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Now in its second edition, Forensic DNA Evidence Interpretation is the most comprehensive resource for DNA casework available today. Written by leaders in the fields of biology and statistics, including a contribution from Peter Gill, the father of DNA analysis, the book emphasizes the interpretation of test results and provides the necessary formulae in an easily accessible manner. This latest edition is fully updated and includes current and emerging techniques in this fast-moving field. The book begins by reviewing all pertinent biology, and then provides information on every aspect of DNA analysis. This includes modern interpretation methods and contemporary population genetic models available for estimating DNA frequencies or likelihood ratios. Following a chapter on procedures for validating databases, the text presents overviews and performance assessments of both modern sampling uncertainty methods and current paternity testing techniques, including new guidelines on paternity testing in alignment with the International Society for Forensic Genetics. Later chapters discuss the latest methods for mixture analysis, LCN (ultra trace) analysis and non-autosomal (mito, X, and Y) DNA analysis. The text concludes with an overview of procedures for disaster victim identification and information on DNA intelligence databases. Highlights of the second edition include: New information about PCR processes, heterozygote balance and back and forward stuttering New information on the interpretation of low template DNA, drop models and continuous models Additional coverage of lineage marker subpopulation effects, mixtures and combinations with autosomal markers This authoritative book provides a link among the biological, forensic, and interpretative domains of the DNA profiling field. It continues to serve as an invaluable resource that allows forensic scientists, technicians, molecular biologists and attorneys to use forensic DNA evidence to its greatest potential.
In the spring of 2011, a diverse group of scientists gathered at Cornell University to discuss their research into the nature and origin of biological information. This symposium brought together experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. This volume presents new research by those invited to speak at the conference. The contributors to this volume use their wide-ranging expertise in the area of biological information to bring fresh insights into the many explanatory difficulties associated with biological information. These authors raise major challenges to the conventional scientific wisdom, which attempts to explain all biological information exclusively in terms of the standard mutation/selection paradigm. Several clear themes emerged from these research papers: 1) Information is indispensable to our understanding of what life is; 2) Biological information is more than the material structures that embody it; 3) Conventional chemical and evolutionary mechanisms seem insufficient to fully explain the labyrinth of information that is life. By exploring new perspectives on biological information, this volume seeks to expand, encourage, and enrich research into the nature and origin of biological information.
This book combines linguistic and historical approaches with the latest techniques of DNA analysis and shows 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 while others spread across the globe. They use recent advances in DNA testing to investigate whether particular surnames have single, dual, or multiple origins, and to find out if the various forms of a single 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 identifty the name of the same individual or family spelt in various ways in different times and places. The final chapter of this paperback edition, looking at the use of genetics in historical research, has been updated to include new work on the DNA of Richard III.
Pooling designs have been widely used in various aspects of DNA sequencing. In biological applications, the well-studied mathematical problem called ?group testing? shifts its focus to nonadaptive algorithms while the focus of traditional group testing is on sequential algorithms. Biological applications also bring forth new models not previously considered, such as the error-tolerant model, the complex model, and the inhibitor model. This book is the first attempt to collect all the significant research on pooling designs in one convenient place. The coverage includes many real biological applications such as clone library screening, contig sequencing, exon boundary finding and protein?protein interaction detecting and introduces the mathematics behind it.
DNA Microarrays is intended for scientists who are entering the field, as well as those already familiar with the technology, but interested in new applications and methods. All up-to-date microarray platforms and their various applications are introduced, presenting the successive stages of microarray technology, from array production to the data analysis. There is extensive discussion of array applications in a broad range of studied organisms from yeast to humans
The first edition of this book was the first on the physics of DNA to go beyond the simple (simplified) 'linear' approach, and it has since been found that the inclusion of nonlinear effects leads to a significantly improved interpretation of experimental data. This new edition naturally retains this approach, but has been completely revised, updated and expanded to cover recent developments.
Beginning with introductory chapters on DNA structure and dynamics, the book also includes a comparison between linear and nonlinear approaches to the DNA molecule, a chapter devoted to the statistics of nonlinear excitations of DNA, and examples for the interpretation of experimental data on the dynamics of DNA in terms of nonlinear theory.
Essential reading for researchers in biophysics and nonlinear physics, allowing biologists, chemists and physicists to continue developing new and improved techniques of investigating the DNA molecule.
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.
This major new work is an invaluable laboratory manual for all scientists involved with computational genomics. Topics covered include database searches, sequence analysis and comparison, multiple sequence analysis, large-scale EST analysis, genome browsing, protein structure prediction, mircroarray data analysis, and proteomics. The book is also useful as a teaching reference for graduates and undergraduate students.
This book handles an emerging, central issue in molecular genetics and the development of eukaryotes: the control of gene expression by small species of RNA. As an exciting new field of endeavor, it is the first book by a single author to deal comprehensively with RNA silencing. The book provides the historical background of the field preceding the seminal work by Fire and associates in 1998 on the impact of small double-stranded RNA on the expression of nematode genes, which is considered the beginning of RNA silencing research, RNA silencing is described in a wide range of plants and animals including protozoa, simple metazoa, insects, non-mammalian vertebrates, and mammals. In each case the, experimental results are provided with the accompanying background and with illustrations. There is also an appendix on the prospective use of RNA silencing in gene therapy, which is intended as a guide for investigators wishing to explore this possibility.
A guide to machine learning approaches and their application to the analysis of biological data. An unprecedented wealth of data is being generated by genome sequencing projects and other experimental efforts to determine the structure and function of biological molecules. The demands and opportunities for interpreting these data are expanding rapidly. Bioinformatics is the development and application of computer methods for management, analysis, interpretation, and prediction, as well as for the design of experiments. Machine learning approaches (e.g., neural networks, hidden Markov models, and belief networks) are ideally suited for areas where there is a lot of data but little theory, which is the situation in molecular biology. The goal in machine learning is to extract useful information from a body of data by building good probabilistic models-and to automate the process as much as possible. In this book Pierre Baldi and Soren Brunak present the key machine learning approaches and apply them to the computational problems encountered in the analysis of biological data. The book is aimed both at biologists and biochemists who need to understand new data-driven algorithms and at those with a primary background in physics, mathematics, statistics, or computer science who need to know more about applications in molecular biology. This new second edition contains expanded coverage of probabilistic graphical models and of the applications of neural networks, as well as a new chapter on microarrays and gene expression. The entire text has been extensively revised.
Forensic DNA Applications: An Interdisciplinary Perspective was developed as an outgrowth of a conference held by the International Society of Applied Biological Sciences. The topic was human genome based applications in forensic science, anthropology, and individualized medicine. Assembling the contributions of contributors from numerous regions around the world, this volume is designed as both a textbook for forensic molecular biology students and a reference for practitioners and those in the legal system.
The book begins with the history and development of DNA typing and profiling for criminal and civil purposes. It discusses the statistical interpretation of results with case examples, mitochondrial DNA testing, Y single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), and X SNP and STR testing. It also explores low copy number DNA typing, mixtures, and quality assurance and control.
The second section examines the collection and preservation of biological evidence under a variety of different circumstances and the identification of human remains including in mass disaster settings. It discusses applications to bioterrorism investigations, animal DNA testing in criminal cases, pedigree questions and wildlife forensic problems, applications in forensic entomology, and forensic botany.
The third section explores recent developments and new technologies, including the rigorous identification of tissue of origin, mtDNA profiling using immobilized probe strips, chips and next-generation sequencing, the use of SNPs to ascertain phenotypic characteristics, and the "molecular autopsy" that looks at aspects of toxicogenetics and pharmacogenetics.
The book concludes with a discussion on law, ethics, and policy. It examines the use of DNA evidence in the criminal justice system in both the United States and Europe, ethical issues
in forensic laboratory practices, familial searches, DNA databases, ancestry searches, physical phenotyping, and report writing. The contributors also examine DNA applications in immigration and human trafficking cases and international perspectives on DNA databases."
In this book, the authors present current research in the study of DNA replication and mutation, including connections between BLM and the Fanconi anemia pathway in the repair of replication fork damage; the mutagenic potential of methacrylates used in restorative dentistry; DNA mutation of the progranulin gene in familial frontotemporal lobar degeneration; effect of DNA polymerase a-inhibitor dehydroaltenusin on DNA replication in cultured cells; gel-based methods of DNA-binding zinc II complexes in the detection of DNA mutations and DNA mutations and genetic coding.
This timely volume explores the use of CRISPR-Cas9 for genome editing, presenting cutting-edge techniques and their applications in treatment of disease. The chapters describe latest methods such as use of targetable nucleases, investigation of the non-coding genome, mouse genome editing, increasing of knock-in efficiency in mouse zygotes, and generation of reporter stem cells; the text contextualizes these methods in treatment of cardiovascular disease, diabetes mellitus, retinitis pigmentosa, and others. The final chapters round out the book with a discussion of controversies and future directions. Genome Editing is an essential, of-the-moment contribution to this rapidly growing field. Drawing from a wealth of international perspectives, it presents novel techniques and applications for the engineering of the human genome. This book is essential reading for all clinicians and researchers in stem cells, regenerative medicine, genomics, biochemical and biomedical engineering- especially those interested in learning more about genome editing and applying it in a targeted, specific way.
Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practices and analyses based on environmental DNA.
Current research in genomics and pharmacogenomics is increasingly highlighting the need to move towards stratified disease descriptions and individualized treatment plans. This book explains how a confluence of recent biological, technological and methodological developments is making it possible to provide personalized diagnoses and treatments. By virtue of treating each person's condition as unique, personal genomics and personalized medicine require health professionals to understand the nature of the data, its health implications, and its limitations. This book provides a detailed scientific treatment of the emerging disciplines of personal genomics and personalized medicine. It also includes a comprehensive treatment of both the promises and challenges of personal genomics and medicine from technological, societal and medical perspectives. It offers a wide-ranging review of the state of the art across all aspects of a highly multi-disciplinary subject. This book will be immensely useful for practicing health professionals and researchers, as well as senior undergraduates and graduate students in biomedical sciences. Contents: From DNA Sequence to Physiology DNA Sequence Variations, Their Prevalence, and Effects on Cellular Biochemistry Environmental and Life-History Effects The Impact of Inter-Individual Biochemical Differences on Health Outcomes DNA Testing and Sequencing Technologies Measuring the Impact of Environmental Factors on Health Characterizing the Effects of Genetic and Environmental Factors on Cellular Function Translating Personal Genomics and Personalized Medicine into Clinical Practice Organizational, Legal and Ethical Challenges Coda Engineering the Future of Medicine
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).
The aim of molecular diagnostics is preferentially to detect a developing disease before any symptoms appear. There has been a significant increase, fueled by technologies from the human genome project, in the availability of nucleic acid sequence information for all living organisms including bacteria and viruses. When combined with a different type of instrumentation applied, the resulting diagnostics is specific and sensitive. Nucleic acid-based medical diagnosis detects specific DNAs or RNAs from the infecting organism or virus and a specific gene or the expression of a gene associated with a disease. Nucleic acid approaches also stimulate a basic science by opening lines of inquiry that will lead to greater understanding of the molecules at the center of life. One can follow Richard Feynman's famous statement "What I cannot create, I do not understand."
Current research in genomics and pharmacogenomics is increasingly highlighting the need to move towards stratified disease descriptions and individualized treatment plans. This book explains how a confluence of recent biological, technological and methodological developments is making it possible to provide personalized diagnoses and treatments.By virtue of treating each person's condition as unique, personal genomics and personalized medicine require health professionals to understand the nature of the data, its health implications, and its limitations.This book provides a detailed scientific treatment of the emerging disciplines of personal genomics and personalized medicine. It also includes a comprehensive treatment of both the promises and challenges of personal genomics and medicine from technological, societal and medical perspectives. It offers a wide-ranging review of the state of the art across all aspects of a highly multi-disciplinary subject. This book will be immensely useful for practicing health professionals and researchers, as well as senior undergraduates and graduate students in biomedical sciences.
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.
Metagenomic analysis has extraordinary potential to improve our understanding of microbial populations in their natural environment and identify novel genes of interest. The key feature of such analyses is that they are performed using metagenomic libraries constructed from total DNA isolated from a particular niche rather than a laboratory culture. Thus, metagenomic analyses potentially allow access to all the genetic resources present in an environment, regardless of whether or not they belong to micro-organisms that can be cultured in the laboratory. Sequence-based metagenomic analyses rely on comparisons with databases of known genomic sequences whilst functional analyses rely on screening libraries on the basis of the phenotypes cloned DNA can confer to host bacteria. Therefore, functional analysis allows the identification of novel genes with functions that could not have been predicted from their DNA sequence. This book discusses metagenomics' methods, applications and perspectives.
Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline.
This book describes how genomics has revolutionized our scientific understanding of agriculturally important plant-associated bacteria. Each chapter focuses on the genomics of particular bacteria: the first described plant pathogen, "Erwinia amylovora"; phytoplasmas lacking cell walls; fastidious, phloem-restricted liberibacters; "Pseudomonas syringae," which is a genetically tractable model system; "Xanthomonas citri," which causes a disease that can devastate citrus crops and "Pseudomonas fluorescens," which can protect plants from diseases.
Topics considered in this volume include the importance of horizontal gene transfer in originating new bacterial strains and species and advances in transcriptomics that allow us to describe the complex regulatory networks critical to plant-microbe interactions. The availability of the "Xanthomonas oryzae" genome has led to new technologies in genome editing, which will revolutionize approaches to genetic engineering, even in eukaryotes. The contributions show how genomics has greatly accelerated progress toward understanding the biology of these bacteria and how that understanding can be translated into novel crop protection methods.
Due to its data handling and modeling capabilities as well as its flexibility, R is becoming the most widely used software in bioinformatics. R Programming for Bioinformatics explores the programming skills needed to use this software tool for the solution of bioinformatics and computational biology problems. Drawing on the author's first-hand experiences as an expert in R, the book begins with coverage on the general properties of the R language, several unique programming aspects of R, and object-oriented programming in R. It presents methods for data input and output as well as database interactions. The author also examines different facets of string handling and manipulations, discusses the interfacing of R with other languages, and describes how to write software packages. He concludes with a discussion on the debugging and profiling of R code. With numerous examples and exercises, this practical guide focuses on developing R programming skills in order to tackle problems encountered in bioinformatics and computational biology.
Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, "ancient DNA" (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.
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