Bioinformatics has ignited the imagination of scientists, entrepreneurs and the general public. At the meeting place of two fast growth disciplines, biology and computer science Bioinformatics is one of the cornerstones of the new biology. It is clearly pivotal to the translation of high throughput projects such the human genome project into useful knowledge. Yet despite all this attention, there is no consensus on what exactly is Bioinformatics. There are several canonical topics, such as gene structure prediction, protein functional classification or structure prediction. The present book explores new frontiers in bioinformatics, such as Glycomics or the computational modeling of genetic processes. We also discuss confounding factors that we find crucial to the development of the field, such as the ability to protect and restrict intellectual property in the field, or the challenges involved in educating bioinformatics users. Finally, we touch upon some fundamental questions, such as what information is and how it is captured in biological systems. By bringing to the readers such a broad spectrum of reviews, we hope to capture the vibrant spirit of this young science and to truly represent the fast pace with which it is still developing.

This volume presents an overview of recent developments in systems biology and their applications in cancer-related research. The ongoing advances in our understanding of genomics and proteomics, coupled with the development of new and more robust tools, have led to an emphasis on analyzing biological systems at multiple levels. Thus, there is a need to integrate different types of data into a comprehensive "systems" view.

Written by active researchers in the emerging areas, this book gives senior undergraduate students, graduate students and new researchers an idea of where the frontiers of systems biology are and an opportunity to learn high-throughput techniques in use. One of the particular emphases of the book is to elucidate the molecular mechanisms in cancer. The discovery of biomarkers and anti-cancer drugs using systems biology approach is also extensively discussed.

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.

The discovery of the spatial structure of the double-stranded DNA molecule is one of the greatest achievements of science. It would not be an exaggeration to say that the DNA double helix is a distinguished symbol of modern biology.
Divided into three parts, DNA Liquid-Crystalline Dispersions and Nanoconstructions covers the information presently available on the condensation of various forms of DNA and describes practical applications of the peculiar properties of the liquid-crystalline particles.

• Part 1 describes the main methods used for condensation of linear high- and low-molecular mass DNA, including their complexes with polycations and circular DNA
• Part 2 compares the state and reactivity of double-stranded nucleic acid molecules fixed spatially in the liquid-crystalline as well as the same molecules under intracellular conditions
• Part 3 explains how the discovery of the fundamental principles underlying the formation of nucleic acid liquid-crystalline dispersion particles opens a gate for the operational use of these principles in the area of nanotechnology and biosensorics

With detailed coverage of DNA liquid crystals, this book provides an understanding of the information presently available on the condensation of various forms of DNA. Double-stranded nucleic acids, spatially organized in a liquid-crystalline structure, represent an important polyfunctional tool for molecular biology and nanobiotechnology. The possibility of programmed and controlled variations in the properties of these molecules and in the characteristics of their liquid-crystalline dispersions, provides wide options for the formation of biologically active three-dimensional structures with unique, widely applicable properties.

Mapping the genomic landscapes is one of the most exciting frontiers of science. We have the opportunity to reverse engineer the blueprints and the control systems of living organisms. Computational tools are key enablers in the deciphering process. This book provides an in-depth presentation of some of the important computational biology approaches to genomic sequence analysis. The first section of the book discusses methods for discovering patterns in DNA and RNA. This is followed by the second section that reflects on methods in various ways, including performance, usage and paradigms.

Epigenetics in Organ Specific Disorders, a new volume in the Translational Epigenetics series, provides a foundational overview and nuanced analysis of epigenetic gene regulation distinct to each organ type and organ specific disorders, fully elucidating the epigenetics pathways that promote and regulate disease. After a brief introduction, chapter authors compare epigenetic regulations across normal and disease conditions in different organ tissues, exploring similarities and contrasts. The role of epigenetic mechanisms in stem cells, cell-matrix interactions and cell proliferation, cell migration, cellular apoptosis, necrosis, pyknosis, tumor suppression, and immune responses across different organ types are examined in-depth. Organ specific epigenetic mechanisms and biomarkers of early use in developing drugs, which can selectively target the organ of interest, are also explored to enable new precision therapies.

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"

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.

How genes are not the only basis of heredity-and what this means for evolution, human life, and disease For much of the twentieth century it was assumed that genes alone mediate the transmission of biological information across generations and provide the raw material for natural selection. In Extended Heredity, leading evolutionary biologists Russell Bonduriansky and Troy Day challenge this premise. Drawing on the latest research, they demonstrate that what happens during our lifetimes--and even our grandparents' and great-grandparents' lifetimes-can influence the features of our descendants. On the basis of these discoveries, Bonduriansky and Day develop an extended concept of heredity that upends ideas about how traits can and cannot be transmitted across generations. By examining the history of the gene-centered view in modern biology and reassessing fundamental tenets of evolutionary theory, Bonduriansky and Day show that nongenetic inheritance-involving epigenetic, environmental, behavioral, and cultural factors-could play an important role in evolution. The discovery of nongenetic inheritance therefore has major implications for key questions in evolutionary biology, as well as human health. Extended Heredity reappraises long-held ideas and opens the door to a new understanding of inheritance and evolution.

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.

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.

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).

'A book that would have had Darwin swooning - anyone seriously interested in who we are and how we function should read this.' Guardian At the beginning of this century enormous progress had been made in genetics. The Human Genome Project finished sequencing human DNA. It seemed it was only a matter of time until we had all the answers to the secrets of life on this planet. The cutting-edge of biology, however, is telling us that we still don't even know all of the questions. How is it that, despite each cell in your body carrying exactly the same DNA, you don't have teeth growing out of your eyeballs or toenails on your liver? How is it that identical twins share exactly the same DNA and yet can exhibit dramatic differences in the way that they live and grow? It turns out that cells read the genetic code in DNA more like a script to be interpreted than a mould that replicates the same result each time. This is epigenetics and it's the fastest-moving field in biology today. The Epigenetics Revolution traces the thrilling path this discipline has taken over the last twenty years. Biologist Nessa Carey deftly explains such diverse phenomena as how queen bees and ants control their colonies, why tortoiseshell cats are always female, why some plants need a period of cold before they can flower, why we age, develop disease and become addicted to drugs, and much more. Most excitingly, Carey reveals the amazing possibilities for humankind that epigenetics offers for us all - and in the surprisingly near future.

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.

How could a relatively simple chemical code give rise to the complexity of a human being? How could our human genome have evolved? And how does it actually work? Over the past 50 years we have deciphered the inner workings of the human genome. From the basic structure of DNA through to the complete sequence of the code, what first appeared to be simple is actually a complex and beautiful three-dimensional world that makes each of us who we are. In The Mysterious World of the Human Genome acclaimed science writer Frank Ryan leads us through the most exciting scientific discoveries of the last 50 years, revealing how this science has unlocked the cure of some genetic diseases, developed the use of DNA in forensic science and paternity testing, helped us trace our ancestors and provided a definitive map for the movement of humans out of Africa. This scientific journey has had a profound impact on our understanding of the evolution of life itself, through the role of the most ancient of organisms in our basic biology all the way to the revelation that our most recent ancestor, Homo neanderthalensis, lives on in many of us. In the ever more complicated world of the human genome, this is the first book to explain how the human genome actually works as a whole and how that knowledge will have a profound effect on our understanding of where we have come from and where we are likely to be going in the future.

"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.

Handbook of Epigenetics: The New Molecular and Medical Genetics, Third Edition provides a comprehensive analysis of epigenetics, from basic biology to clinical application. This new edition has been fully revised to cover the latest and evolving topics in epigenetics, with chapters updated and new chapters added on topics such as single-cell epigenetics, DNA methylation clocks in age-related diseases, transposable elements and epigenetics, X chromosome inactivation, and the epigenetics of drug addiction, among other topics. Throughout this edition, greater emphasis falls on epigenomic analyses and incorporating multi-omics approaches rather than gene-specific analyses. In addition, this edition has also been enhanced with step-by-step instructions in research methods, as well as easy-to-digest disease case studies and clinical trials that provide context and applied examples of recent advances in disease understanding and epigenetic therapeutics. These features empower researchers to reproduce the approaches and studies discussed and aid clinical translation. Live links across chapters tie in relevant external datasets and resources.

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.

Although scientists recognize the role of epigenetic mechanisms in DNA damage response, the complex, mechanistic interplay between chromatin regulation and DNA repair is still poorly understood. Comprehending how these processes are connected in time and space and play out in developmental processes may reveal novel directions for new research and disease treatment. Epigenetics and DNA Damage, a new volume in the Translational Epigenetics series, offers a thorough grounding in the relationship between DNA Damage, epigenetic modifications, and chromatin regulation. Early chapters address the basic science of DNA damage and its association with various epigenetic mechanisms, including DNA methylation, post-translational histone modifications, histone variants, chromatin remodeling, miRNAs, and lncRNAs. This is followed by a close discussion of DNA damage and epigenetics in metabolism, aging, cellular differentiation, immune function, stem cell biology, and cancer, tying recent research to translational application in disease understanding. Later chapters examine possible epigenetic therapies combining DNA damage induction and epigenetic alteration, as well as instructive chapters on how to analyze DNA damage and epigenetic alterations in new research.

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 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.

Providing an interface between dry-bench bioinformaticians and wet-lab biologists, DNA Methylation Microarrays: Experimental Design and Statistical Analysis presents the statistical methods and tools to analyze high-throughput epigenomic data, in particular, DNA methylation microarray data. Since these microarrays share the same underlying principles as gene expression microarrays, many of the analyses in the text also apply to microarray-based gene expression and histone modification (ChIP-on-chip) studies. After introducing basic statistics, the book describes wet-bench technologies that produce the data for analysis and explains how to preprocess the data to remove systematic artifacts resulting from measurement imperfections. It then explores differential methylation and genomic tiling arrays. Focusing on exploratory data analysis, the next several chapters show how cluster and network analyses can link the functions and roles of unannotated DNA elements with known ones. The book concludes by surveying the open source software (R and Bioconductor), public databases, and other online resources available for microarray research. Requiring only limited knowledge of statistics and programming, this book helps readers gain a solid understanding of the methodological foundations of DNA microarray analysis.