify recent and ongoing transposition events. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Transposable Elements: Methods and Protocols seeks to aid scientists in the further study of transposons by providing essential background information and specific experimental protocols.

The sequencing of the human genome was a pivotal event in science that opened the door to exploring the structure and function of genes and their regulation. The activation or suppression of transcribed genes is critical to the orchestration of everyday biological processes at the cellular, tissue, and physiological levels. The rapid advance of science and technology has yielded the development of the microarray technique, which has propelled a much deeper understanding of the genome. By combining these technological advances in microarrays with statistical and bioinformatics software, investigators are now able to perform scientific investigations geared towards answering unique biological problems that encompass many fields of research from genetics and evolution to molecular medicine, health, and disease. This book provides an overview of the use and application of microarrays throughout the life sciences to address diverse complex biological questions. In this collection, authors present information on using microarrays to unlock molecular mechanisms and gene expression patterns associated with research areas ranging from biodefense, pathological changes, and monitoring antimicrobial resistance genes to diagnostics, marine biodiversity, and dermal toxicology.

This book provides an evolutionary conceptual framework for comparative genomics, with the ultimate objective of understanding the loss and gain of genes during evolution, the interactions among gene products, and the relationship between genotype, phenotype and the environment. The many examples in the book have been carefully chosen from primary research literature based on two criteria: their biological insight and their pedagogical merit. The phylogeny-based comparative methods, involving both continuous and discrete variables, often represent a stumbling block for many students entering the field of comparative genomics. They are numerically illustrated and explained in great detail. The book is intended for researchers new to the field, i.e., advanced undergraduate students, postgraduates and postdoctoral fellows, although professional researchers who are not in the area of comparative genomics will also find the book informative.