Sequencing Apple's DNA

Written by leading experts from industry and academia, this first single comprehensive resource addresses recent developments in next generation DNA sequencing technology and their impact on genome research, drug discovery and health care. As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing.

Tag-based approaches were originally designed to increase the throughput of capillary sequencing, where concatemers of short sequences were first used in expression profiling. New Next Generation Sequencing methods largely extended the use of tag-based approaches as the tag lengths perfectly match with the short read length of highly parallel sequencing reactions. Tag-based approaches will maintain their important role in life and biomedical science, because longer read lengths are often not required to obtain meaningful data for many applications. Whereas genome re-sequencing and de novo sequencing will benefit from ever more powerful sequencing methods, analytical applications can be performed by tag-based approaches, where the focus shifts from 'sequencing power' to better means of data analysis and visualization for common users. Today Next Generation Sequence data require powerful bioinformatics expertise that has to be converted into easy-to-use data analysis tools. The book's intention is to give an overview on recently developed tag-based approaches along with means of their data analysis together with introductions to Next-Generation Sequencing Methods, protocols and user guides to be an entry for scientists to tag-based approaches for Next Generation Sequencing.

An up-to-date and comprehensive treatment of the fundamentals of scheduling theory, including recent advances and state-of-the-art topics Principles of Sequencing and Scheduling strikes a unique balance between theory and practice, providing an accessible introduction to the concepts, methods, and results of scheduling theory and its core topics. With real-world examples and up-to-date modeling techniques, the book equips readers with the basic knowledge needed for understanding scheduling theory and delving into its applications. The authors begin with an introduction and overview of sequencing and scheduling, including single-machine sequencing, optimization and heuristic solution methods, and models with earliness and tardiness penalties. The most current material on stochastic scheduling, including correct scheduling of safety time and the use of simulation for optimization, is then presented and integrated with deterministic models. Additional topical coverage includes: Extensions of the basic model Parallel-machine models Flow shop scheduling Scheduling groups of jobs The job shop problem Simulation models for the dynamic job shop Network methods for project scheduling Resource-constrained project scheduling Stochastic and safe scheduling Extensive end-of-chapter exercises are provided, some of which are spreadsheet-oriented, and link scheduling theory to the most popular analytic platform among today's students and practitioners—the Microsoft Office Excel® spreadsheet. Extensive references direct readers to additional literature, and the book's related Web site houses material that reinforces the book's concepts, including research notes, data sets, and examples from the text. Principles of Sequencing and Scheduling is an excellent book for courses on sequencing and scheduling at the upper-undergraduate and graduate levels. It is also a valuable reference for researchers and practitioners in the fields of statistics, computer science, operations research, and engineering.

OGENOTYPING BY SEQUENCING FOR CROP IMPROVEMENT A thoroughly up-to-date exploration of genotyping-by-sequencing technologies and related methods in plant science In Genotyping by Sequencing for Crop Improvement, a team of distinguished researchers delivers an in-depth and current exploration of the latest advances in genotyping-by-sequencing (GBS) methods, the statistical approaches used to analyze GBS data, and its applications, including quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS) in crop improvement. This edited volume includes insightful contributions on a variety of relevant topics, like advanced molecular markers, high-throughput genotyping platforms, whole genome resequencing, QTL mapping with advanced mapping populations, analytical pipelines for GBS analysis, and more. The distinguished contributors explore traditional and advanced markers used in plant genotyping in extensive detail, and advanced genotyping platforms that cater to unique research purposes are discussed, as is the whole-genome resequencing (WGR) methodology. The included chapters also examine the applications of these technologies in several different crop categories, including cereals, pulses, oilseeds, and commercial crops. Genotyping by Sequencing for Crop Improvement also offers: A thorough introduction to molecular marker techniques and recent advancements in the technology Comprehensive explorations of the genotyping of seeds while preserving their viability, as well as advances in genomic selection Practical discussions of opportunities and challenges relating to high throughput genotyping in polyploid crops In-depth examinations of recent advances and applications of GBS, GWAS, and GS in cereals, pulses, oilseeds, millets, and commercial crops Perfect for practicing plant scientists with an interest in genotyping-by-sequencing technology, Genotyping by Sequencing for Crop Improvement will also earn a place in the libraries of researchers and students seeking a one-stop reference on the foundational aspects of – and recent advances in – genotyping-by-sequencing, genome-wide association studies, and genomic selection.

Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.

How to design, execute, and interpret experiments for protein sequencing using mass spectrometry The rapid expansion of searchable protein and DNA databases in recent years has triggered an explosive growth in the application of mass spectrometry to protein sequencing. This timely and authoritative book provides professionals and scientists in biotechnology research with complete coverage of procedures for analyzing protein sequences by mass spectrometry, including step-by-step guidelines for sample preparation, analysis, and data interpretation. Michael Kinter and Nicholas Sherman present their own high-quality, laboratory-tested protocols for the analysis of a wide variety of samples, demonstrating how to carry out specific experiments and obtain fast, reliable results with a 99% success rate. Readers will get sufficient experimental detail to apply in their own laboratories, learn about the proper selection and operation of instruments, and gain essential insight into the fundamental principles of mass spectrometry and protein sequencing. Coverage includes: Peptide fragmentation and interpretation of product ion spectra Basic polyacrylamide gel electrophoresis Preparation of protein digests for sequencing experiments Mass spectrometric analysis using capillary liquid chromatography Techniques for protein identification by database searches Characterization of modified peptides using tandem mass spectrometry And much more

Includes a Foreword by Dr. James D. Watson, the co-discoverer of the DNA double helix, and Dr. Jan A. Witkowski. «From the Foreword by Drs. Watson and Witkowski: 'DNA: Forensic and Legal Applications is a comprehensive and invaluable guide to the field, covering topics ranging from collecting samples in the field to presenting the complex results to a jury. We are sure that it will play its part in promoting this most powerful tool in the forensic scientist's armamentarium.'» DNA: Forensic and Legal Applications covers the technology and laws related to DNA, as well as the use of DNA evidence in the legal system. This combination of science and law makes it the first comprehensive title of its kind and an appropriate reference for those with both elementary and advanced knowledge of the topic. It draws together in one source information that would previously have required extensive research and reliance on experts to obtain, offering both breadth and depth in a clear style without s acrificing scholarly goals. With material from both scientific and legal areas, DNA: Forensic and Legal Applications covers the latest advances in technology. It provides an ideal text for forensic scientists and students of forensic science, analytical chemists, lawyers, judges, police officers, and detectives.

DNA ORIGAMI Discover the impact and multidisciplinary applications of this subfield of DNA nanotechnology DNA origami refers to the technique of assembling single-stranded DNA template molecules into target two- and three-dimensional shapes at the nanoscale. This is accomplished by annealing templates with hundreds of DNA strands and then binding them through the specific base-pairing of complementary bases. The inherent properties of these DNA molecules—molecular recognition, self-assembly, programmability, and structural predictability—has given rise to intriguing applications from drug delivery systems to uses in circuitry in plasmonic devices. The first book to examine this important subfield, DNA Origami brings together leading experts from all fields to explain the current state and future directions of this cutting-edge avenue of study. The book begins by providing a detailed examination of structural design and assembly systems and their applications. As DNA origami technology is growing in popularity in the disciplines of chemistry, materials science, physics, biophysics, biology, and medicine, interdisciplinary studies are classified and discussed in detail. In particular, the book focuses on DNA origami used for creating new functional materials (combining chemistry and materials science; DNA origami for single-molecule analysis and measurements (as applied in physics and biophysics); and DNA origami for biological detection, diagnosis and therapeutics (medical and biological applications). DNA Origami readers will also find: A complete guide for newcomers that brings together fundamental and developmental aspects of DNA origami technology Contributions by a leading team of experts that bring expert views from different angles of the structural developments and applications of DNA origami An emerging and impactful research topic that will be of interest in numerous multidisciplinary areas A helpful list of references provided at the end of each chapter to give avenues for further study Given the wide scope found in this groundbreaking work, DNA Origami is a perfect resource for nanotechnologists, biologists, biophysicists, chemists, materials scientists, medical scientists, and pharmaceutical researchers.

With its focus on a completely novel class of pharmaceuticals, this book collates the hitherto scarce literature about DNA drug formulation keenly desired by biotechnologists, molecular biologists and pharmacists, as well as those working in the biotechnological and pharmaceutical industries. As such, this volume presents a wide range of gene delivery systems needed for different therapeutic applications. It fills the gap between research and clinical trials and describes pharmaceutical fundamentals for the development of efficient DNA pharmaceuticals.