Candid, provocative, and disarming, this is the widely-praised memoir of the co-discoverer of the double helix of DNA.

The State of the Art in Transcriptome Analysis RNA sequencing (RNA-seq) data offers unprecedented information about the transcriptome, but harnessing this information with bioinformatics tools is typically a bottleneck. RNA-seq Data Analysis: A Practical Approach enables researchers to examine differential expression at gene, exon, and transcript levels and to discover novel genes, transcripts, and whole transcriptomes. Balanced Coverage of Theory and Practice.Each chapter starts with theoretical background, followed by descriptions of relevant analysis tools and practical examples. Accessible to both bioinformaticians and nonprogramming wet lab scientists, the examples illustrate the use of command-line tools, R, and other open source tools, such as the graphical Chipster software. The Tools and Methods to Get Started in Your Lab. Taking readers through the whole data analysis workflow, this self-contained guide provides a detailed overview of the main RNA-seq data analysis methods and explains how to use them in practice. It is suitable for researchers from a wide variety of backgrounds, including biology, medicine, genetics, and computer science. The book can also be used in a graduate or advanced undergraduate course.

Genome sequencing is one of the most exciting scientific breakthroughs of the past thirty years. But what precisely does it involve and how is it developing? In this brilliantly wide-ranging, one-stop guide WIRED journalist Rachael Pells explains the science behind genomics. She analyses its practical applications in medical diagnosis and the treatment of conditions that range from cancer to severe allergic reactions to cystic fibrosis. She considers its potential to help with advances in agriculture and environmental science. She explores the ethics of genetic modification and the dangers involved when humans 'play God'. And she addresses the fundamental question: to what extent will future advances transform human longevity and the quality of life.

Fixing Your Damaged and Incorrect Genes is a book about a well-established biological process called DNA REPAIR. The book describes the multiple and varied biochemical strategies by which damaged or incorrect nucleotides are removed from DNA or are corrected. The book includes multiple figures of notable past and present scientists in the field. The book is uniquely focused on an audience of non-biologists and is written in simple language with minimal use of technical terms. It contains an extensive glossary that provides explanations of key words that readers are encouraged to refer to as they read. Fixing Your Damaged and Incorrect Genes is unique, there being no previously published books for non-biologists on the topic of DNA repair.

This book describes the driving forces behind the evolutionary process at the molecular and genome levels, the effects of the various molecular mechanisms on the structure of genes, proteins, and genomes, the methodology and the analytical tools involved in dealing with molecular data from an evolutionary perspective, and the logic of evolutionary hypothesis testing. Evolutionary phenomena at the molecular level are detailed in a way that can be understood without much prerequisite knowledge of molecular biology, evolution, or mathematics. Numerous examples that support and clarify the theoretical arguments and methodological discussions are included.

There have been remarkable advances towards discovering agents that exhibit selectivity and sequence-specificity for DNA, as well as understanding the interactions that underlie its propensity to bind molecules. This progress has important applications in many areas of biotechnology and medicine, notably in cancer treatment as well as in future gene targeting therapies. The editor and contributing authors are leaders in their fields and provide useful perspectives from diverse and interdisciplinary backgrounds on the current status of this broad area. The role played by chemistry is a unifying theme. Early chapters cover methodologies to evaluate DNA-interactive agents and then the book provides examples of DNA-interactive molecules and technologies in development as therapeutic agents. DNA-binding metal complexes, peptide and polyamide–DNA interactions, and gene targeting tools are some of the most compelling topics treated in depth. This book will be a valuable resource for postgraduate students and researchers in chemical biology, biochemistry, structural biology and medicinal fields. It will also be of interest to supramolecular chemists and biophysicists.

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

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

MicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression. Thousands of miRNAs have been identified in different organisms including viruses, insects, plants and animals. MiRNAs has emerged as key regulators of important biological processes. The differential expression of miRNAs in various human diseases has made them potential candidates for developing novel therapies and personalized medicines. This book is focused on microRNA let-7, the second miRNA discovered in the year 2000 and one of the most studied miRNA. This book discusses various aspects of miRNA let-7 starting from its discovery, biogenesis, transcriptional and posttranscriptional regulation to its crucial role in various fundamental cellular processes such as development, stem cell maintenance and differentiation, regulation of signalling pathways in cancer, drug resistance and therapeutic potential in different human diseases.

This book examines the peculiarities of the circular dichroism (CD) spectra of the double-stranded (ds) DNA cholesteric liquid-crystalline dispersions (CLCDs). The main physico-chemical properties formed as a result of the phase exclusion of these molecules in water-salt or water-salt-polymer-containing solutions are examined. In addition, the main principles of the theory of optical properties of imperfect, absorbing, cholesteric liquid crystals is discussed.

Genome stability of every species depends on complex interaction of predefined and environmentally induced genetic and epigenetic states. Predefined states consist of chromatin structure and cell metabolic processes such as DNA repair, radical scavenging and cell signalling, whereas induced states depend on interactions with the environment. Organisms are able to respond to a changing environment by various alterations in their somatic cells as well as in their germline and progeny. In this book, we will describe various phenomena associated with the maintenance of genome stability. These include genetic and epigenetic responses to various stresses in exposed cells and organisms, bystander and, bystander-like effects, transgenerational changes in genome stability and stress tolerance in bacteria, plants and animals.

This volume presents original research results from the leading edge of DNA research. It includes articles which have been carefully selected to present substantial research results across a broad spectrum of topics.

Numerous physical and chemical stress factors, endogenous or exogenous, challenge living organisms. Metabolisation processes generate highly reactive intermediates which can covalently bind to DNA, resulting in bulky addition products called "adducts." DNA adduct formation appears to be a general response of plants to organic chemical exposure, whether in controlled conditions or in the field. In particular, common carcinogenic pollutants and pesticides promote the formation of DNA adducts in plants. The authors of this book examine the development of DNA adducts, as well as the ways in which they can be eliminated due to DNA repair pathways. In this book, the data from in vivo transgenic assays is also examined, which can help to clarify specific pre-mutagenic adducts, DNA repair functions and mutational events that may be involved in the mutagenicity of human carcinogens. Other chapters in this book identify and discuss novel anthracyclines capable of forming DNA adducts, the role of DNA adducts as early biomarkers in the screening and development of marine anticancer drugs, the genotoxicity, such as DNA adduct formation, of air pollutants and its assessment by in vivo mutagenesis and a discussion of oxidative DNA damage, which can play an important role in the carcinogenic processes of PAHs and aromatic amines, in addition to bulky-DNA adducts formation.

Ribonucleotide reductase (RNR), a universal enzyme present in essentially all living cells and organisms, has a central role in DNA replication and repair by catalysing production of deoxyribonucleotides from the corresponding ribonucleotides. Three major classes of RNRs are known, differing in their cofactor requirements: class I RNRs (with subclasses Ia and Ib) carry a stable tyrosyl radical and are oxygen-dependent, class II RNRs require the vitamin B12 cofactor 5'-deoxyadenosylcobalamin and are oxygen-independent, and class III RNRs carry a stable glycyl radical and are oxygen-sensitive. Despite these differences, all classes have a similar reaction mechanism and the same highly specific catalytic core structure, indicating that they evolved from a common ancestor. Biochemical studies of RNRs from selected model organisms in combination with the vast number of deduced RNR sequences from publicly available complete genomic sequences show that whereas eukaryotes and their viruses with few exceptions contain only class Ia RNRs, all three major RNR classes are found among prokaryotes and bacteriophages and quite often one organism encodes more than one class of RNR. They are compiled in an open access database, called RNRdb for Ribonucleotide Reductase database that is available at http://rnrdb.molbio.su.se. RNRs are produced in a strictly controlled way depending upon growth phase and environmental cues. The authors describe a comprehensive summary of how the expression of RNR genes is regulated in several eubacterial organisms and in yeast. Due to RNR's importance for the realisation of DNA replication, it has been recognised as a possible target for antiproliferative therapy. The authors present a comprehensive summary of RNR-specific inhibitors that have reached clinical trials and/or are currently used in clinical therapy.

This book presents the latest research on DNA damage, which due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumour suppresser genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumour formation. The vast majority of DNA damage affects the primary structure of the double helix; that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage.

Genetic vectors are plasmids, bacteriophages, or viruses used during recombinant DNA techniques that transport foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain a genetic marker to facilitate their selective recognition. This book presents new and important research from around the globe

Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.

Inferring the precise locations and splicing patterns of genes in DNA is a difficult but important task, with broad applications to biomedicine. The mathematical and statistical techniques that have been applied to this problem are surveyed and organized into a logical framework based on the theory of parsing. Both established approaches and methods at the forefront of current research are discussed. Numerous case studies of existing software systems are provided, in addition to detailed examples that work through the actual implementation of effective gene-predictors using hidden Markov models and other machine-learning techniques. Background material on probability theory, discrete mathematics, computer science, and molecular biology is provided, making the book accessible to students and researchers from across the life and computational sciences. This book is ideal for use in a first course in bioinformatics at graduate or advanced undergraduate level, and for anyone wanting to keep pace with this rapidly-advancing field.

A collection of essays, speeches, and reports by J D Watson, author of The Double Helix, a book which famously tells the story of his co-discovery with Crick of the structure of DNA in 1953. The pieces in this book deal with Watson's early life and career, science and politics, the advance of molecular genetics, genetics and society, the recombinant DNA debate, the prospects for curing cancer over the next decade, and how human genetic knowledge is likely to be used, for good or bad. Availability in USA and Canada: Cold Spring Harbour Laboratory Press has the exclusive distribution rights for this title in the U.S and Canada. Please Contact Cold Spring Harbor Laboratory Press, 10 Skyline Drive, Plainview, NY 11803 USA Tel: 516-349-1930 Fax: 516-349-1946 http://www.cshl.org/books/passndna.htm

Mapping and, ultimately, deciphering the human genome is a major human and scientific adventure that involves thousands of researchers world-wide and considerable funds. Bertrand Jordan, an active scientist in this field, became also a privileged observer through a sabbatical year devoted to visiting nearly a hundred participating laboratories around the world. This placed him in an ideal position to see, discuss, record and analyse progress and difficulties in this endeavour. These observations are the basis for a regular feature, "Chroniques Genomiques" (Tales of the Genome) published in the French periodical medecine/sciences. This book is an integrated, expanded and updated version of the 1990-1993 chronicles. It provides a technically detailed but accessible account of the "Genome World" from the viewpoint of a practising scientist. It describes the strategies implemented in settings that range from small laboratories to semi-industrial installations such as "Genethon", and the associated questions in terms of national policies, economic stakes and ethical issues.

Quantitative traits-be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene-usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences.

Over the last twenty years, genome-wide association studies (GWAS) have revealed a great deal about the genetic basis of a wide range of complex diseases and they will undoubtedly continue to have a broad impact as we move to an era of personalised medicine. This authoritative text, written by leaders and innovators from both academia and industry, covers the basic science as well as the clinical, biotechnological and pharmaceutical potential of these methods. With special emphasis given to highlighting pharmacogenomics and population genomics studies using next-generation technology approaches, this is the first book devoted to combining association studies with single nucleotide polymorphisms, copy number variants, haplotypes and expressed quantitative trait loci. A reliable guide for newcomers to the field as well as for experienced scientists, this is a unique resource for anyone interested in how the revolutionary power of genomics can be applied to solve problems in complex disease.

Over the last decade there has been a rapid development of molecular techniques, with an increasing range of instrumentation now available. The development of accompanying reference literature has not kept pace with technological advances and this poses significant challenges to the analyst. Essentials of Nucleic Acid Analysis sets out to guide the analyst through the steps needed to obtain good quality results in DNA analysis. The underlying principles for achieving this goal were formulated by LGC (formerly the Laboratory of the Government Chemist) as the six principles for ensuring valid analytical measurement, which are detailed in the introduction. The reader is also provided with guidelines for method validation and quality control of established and emerging DNA measurement techniques. The authors of each chapter are practitioners of the art of DNA analysis in areas where the quality of the result is critical. Technical details and examples of application of key techniques in nucleic acid analysis are provided while highlighting best practice, available standards and practical advice on improving measurement quality. This book provides an indispensable handbook and premier reference for those working in the widely varying areas and specifically in the fields of food analysis and forensic applications.

"We are sure that DNA: Forensic and Legal Applications will play its part in promoting this most powerful tool in the forensic scientist's armamentarium."
-James Watson, PhD
-Jan Witkowski. PhD

Because it consists of a number of complex steps and procedures subject to both scientific and legal standards, the collection, analysis, presentation, and interpretation of DNA evidence remains a complex process. Any procedural or documentary misstep can potentially render key evidence or testimony useless. To avoid such costly errors, scientists, law enforcement personnel, attorneys, and judges all must possess a detailed knowledge of how forensic DNA works, from the crime scene to the laboratory to the courtroom and beyond.

DNA: Forensic and Legal Applications provides the most comprehensive and up-to-date guide to this important and increasingly prevalent legal tool. Designed to reach readers in both legal and scientific fields, this text gives a global view of the practical issues involved in the forensic use of DNA. In clear, nontechnical language, the text covers:

• A scientific overview of DNA and common DNA tests
• Techniques used by criminalists on the path from crime scene to final laboratory analysis
• Procedures used to analyze biological evidence
• Human genetics, population genetics, and statistics in the context of DNA testing and genetic profiling
• Understanding and interpreting DNA evidence with respect to past and present law
• Concepts and procedures used in challenging or defending DNA evidence
• Postconviction appeals based on analysis of existing DNA evidence, including a discussion of The InnocenceProject
• The future of DNA technology with respect to legal evidence gathering and analysis

In a unique combination of legal practice and scientific analysis, DNA: Forensic and Legal Applications provides forensic scientists, potential expert witnesses, and professionals in the criminal justice system with the definitive resource on the methods of DNA analysis as well as the handling, potential, and limitations of DNA evidence.

This book introduces a discrete optimisation technique in four applications: classic Traveller Salesperson Problem (TSP), Multilocus Genetic Mapping, Multilocus Consensus Genetic Mapping, and Physical Mapping. Each of the four sections contains the problem formulation, description of the algorithm, and experimental results. The foregoing problems are solved on the basis of Guided Evolution Strategy (GES) algorithm. The algorithm was implemented in MultiPoint package (http://multiqtl.com). The developed analytical tools were applied in many genome mapping projects.