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.

Engineered Nanopores for Bioanalytical Applications is the first book to focus primarily on practical analytical applications of nanopore development. These nanoscale analytical techniques have exciting potential because they can be used in applications such as DNA sequencing, DNA fragment sizing, DNA/protein binding, and protein/protein binding.This book provides a solid professional reference on nanopores for readers in academia, industry and engineering and biomedical fields. In addition, the book describes the instrumentation, fabrication, and experimental methods necessary to carry out nanopore-based experiments for developing new devices. - Includes application case studies for detection, identification and analysis of biomolecules and related functional nanomaterials - Introduces the techniques of manufacturing solid state materials with functional nanopores - Explains the use of nanopores in DNA sequencing and the wider range of applications from environmental monitoring to forensics

This book covers the latest techniques that enable us to study the genome in detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism

Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra

Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

This volume provides comprehensive dry and wet experiments, methods, and applications on nanopore sequencing. Chapters guide readers through bioinformatic procedures, genome sequencing, analysis of repetitive regions, structural variations, rapid and on-site microbial identification, epidemiology, and transcriptome analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Nanopore Sequencing: Methods and Protocols aims to be comprehensive guide for researchers.