Bioinformatics of Genome Regulation and Structure covers:

-regulatory genomic sequences: databases, knowledge bases, computer analysis, modeling, and recognition;
-large-scale genome analysis and functional annotation;
-gene structure detection and prediction;
-comparative and evolutionary genomics;
-computer analysis of genome polymorphism and evolution; computer analysis and modeling of transcription, splicing, and translation; structural computational biology: structure-function organization of genomic DNA, RNA, and proteins;
-gene networks, signal transduction pathways, and genetically controlled metabolic pathways: principles of organization, operation, and evolution;
-data warehousing, knowledge discovery and data mining; and,
-analysis of basic patterns of genome operation, organization, and evolution. The data presented may be used while solving a wide range of problems, both basic and applied, in various directions of molecular biology, molecular genetics, biotechnology, pharmacogenetics, pharmacology, and adjacent fields of medicine, veterinary, and agrobiology.

This unique introduction to the growing field of microfluidics applied to genomics provides an overview of the latest technologies and emphasizes its potential in answering important biological questions. Written by a physicist and a biologist, it offers a more comprehensive view than the previous literature. The book starts with key ideas in molecular biology, developmental biology and microtechnology before going on to cover the specifics of single cell analysis and microfluidic devices for single cell molecular analysis. Review chapters discuss the state-of-the art and will prove invaluable to all those planning to develop microdevices for molecular analysis of single cells. Methods allowing complete analysis of gene expression in the single cell are stressed - as opposed the more commonly used techniques that allow analysis of only a few genes at a time. As pioneers in the field, the authors understand how critical it is for a physicist to understand the biological issues and questions related to single cell analysis, as well for biologists to understand what microfluidics is all about. Aimed predominantly at graduate students, this book will also be of significant interest to scientists working in or affiliated with this field.

This volume contains 18 peer-reviewed papers based on the presentations at the 10th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2010) held at Kyoto University from July 26 to July 28, 2010. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs:

* Boston Graduate Program in Bioinformatics, Boston University

* Berlin The International Research Training Group (IRTG) "Genomics and Systems Biology of Molecular Networks"

* Kyoto The JSPS International Training Program (ITP) "International Research and Training Program of Bioinformatics and Systems Biology"

* Tokyo Global COE Program "Center of Education and Research for Advanced Genome-Based Medicine"

Bacterial Genomes provides an in-depth review of the latest research on the structure and stability of microbial genomes, and the techniques used to analyze and "fingerprint" them. Maps of a variety of microorganisms are featured, along with articles describing their construction and relevant features. Extensive tables summarizing the different types of techniques available to analyze the genomes of these microorganisms are also presented. Among those who will find this text most useful are genome researchers, microbiologists, molecular biologists, bacteriologists, infectious disease researchers, and molecular evolutionary biologists. Researchers and students working in the field of molecular evolution in general will also be interested in this book since microbes are such popular model systems.

The Genome Incorporated examines the proliferation of human genomics across contemporary media cultures. It explores questions about what it means for a technoscience to thoroughly saturate everyday life, and places the interrogation of the science/media relationship at the heart of this enquiry. The book develops a number of case studies in the mediation and consumption of genomics, including: the emergence of new direct-to-the-consumer bioinformatics companies; the mundane propagation of testing and genetic information through lifestyle television programming; and public and private engagements with art and science institutions and events. Through these novel sites, this book examines the proliferating circuits of production and consumption of genetic information and theorizes this as a process of incorporation. Its wide-ranging case studies ensure its appeal to readers across the social sciences.

This volume contains papers presented at the 20th International Conference on Genome Informatics (GIW 2009) held at the Pacifico Yokohama, Japan from December 14 to 16, 2009. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein structure prediction, genetic regulatory networks, bioinformatic algorithms, comparative genomics, and biomolecular data integration and analysis. Boasting a history of 20 years, GIW is the longest-running international bioinformatics conference.A total of 18 contributed papers were selected for presentation at GIW 2009 and for inclusion in this book. In addition, this book contains abstracts from the five invited speakers: Sean Eddy (HHMI's Janelia Farm, USA), Minoru Kanehisa (Kyoto University, Japan), Sang Yup Lee (KAIST, Korea), Hideyuki Okano (Keio University, Japan) and Mark Ragan (University of Queensland, Australia).

Numerous and charismatic, the Lepidoptera is one of the most widely studied groups of invertebrates. Advances in molecular tools and genomic techniques have reduced the need for large sizes and mass-rearing, and lepidopteran model systems are increasingly used to illuminate broad-based experimental questions as well as those peculiar to butterflies and moths. Molecular Biology and Genetics of the Lepidoptera presents a wide-ranging collection of studies on the Lepidoptera, treating them as specialized insects with distinctive features and as model systems for carrying out cutting-edge research. Leading researchers provide an evolutionary framework for placing moths and butterflies on the Tree of Life. The book covers progress in deciphering the silkworm genome and unraveling lepidopteran sex chromosomes. It features new information on sex determination, evolution, and the development of butterfly wing patterns, eyes, vision, circadian clocks, chemoreceptors, and sexual communication. The contributors discuss the genetics and molecular biology of plant host range and prospects for controlling the major crop pest genus Helicoverpa. They also explore the rise of insecticide resistance, the innate immune response, lepidopteran minihosts for testing human pathogens and antibiotics, and the use of intrahemocoelic toxins for control. The book concludes with coverage of polyDNA virus-carrying parasitoid wasps, and the cloning of the first virus resistance gene in the silkworm. Understanding the biology and genetics of butterflies and moths may lead to new species-selective methods of control, saving billions of dollars in pesticide use and protecting environmental and human health-making the sections on strategies for pest management extremely important. This book will open up new paths to the research literature for a broad audience, including entomologists, evolutionary and systematic biologists, geneticists, physiologists, biochemists, and molecular biologists.

DNA microarray technology has become a useful technique in gene expression analysis for the development of new diagnostic tools and for the identification of disease genes and therapeutic targets for human cancers. Appropriate control for DNA microarray experiment and reliable analysis of the array data are key to performing the assay and utilizing the data correctly. The most difficult challenge has been the lack of a powerful method to analyze the data for all genes (more than 30,000 genes) simultaneously and to use the microarray data in a decision-making process. In this book, the authors describe DNA microarray technology and data analysis by pointing out current advantages and disadvantages of the technique and available analytical methods. Crucially, new ideas and analytical methods based on the authors' own experience in DNA microarray study and analysis are introduced. It is believed that this new way of interpreting and analyzing microarray data will bring us closer to success in decision-making using the information obtained through the DNA microarray technology.

Discusses the impact of DNA methylation in human health and disease Includes concepts, experimental models, and clinical uses of demethylating agents Presents the most current research on the impact of DNA methylation in cancer Features the work of the foremost leaders in the field Understanding the complex roles of DNA methylation is currently an active field of research. DNA Methylation: Approaches, Methods, and Applications presents the most current research on the impact of DNA methylation in human disease, particularly cancer. Written by leaders in the field, this state-of-art reference delineates the best techniques to use when addressing questions concerning the cytocine methylation status of genomic DNA. It includes concepts, experimental models, and clinical uses of demethylating agents. The book provides a balance between articles clarifying methodological details and more general review chapters that offer broad biological perspectives on DNA methylation.

"Genomics in Asia" focuses on issues dealing with the development and application of molecular biology and bioengineering technologies in Asian societies and cultures. The workshop on which this book is based aimed to gain an insight into bioethical issues with relation to the dynamics of Asian societies, cultures and religions. It was to generate debate on Asian Genomics and create a basis for comparative research into the relationship between the development and application of modern genetics, cultural values, and local interests in Asian societies. The papers first of all reflect a great variety of bioethical views discussed from the angle of different disciplinary and cultural backgrounds, creating a basis on which a further comparison between different local knowledge systems in relation to genomic practices will be feasible.

This book provides insights on research into the social, political and ethical aspects of genomics, and reflects the bioethical experiences of researchers from Japan, China, the Philippines, Thailand, Taiwan, Pakistan, India and Malaysia. The subjects of discussion vary from genetics in China to religious perspectives on cloning and genetic therapy. Themes include the commercial and medical application of new bioengineering technologies, such as the impact of preventive genetic medicine, genetic counselling, genetically modified organisms [GMOs] and stem-cell research on wealth distribution, cultural traditions, social well-being, and political and legal regulations and institutions. In the study of bioengineering in Asia, various perspectives were brought together at a concrete research level. The authors tried to avoid macro-concepts incorporated bydichotomies of East and West and to acquire new insights into the relationship between local knowledge systems and cultures and interests groups on the one hand and the constellation of various interests of scientific research, governments and MNCs on the other.

This volume contains 31 peer-reviewed papers based on the presentations at the 7th International Annual Workshop on Bioinformatics and Systems Biology (IBSB 2007) held at the Human Genome Center, Institute of Medical Science, University of Tokyo from July 31 to August 2, 2007. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs and partner institutions:* Boston (Charles DeLisi) - Graduate Program in Bioinformatics, Boston University* Berlin (Herman-Georg Holzhutter) - The International Research Training Group (IRTG) "Genomics and Systems Biology of Molecular Networks"* Kyoto/Tokyo (Minoru Kanehisa/Satoru Miyano) - Joint Bioinformatics Education Program of Kyoto University and University of Tokyo.This volume is dedicated to the memory of Prof. Dr. Dr. h.c. Reinhart Heinrich, a former Professor at Humboldt University Berlin and a co-founder of this workshop.

This volume contains papers presented at the 18th International Conference on Genome Informatics (GIW 2007) held at the Biopolis, Singapore from December 3 to 5, 2007. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein folding prediction, gene regulatory network, clustering algorithms, comparative genomics, and text mining. Boasting a history of 18 years, GIW is likely the longest-running international bioinformatics conference.A total of 16 papers were selected for presentation at GIW 2007 and inclusion in this book. The notable authors include Ming Li (University of Waterloo, Canada), Minoru Kanehisa (Kyoto University, Japan), Vladimir Kuznetsov (Genome Institute of Singapore), Tao Jiang (UC Riverside, USA), Christos Ouzounis (European Bioinformatics Institute, UK), and Satoru Miyano (University of Tokyo, Japan). In addition, this book contains abstracts from the five invited speakers: Frank Eisenhaber (Bioinformatics Institute, Singapore), Sir David Lane (Institute of Molecular and Cell Biology, Singapore), Hanah Margalit (The Hebrew University of Jerusalem, Israel), Lawrence Stanton (Genome Institute of Singapore), and Michael Zhang (Cold Spring Harbor Laboratory, USA).

This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. Chapters explain how to convert raw experimental data into 3D conformations, and how to use models to better understand biophysical mechanisms that control chromosome conformation. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, the entire human genome, epigenome folding, chromosome structure and dynamics, and predicting 3D genome structure.

Modern DNA microarray technologies have evolved over the past 25 years to the point where it is now possible to take many million measurements from a single experiment. These two volumes, Parts A & B in the Methods in Enzymology series provide methods that will shepard any molecular biologist through the process of planning, performing, and publishing microarray results.
Part A starts with an overview of a number of microarray platforms, both commercial and academically produced and includes wet bench protocols for performing traditional expression analysis and derivative techniques such as detection of transcription factor occupancy and chromatin status. Wet-bench protocols and troubleshooting techniques continue into Part B. These techniques are well rooted in traditional molecular biology and while they require traditional care, a researcher that can reproducibly generate beautiful Northern or Southern blots should have no difficulty generating beautiful array hybridizations.
Data management is a more recent problem for most biologists. The bulk of Part B provides a range of techniques for data handling. This includes critical issues, from normalization within and between arrays, to uploading your results to the public repositories for array data, and how to integrate data from multiple sources. There are chapters in Part B for both the debutant and the expert bioinformatician.
- Provides an overview of platforms
- Includes experimental design and wet bench protocols
- Presents statistical and data analysis methods, array databases, data visualization and meta analysis

The results obtained from, and techniques used in, different fields of science, such as mathematics, physics and biology are selected, gathered and analyzed to provide an introduction to the developing field of research into the nonlinear physics of DNA. The DNA molecule, which has been traditionally studied by techniques developed through molecular biology, is considered here rather from a physicist's viewpoint, as a nonlinear dynamical system. This is a complimentary way of looking at the molecule, and is arrived at following both a theoretical analysis of interactions and motions in DNA, and as a result of interpretation of experimental data. It is shown that this "nonlinear physics" approach allows one to explain some of the mechanisms of DNA functioning, and that it can offer possibilities in the study and interpretation of genetic codes. This text introduces all those involved in the study of the DNA molecule from a traditional, molecular biology viewpoint, to some of the results and developments which have been realized using a nonlinear physics approach, and should also allow biologists, biochemists and physicists to continue to develop non-traditional techniques of investigating the DNA molecule.

This book focuses on the development and application of the latest advanced data mining, machine learning, and visualization techniques for the identification of interesting, significant, and novel patterns in gene expression microarray data.
Biomedical researchers will find this book invaluable for learning the cutting-edge methods for analyzing gene expression microarray data. Specifically, the coverage includes the following state-of-the-art methods:
- Gene-based analysis: the latest novel clustering algorithms to identify co-expressed genes and coherent patterns in gene expression microarray data sets
- Sample-based analysis: supervised and unsupervised methods for the reduction of the gene dimensionality to select significant genes. A series of approaches to disease classification and discovery are also described
- Pattern-based analysis: methods for ascertaining the relationship between (subsets of) genes and (subsets of) samples. Various novel pattern-based clustering algorithms to find the coherent patterns embedded in the sub-attribute spaces are discussed
- Visualization tools: various methods for gene expression data visualization. The visualization process is intended to transform the gene expression data set from high-dimensional space into a more easily understood two- or three-dimensional space.

A thoroughly updated version of the successful first edition with a new chapter on Real-Time PCR, more prokaryotic applications, and more detail in the complex mutagenesis sections. Information on PCR applications in genomics and proteomics have been expanded and integrated throughout the text. There is also advice on available products and specific pointers to the most appropriate methods. As with the first edition, this will be an ideal practical introduction and invaluable guide to PCR and its applications.

Despite rapidly expanding interest in potential applications of surrogate tissue analysis and intense competition to identify and validate biomarkers in appropriate surrogate tissues, very few peer reviewed publications describing the use of this approach have appeared in the scientific press. One of the first publications on this topic, Surrogate Tissue Analysis: Genomic, Proteomic, and Metabolomic Approaches describes initial applications and considerations for "omic" technologies in the field of surrogate tissue analysis. Highlighting important issues to consider when conducting profiling studies to identify novel biomarkers, the first section covers transcriptional approaches in surrogate tissues. It provides a review of important issues in peripheral blood profiling, summarizes results achieved when evaluations of various blood preparation platforms are used for the purpose of transcriptional profiling, and covers the relatively novel application of transcriptional profiling in neurological and oncological disease settings. The second section focuses on proteomic and protein-based methods for identifying markers in surrogate tissues, highlighting immunoassay and mass-spectrometry approaches for assessment of proteins in serum and other fluids, with a focus on the implications of protein-based biomarkers for detecting and monitoring early stages of cancer. The third section explores metabolomic approaches along with other novel molecular screens that can be applied in surrogate tissues to find biomarkers, and examines in detail the rapid development of metabolomics into a powerful technique for biomarker identification. The authors conclude with coverage of regulatory considerations, economic impact, and pan-omic strategies which will undoubtedly impact surrogate tissue analysis in the future. They explore current concepts in pan-omic approaches during drug development where a compendium of data generated by multiple profiling approaches are assessed and evaluated with its impact on the field of systems biology. The last chapter rounds out the coverage with a brief look ahead towards future analytical issues that will likely arise in the field of surrogate tissue analysis. The book is both an introduction to the various "omic" technologies in this young field and a fundamental reference for scientists interested in identifying biomarkers in surrogate tissues.

Research into DNA and the development of powerful techniques to produce DNA profiles enable experts to appear in court and give compelling. scientific evidence in many types of case. This book gives the legal practitioner a complete account of the issues involved in taking DNA evidence into court. It helps lawyers to ask important and probing questions when faced with such evidence in court. This second edition has been thoroughly updated to take account of recent legislation and case law.

The functional properties of any molecule are directly related to, and affected by, its structure. This is especially true for DNA, the molecular that carries the code for all life on earth.
The third edition of Understanding DNA has been entirely revised and updated, and expanded to cover new advances in our understanding. It explains, step by step, how DNA forms specific structures, the nature of these structures and how they fundamentally affect the biological processes of transcription and replication.
Written in a clear, concise and lively fashion, Understanding DNA is essential reading for all molecular biology, biochemistry and genetics students, to newcomers to the field from other areas such as chemistry or physics, and even for seasoned researchers, who really want to understand DNA.
* Describes the basic units of DNA and how these form the double helix, and the various types of DNA double helix
* Outlines the methods used to study DNA structure
* Contains over 130 illustrations, some in full color, as well as exercises and further readings to stimulate student comprehension

Updated and revised, this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques to study premature chromatin condensation and the use of comparative genomic hybridization to assess genomic aberration are included as well. Novel techniques for imaging chromatin using atomic force microscopy and the isolation of specific genomic regions using engineered DNA binding molecules generated by CRISPR are then examined. That section is followed by protocols to analyze DNA and histone modifications, while the third section includes methods to study DNA replication and repair, in the context of chromatin. Last but not least, protocols for studying chromatin and its relation with transcriptional regulation are presented in a fourth section. 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 up-to-date, Chromatin Protocols, Third Edition aims to help researchers in facilitating in-depth molecular analysis of various aspects of chromatin structure and function.

Combining elements of biochemistry, molecular biology, and immunology, artificial DNA can be employed in a number of scientific disciplines. Some of the varied applications include site-specific mutagenesis, hybridization, amplification, protein engineering, anti-sense technology, DNA vaccines, protein vaccines, recombinant antibodies, screening for genetic and pathogenic diseases, development of materials with new biochemical and structural properties, and many more.

Artificial DNA: Methods and Applications introduces the concept of artificial DNA that has been rationally designed and explains how it may be exploited in order to develop products that will achieve your intended purpose. The first part of the book covers methods of oligonucleotide synthesis and direct applications of synthetic DNA. The second part describes methods of gene assembly from synthetic oligonucleotides and applications of synthetic genes. The authors also discuss the different trends and future developments within each application area .

With state-of-the art research, the contributing authors describe how to engineer proteins using rational and semi-rational design to exhibit the desired traits and detail the various amplification reactions and hybridization techniques for modeling evolution and for use in basic research. The only text devoted to this subject, Artificial DNA offers a comprehensive review that allows you to understand the strategy, design, and applications of synthetic oligonucleotides.

Supramolecular chemistry is the outburst topic of the next generation of science. While the majority of biomedical research efforts to date have centered on utilizing well-known polymeric materials, the recent progress in supramolecular chemistry has introduced a fascinating new field of macromolecular architecture.

Supramolecular Design for Biological Applications focuses on modulating, altering, and mimicking biological functions with a new family of molecular assemblies. The authors provide innovative ideas and concepts for developing novel biomaterials that could be applied in diagnosis, drug carrier operations, and environmental protection. This reference is comprehensive, presenting principles, applications, recent advances, and future directions. Each chapter includes clear and informative illustrations of molecular architectures. The writing is scientific but allows for easy comprehension of the differences in molecular interactions, dimensions, and supramolecular architecture.

Supramolecular Design for Biological Applications will advance the understanding of supramolecular-structured biomaterials and associated issues regarding biological functions. By explaining recent trends and molecular interactions, this book will enable you to initiate new research for nano-scale science and technology in the 21st century.

In today's world, we are witnessing simultaneous breakthroughs in reproductive technologies, genomics, and molecular biology. Advances in molecular genetic technology and understanding of the bovine genome have led to the development of tools that can be used to enhance profitability on cow-calf enterprises. Factors Affecting Calf Crop: Biotechnology of Reproduction provides a detailed compilation of current and forthcoming technology for managing reproduction in cattle.

The book discusses topics such as: approved techniques for controlling the estrous cycle in cattle; managing follicular growth with progesterone, estrogens, and prostaglandins; freezing, thawing, and transfer of cattle embryos; application of embryo transfer to the beef cattle industry; embryo transfer in topically adapted cattle; new factors affecting bull fertility; embryo collection and utilization technology, in vitro fertilization, somatic cell cloning, and genetic technologies; uses of real-time ultrasound; and sexed semen.

Over 25 leading animal scientists have combined their expertise to produce the first single-source reference that covers successful reproductive techniques that will, most likely, be the wave of the future. Expansive in scope, the book addresses current biotechnologies as they impact the production of beef cattle. Written at a level to appeal to the researcher, commercial producer, or student, Factors Affecting Calf Crop: Biotechnology of Reproduction presents you with a wealth of technologies applicable to animal agriculture.

What are the genomic signatures of adaptations in DNA? How often does natural selection dictate changes to DNA? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? Molecular population genetics seeks to answer such questions by explaining genetic variation and molecular evolution from micro-evolutionary principles. It provides a way to learn about how evolution works and how it shapes species by incorporating molecular details of DNA as the heritable material. It enables us to understand the logic of how mutations originate, change in abundance in populations, and become fixed as DNA sequence divergence between species. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today's life scientists. These concepts apply in analysis of personal genomics, genome-wide association studies, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This book introduces, in an accessible way, the bare essentials of the theory and practice of molecular population genetics.