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 studiesServes as a historical repository of general use supervised classification methods as well as newer contemporary methodsBrings the reader quickly up to speed on the various classification methods by implementing the programming pseudo-code and source code provided in the bookDescribes 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.

The field of forensic DNA analysis has grown immensely in the past two decades and genotyping of biological samples is now routinely performed in human identification (HID) laboratories. Application areas include paternity testing, forensic casework, family lineage studies, identification of human remains, and DNA databasing. Forensic DNA Analysis: Current Practices and Emerging Technologies explores the fundamental principles and the application of technologies for each aspect of forensic DNA analysis. The book begins by discussing the value of DNA evidence and how to properly recognize, document, collect, and store it. The remaining chapters examine: The most widely adopted methods and the best practices for DNA isolation from forensic biological samples and human remains Studies carried out on the use of both messenger RNA and small (micro) RNA profiling Real-time polymerase chain reaction (PCR) methods for quantification and assessment of human DNA prior to genotyping Capillary electrophoresis (CE) as a tool for forensic DNA analysis Next-generation short tandem repeat (STR) genotyping kits for forensic applications, the biological nature of STR loci, and Y-chromosome STRs (Y-STRs) Mitochondrial DNA (mtDNA) sequence analysis Single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in typing highly degraded DNA Deep-sequencing technologies The current state of integrated systems in forensic DNA analysis The book concludes by discussing various aspects of sample-processing training and the entities that provide such training programs. This volume is an essential resource for students, researchers, teaching faculties, and other professionals interested in human identification/forensic DNA analysis.

With the advent of new technologies and acquired knowledge, the number of fields in omics and their applications in diverse areas are rapidly increasing in the postgenomics era. Such emerging fields-including pharmacogenomics, toxicogenomics, regulomics, spliceomics, metagenomics, and environomics-present budding solutions to combat global challenges in biomedicine, agriculture, and the environment. OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences provides valuable insights into the applications of modern omics technologies to real-world problems in the life sciences. Filling a gap in the literature, it offers a broad, multidisciplinary view of current and emerging applications of omics in a single volume. Written by highly experienced active researchers, each chapter describes a particular area of omics and the associated technologies and applications. Topics covered include: Proteomics, epigenomics, and pharmacogenomics Toxicogenomics and the assessment of environmental pollutants Applications of plant metabolomics Nutrigenomics and its therapeutic applications Microalgal omics and omics approaches in biofuel production Next-generation sequencing and omics technology for transgenic plant analysis Omics approaches in crop improvement Engineering dark-operative chlorophyll synthesis Computational regulomics Omics techniques for the analysis of RNA splicing New fields, including metagenomics, glycomics, and miRNA Breast cancer biomarkers for early detection Environomics strategies for environmental sustainability This timely book explores a wide range of omics application areas in the biomedical, agricultural, and environmental sciences. Throughout, it highlights working solutions as well as open problems and future challenges. Demonstrating the diversity of omics, it introduces readers to state-of-the-art developments and trends in omics-driven research.

The field of materials science and technology has undergone revolutionary advances due to the development of novel analytical tools, functional materials, and multidisciplinary approaches to engineering. Additionally, theoretical predictions combined with increasingly improved models and computational capabilities are making impressive contributions to the progress of materials science and technology. In particular, the materials science of DNA has emerged as a vital area of research and is expected to immensely broaden the horizon of material science and nanotechnology in this century. Materials Science of DNA highlights the most important subjects and perspectives in the field, with the aim of stimulating the interdisciplinary community and bringing this intensively interesting, emerging field of molecular-scale materials science to maturation. The editors have not only been involved in the research of materials science of DNA for the past decade, but also lead the series of International Biotronics Workshops supported by the US Air Force Research Laboratory. Biotechnology and DNA-based biopolymers are not only applicable for genomic sequencing and clinical diagnosis and treatment, but can also have a major impact on nonbiotech applications-such as electronics and photonics- opening up a whole new field for bioengineering. New concepts and insights gained from DNA research are expected to prove genuinely useful in a variety of devices in nano, micro, and macro dimensions in the future. Where silicon has been the building block of inorganic electronics and photonics, DNA holds promise to become the building block for organic electronics and photonics.

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.

The story of the most significant biological breakthrough of the century - the discovery of the structure of DNA. 'It is a strange model and embodies several unusual features. However, since DNA is an unusual substance, we are not hesitant in being bold' By elucidating the structure of DNA, the molecule underlying all life, Francis Crick and James Watson revolutionised biochemistry. At the time, Watson was only 24. His uncompromisingly honest account of those heady days lifts the lid on the real world of great scientists, with their very human faults and foibles, their petty rivalries and driving ambition. Above all, he captures the extraordinary excitement of their desperate efforts to beat their rivals at King's College to the solution to one of the great enigmas of the life sciences.

John Butler, bestselling author of Forensic DNA Typing, now applies his expertise on the subject of DNA analysis into an introductory textbook. Fundamentals of Forensic DNA Typing walks students step-by-step through the DNA analysis process beginning with collection of evidence at a crime scene to the statistical interpretation of the results. Also included are brief discussions of such news worthy topics as victim identification from the September 11, 2001 attacks, the identification of the remains of the Romanovs, the last Russian Royal family, and the O.J. Simpson case. New applications, such as genetic genealogy and tracing domestic pet hairs to perpetrators, are also detailed. With its clear and understandable style and extensive list of online ancillaries and study aids, this textbook will make the subject accessible to students in forensic science courses worldwide.
Includes a glossary with over 400 terms for quick reference of unfamiliar terms as well as an acronym guide to decipher the DNA dialectContinues in the style of Forensic DNA Typing, 2e, with high-profile cases addressed in D.N.A.Boxes-- "Data, Notes & Applications" sections throughoutAncillaries include: instructor manual Web site, with tailored set of 1000+ PowerPoint slides (including figures), links to online training websites and a test bank with key

Growing evidence suggests that epigenetic mechanisms play a central role in stem cell biology and are vital for determining gene expression during cellular differentiation and governing mammalian development. In Stem Cell Epigenetics, leading international researchers examine how chromatin regulation and bona fide epigenetic mechanisms underlie stem cell renewal and differentiation. Authors also explore how the diversity of cell types, including the extent revealed by single cell omic approaches, is achieved, and how such processes may be reversed or managed via epigenetic reprogramming. Topics discussed include chromatin in pluripotency, stem cells and DNA methylation, histone modifications in stem cells and differentiation, higher-order chromatin conformation in pluripotent cells, stem cells and cancer, epigenetics and disease modeling, brain organoids from pluripotent cells, transcriptional regulation in stem cells and differentiation, non-coding RNAs in pluripotency and early differentiation, and diseases caused by epigenetic alterations in stem cells. Additionally, the book discusses the potential implementation of stem cell epigenetics in drug discovery, regenerative medicine, and disease treatment. Stem Cell Epigenetics will provide researchers and physicians with a state-of-the-art map to orient across the frontiers of this fast-evolving field.

Pathological Specimens and Genomic Medicine - Emerging Issues surveys various fields and medical disciplines related to the implementation of the new field of genomic medicine. The book includes sections on specimen processing, the effects of tissue fixation and storage impact on downstream molecular assays, image analysis and its role in the pathology workflow, molecular evaluation of samples, and how to present data to clinicians. The book contains examples of cases where these innovative technologies are applied in the real world, and also presents a look in to the future of the field of genomic medicine.

Unlock the secrets in your DNA!

Discover the answers to your family history mysteries using the most-cutting edge tool available. This plain-English guide is a one-stop resource for how to use DNA testing for genealogy. Inside, you'll find guidance on what DNA tests are available, plus the methodologies and pros and cons of the three major testing companies and advice on choosing the right test to answer your specific genealogy questions. And once you've taken a DNA test, this guide will demystify the often-overwhelming subject and explain how to interpret DNA test results, including how to understand ethnicity estimates and haplogroup designations, navigate suggested cousin matches, and use third-party tools like GEDmatch to further analyze your data. To give you a holistic view of genetic testing for ancestry, the book also discusses the ethics and future of genetic genealogy, as well as how adoptees and others who know little about their ancestry can especially benefit from DNA testing.

The book features:

• Colorful diagrams and expert definitions that explain key DNA terms and concepts such as haplogroups and DNA inheritance patterns
• Detailed guides to each of the major kinds of DNA tests and which tests can solve which family mysteries, with case studies showing how each can be useful
• Information about third-party tools you can use to more thoroughly analyze your test results once you've received them
• Test comparison guides and research forms to help you select the most appropriate DNA test and organize your results and research once you've been tested

Race, while drawn from the visual cues of human diversity, is an idea with a measurable past, an identifiable present, and an uncertain future. The concept of race has been at the center of both triumphs and tragedies in American history and has had a profound effect on the human experience. Race Unmasked revisits the origins of commonly held beliefs about the scientific nature of racial differences, examines the roots of the modern idea of race, and explains why race continues to generate controversy as a tool of classification even in our genomic age. Surveying the work of some of the twentieth century's most notable scientists, Race Unmasked reveals how genetics and related biological disciplines formed and preserved ideas of race and, at times, racism. A gripping history of science and scientists, Race Unmasked elucidates the limitations of a racial worldview and throws the contours of our current and evolving understanding of human diversity into sharp relief.

This up-to-date review of seed genomics, from basic seed biology to practical applications in crop science, provides a thorough background understanding of seed biology from a basic science perspective. A valuable resource for advanced graduate students, post-docs, researchers and professionals in the Plant and Crop Sciences, this book brings together top researchers in the field to cover three general themes: genomic approaches to studying seeds, genomic analysis of basic seed biology, and crop seed genomics.A valuable resource for advanced graduate students, post-docs, researchers and professionals in the Plant and Crop Sciences

People have always sought medical care that is tailored to every individual patient. Alongside with the historical development of institutions of care, the vision of personal and 'holistic' care persisted. Patient-centred medicine, interpersonal communication and shared decision making have become central to medical practice and services. This evolving vision of 'personalized medicine' is in the forefront of medicine, creating debates among ethicists, philosophers and sociologists of medicine about the nature of disease and the definition of wellness, the impact on the daily life of patients, as well as its implications on low-income countries. Is increased 'precision' also an improvement on the personal aspects of care or erosion of privacy? Do 'precise' and 'personalized' approach marginalize public health, and can this care be personalized without attention to culture, economy and society? The book provides a multidisciplinary and interdisciplinary discussion of the ethos and ethics of precision/personal medicine, involving scientists who have shaped the field, in dialogue with ethicists, social scientists and philosophers of science. The contributing scholars come from all over the world and from different cultural backgrounds providing reflective perspectives of history of ideas, critical theory and technology assessment, together with the actual work done by pioneers in the field. It explores issues such as global justice, gender, public health, pharmaceutical industry, international law and religion, and explores themes discussed in relation to personalized medicine such as new-born screening and disorders of consciousness. This book will be of interest to academicians in bioethics, history of medicine, social sciences of medicine as well as general educated readers.

An invaluable resource for computational biologists and researchers from other fields seeking an introduction to the topic, Chromatin: Structure, Dynamics, Regulation offers comprehensive coverage of this dynamic interdisciplinary field, from the basics to the latest research. Computational methods from statistical physics and bioinformatics are detailed whenever possible without lengthy recourse to specialized techniques.

'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.

Population genetics is an inherently quantitative discipline, yet often focuses upon abstract concepts which can be difficult to conceptualize and appropriately visualize at first glance. This book focuses on applying the hugely popular R software specifically to the field, offering an accessible, step-by-step guide to tackling the challenges of achieving effective data interpretation and summary. The authors adopt an engaging "learning by doing" approach that will enable readers to develop an intuitive understanding of key population genetics concepts through the use of R. Beginning with the groundwork of installing and using R (including CRAN and the RStudio IDE), the book works through the use of basic commands for data manipulation. An introduction to basic terminology in population genetics follows, clearly explaining how these fundamental assumptions can provide insights and form basic inferences for real populations. The focus then moves onto statistical tests including writing and running algorithms as functions. Subsequent chapters examine genetic variation, adaptation, and natural selection as well as different approaches to population differences. Importantly, the accompanying set of practical exercises demonstrate that implementing all of these concepts via programming can actually help greatly in understanding them, even if they may at first seem insurmountably complex. Finally, this accessible textbook points the way forwards to other key concepts that are important to understanding modern day population genetics research (in particular coalescent theory) and offers the reader useful launching points for further learning. Population Genetics with R is aimed at students ranging from undergraduate to postgraduate level in the fields of population genetics, ecology, evolutionary biology, conservation genetics, computational biology, and biostatistics.

The latest edition of this highly successful textbook introduces the key techniques and concepts involved in cloning genes and in studying their expression and variation.
The new edition features:
Increased coverage of whole-genome sequencing technologies and enhanced treatment of bioinformatics.Clear, two-colour diagrams throughout.A dedicated website including all figures.

Noted for its outstanding balance between clarity of coverage and level of detail, this book provides an excellent introduction to the fast moving world of molecular genetics.

Genomics and genome technology is having, and continues to have, a major impact on all areas of bioscience research providing insights into the key area of molecular mechanisms of cells in health and disease. This is causing a profound effect on biomedical science and is accelerating the development of new diagnostic applications. This book provides a timely, graduate level introduction to the fast-paced area of genomics and clinical diagnostic technologies and introduces the concept of applications based on this area. The initial chapters focus on principal molecular technologies that underpin the information in the later chapters. In addition to introductory areas of nucleic acids and techniques in molecular biology, bioinformatics and proteomics, other key diagnostic areas such as the use of immunological reagents are covered. The later chapters provide more specialised examples of currently used diagnostic technologies and insights into selected key diagnostic challenges including specific examples of molecular microbial diagnostics and molecular biomarkers in oncology. The running themes through the chapters provides an insight into current and future perspectives in this rapidly evolving field.

The simplicity and lack of redundancy in their regulatory genes have made ascidians one of the most useful species in studying developmental genomics. In Developmental Genomics of Ascidians, Dr. Noriyuki Satoh explains the developmental genomics of ascidians, stresses the simplicity of Ciona developmental system, and emphasizes single-cell level analyses. This book actively accentuates the advantages of using ascidians as model organisms in an up-and-coming field of developmental genomics.

A Primer of Population Genetics and Genomics has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics. Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of current research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention. This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.

The sequencing of the human genome and subsequent elucidation of the molecular pathways that are important in the pathology of disease have provided unprecedented opportunities for the development of new therapeutics. Nucleic acid-based drugs have emerged in recent years to yield extremely promising candidates for drug therapy to a wide range of diseases. Advances in Nucleic Acid Therapeutics is a comprehensive review of the latest advances in the field, covering the background of the development of nucleic acids for therapeutic purposes to the array of drug development approaches currently being pursued using antisense, RNAi, aptamer, immune modulatory and other synthetic oligonucleotides. Nucleic acid therapeutics is a field that has been continually innovating to meet the challenges of drug discovery and development; bringing contributions together from leaders at the forefront of progress, this book depicts the many approaches currently being pursued in both academia and industry. A go-to volume for medicinal chemists, Advances in Nucleic Acid Therapeutics provides a broad overview of techniques of contemporary interest in drug discovery.

This is an introductory text and laboratory manual to be used primarily in undergraduate courses. It is also useful for graduate students and research scientists who require an introduction to the theory and methods of nanopore sequencing. The book has clear explanations of the principles of this emerging technology, together with instructional material written by experts that describes how to use a MinION nanopore instrument for sequencing in research or the classroom.At Harvard University the book serves as a textbook and lab manual for a university laboratory course designed to intensify the intellectual experience of incoming undergraduates while exploring biology as a field of concentration. Nanopore sequencing is an ideal topic as a path to encourage students about the range of courses they will take in Biology by pre-emptively addressing the complaint about having to take a course in Physics or Maths while majoring in Biology. The book addresses this complaint by concretely demonstrating the range of topics - from electricity to biochemistry, protein structure, molecular engineering, and informatics - that a student will have to master in subsequent courses if he or she is to become a scientist who truly understands what his or her biology instrument is measuring when investigating biological phenomena.

Around 200,000 years ago, a man--identical to us in all important respects--lived in Africa. Every person alive today is descended from him. How did this real-life Adam wind up father of us all? What happened to the descendants of other men who lived at the same time? And why, if modern humans share a single prehistoric ancestor, do we come in so many sizes, shapes, and races? Showing how the secrets about our ancestors are hidden in our genetic code, Spencer Wells reveals how developments in the cutting-edge science of population genetics have made it possible to create a family tree for the whole of humanity. We now know not only where our ancestors lived but who they fought, loved, and influenced. Informed by this new science, The Journey of Man is replete with astonishing information. Wells tells us that we can trace our origins back to a single Adam and Eve, but that Eve came first by some 80,000 years. We hear how the male Y-chromosome has been used to trace the spread of humanity from Africa into Eurasia, why differing racial types emerged when mountain ranges split population groups, and that the San Bushmen of the Kalahari have some of the oldest genetic markers in the world. We learn, finally with absolute certainty, that Neanderthals are not our ancestors and that the entire genetic diversity of Native Americans can be accounted for by just ten individuals. It is an enthralling, epic tour through the history and development of early humankind--as well as an accessible look at the analysis of human genetics that is giving us definitive answers to questions we have asked for centuries, questions now more compelling than ever.

Our genome is the blueprint to our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. But it is more than a static information store: our genome is a dynamic, tightly-regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the processes of life? Introduction to Genomics is a fascinating insight into what can be revealed from the study of genomes: how organisms differ or match; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genomics means in terms of our future health and wellbeing. Covering the latest techniques that enable us to study the genome in ever-increasing detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism. Learning features throughout make this book the ideal teaching and learning tool: extensive end of chapter exercises and problems help the student to fully grasp the concepts being presented, while end of chapter weblems (web-based problems) and lab assignments give the student the opportunity to engage with the subject in a hands-on manner. The field of genomics is enabling us to analyze life in more detail than ever before; Introduction to Genomics is the perfect guide to this enthralling subject. Online Resource Centre The Online Resource Centre to accompany Introduction to Genomics features For lecturers: Figures from the book in electronic format For students: Answers to end-of-chapter exercises Guided tour of web sites in genomics Hints to end-of-chapter problems Rotating figures

This book combines linguistic and historical approaches with the latest techniques of DNA analysis and show the insights these offer for every kind of genealogical research. It focuses on British names, tracing their origins to different parts of the British Isles and Europe and revealing how names often remain concentrated in the districts where they first became established centuries ago. In the process the book casts fresh light on the ancient peopling of the British Isles. The authors consider why some names die out, and how others have spread across the globe. They use recent advances in DNA testing to discover whether particular surnames have a single, dual or multiple origins and whether various forms of a name have a common origin. They show how information from DNA can be combined with historical evidence and techniques to distinguish between individuals with the same name and different names with similar spellings and to identify the name of the same individual or family spelt in various ways in different times and places. Clearly written and illustrated with hundreds of examples, this book will be welcomed by all those engaged in genealogical research, including everyone seeking to discover the histories of their names and families.