The Guide to Human Genome Computing is invaluable to scientists who wish to make use of the powerful computing tools now available to assist them in the field of human genome analysis. This book clearly explains access and use of sequence databases, and presents the various computer packages used to analyze DNA sequences, measure linkage analysis, compare and align DNA sequences from different genes or organisms, and infer structural and functional information about proteins from sequence data. This Second Edition contains completely updated material. Rather than a revision of the previous volume, the Second Edition is essentially a new book, based on the subjects which will be of interest over the coming years. This new book is international, both in scope and authorship. - Computing resources for the following are clearly explained: Internet resources - databases etc. - Genetic analysis - Sib-pair studies - Comparative mapping - Radiation hybrids - Sequence ready clone maps - Human genome sequencing - ESTs - Gene prediction - Gene expression
Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.
Significant advances in our knowledge of genetics were made during the twentieth century but in the most recent decades, genetic research has dramatically increased its impact throughout society. Genetic issues are now playing a large role in health and public policy, and new knowledge in this field will continue to have significant implications for individuals and society. Written for the non-majors human genetics course, Human Genetics, Third Edition will increase the genetics knowledge of students who are learning about human genetics for the first time. This thorough revision of the best-selling Human Genome, Second Edition includes entirely new chapters on forensics, stem cell biology, bioinformatics, and societal/ethical issues associated with the field. New special features boxes make connections between human genetics and human health and disease. Carefully crafted pedagogy includes chapter-opening case studies that set the stage for each chapter; concept statements interspersed throughout the chapter that keep first-time students focused on key concepts; and end-of-chapter questions and critical thinking activities. This new edition will contribute to creating a genetically literate student population that understands basic biological research, understands elements of the personal and health implications of genetics, and participates effectively in public policy issues involving genetic information. - Includes topical material on forensics, disease studies, and the human genome project to engage non-specialist students - Full, 4-color illustration program enhances and reinforces key concepts and themes - Uniform organization of chapters includes interest boxes that focus on human health and disease, chapter-opening case studies, and concept statements to engage non-specialist readers
The DNA sequence that comprises the human genome--the genetic blueprint found in each of our cells--is undoubtedly the greatest code ever to be broken. Completed at the dawn of a new millennium, the feat electrified both the scientific community and the general public with its tantalizing promise of new and better treatments for countless diseases, including Alzheimer's, cancer, diabetes, and Parkinson's. Yet what is arguably the most important discovery of our time has also opened a Pandora's box of questions about who we are as humans and how the unique information stored in our genomes can and might be used, making it all the more important for everyone to understand the new science of genomics. In the CURIOSITY GUIDE TO THE HUMAN GENOME, Dr. John Quackenbush, a renowned scientist and professor, conducts a fascinating tour of the history and science behind the Human Genome Project and the technologies that are revolutionizing the practice of medicine today. With a clear and engaging narrative style, he demystifies the fundamental principles of genetics and molecular biology, including the astounding ways in which genes function, alone or together with other genes and the environment, to either sustain life or trigger disease. In addition, Dr. Quackenbush goes beyond medicine to examine how DNA-sequencing technology is changing how we think of ourselves as a species by providing new insights about our earliest ancestors and reconfirming our inextricable link to all life on earth. Finally, he explores the legal and ethical questions surrounding such controversial topics as stem cell research, prenatal testing, forensics, and cloning, making this volume of the Curiosity Guides series an indispensable resource for navigating our brave new genomic world.
This second edition of a very successful text reflects the tremendous pace of human genetics research and the demands that it places on society to understand and absorb its basic implications. The human genome has now been officially mapped and the cloning of animals is becoming a commonplace scientific discussion on the evening news. Join authors Julia Richards and Scott Hawley as they examine the biological foundations of humanity, looking at the science behind the sensation and the current and potential impact of the study of the genome on our society. The Human Genome, Second Edition is ideal for students and non-professionals, but will also serve as a fitting guide for the novice geneticist by providing a scientific, humanistic, and ethical frame of reference for a more detailed study of genetics. New in this edition: · 60% new material, including data from the Human Genome Project and the latest genetics and ethics discussions · Several new case studies and personal stories that bring the concepts of genetics and heredity to life · Simplified treatment of material for non-biology majors · New full-color art throughout the text · New co-author, Julia Richards, joins R. Scott Hawley in this revision
How global biotechnology is redefining "life itself." In the age of global biotechnology, DNA can exist as biological material in a test tube, as a sequence in a computer database, and as economically valuable information in a patent. In The Global Genome, Eugene Thacker asks us to consider the relationship of these three entities and argues that—by their existence and their interrelationships—they are fundamentally redefining the notion of biological life itself. Biological science and the biotech industry are increasingly organized at a global level, in large part because of the use of the Internet in exchanging biological data. International genome sequencing efforts, genomic databases, the development of World Intellectual Property policies, and the "borderless" business of biotech are all evidence of the global intersections of biology and informatics—of genetic codes and computer codes. Thacker points out the internal tension in the very concept of biotechnology: the products are more "tech" than "bio," but the technology itself is fully biological, composed of the biomaterial labor of genes, proteins, cells, and tissues. Is biotechnology a technology at all, he asks, or is it a notion of "life itself" that is inseparable from its use in the biotech industry? The three sections of the book cover the three primary activities of biotechnology today: the encoding of biological materials into digital form—as in bioinformatics and genomics; its recoding in various ways—including the "biocolonialism" of mapping genetically isolated ethnic populations and the newly pervasive concern over "biological security"; and its decoding back into biological materiality—as in tissue engineering and regenerative medicine. Thacker moves easily from science to philosophy to political economics, enlivening his account with ideas from such thinkers as Georges Bataille, Georges Canguilhem, Michel Foucault, Antonio Negri, and Paul Virilio. The "global genome," says Thacker, makes it impossible to consider biotechnology without the context of globalism.
In this visionary look into the future, Freeman Dyson argues that technological changes fundamentally alter our ethical and social arrangements and that three rapidly advancing new technologies--solar energy, genetic engineering, and world-wide communication--together have the potential to create a more equal distribution of the world's wealth. Dyson begins by rejecting the idea that scientific revolutions are primarily concept driven. He shows rather that new tools are more often the sparks that ignite scientific discovery. Such tool-driven revolutions have profound social consequences--the invention of the telescope turning the Medieval world view upside down, the widespread use of household appliances in the 1950s replacing servants, to cite just two examples. In looking ahead, Dyson suggests that solar energy, genetics, and the Internet will have similarly transformative effects, with the potential to produce a more just and equitable society. Solar power could bring electricity to even the poorest, most remote areas of third world nations, allowing everyone access to the vast stores of information on the Internet and effectively ending the cultural isolation of the poorest countries. Similarly, breakthroughs in genetics may well enable us to give our children healthier lives and grow more efficient crops, thus restoring the economic and human vitality of village cultures devalued and dislocated by the global market. Written with passionate conviction about the ethical uses of science,The Sun, the Genome, and the Internetis both a brilliant reinterpretation of the scientific process and a challenge to use new technologies to close, rather than widen, the gap between rich and poor.
"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.
There is growing enthusiasm in the scientific community about the prospect of mapping and sequencing the human genome, a monumental project that will have far-reaching consequences for medicine, biology, technology, and other fields. But how will such an effort be organized and funded? How will we develop the new technologies that are needed? What new legal, social, and ethical questions will be raised? Mapping and Sequencing the Human Genome is a blueprint for this proposed project. The authors offer a highly readable explanation of the technical aspects of genetic mapping and sequencing, and they recommend specific interim and long-range research goals, organizational strategies, and funding levels. They also outline some of the legal and social questions that might arise and urge their early consideration by policymakers.
Recent advances in the biosciences have led to a range of powerful new technologies, particularly nucleic acid, protein and cell-based methodologies. The most recent insights have come to affect how scientists investigate and define cellular processes at the molecular level. This book expands upon the techniques included in the first edition, providing theory, outlines of practical procedures, and applications for a range of techniques. Written by a well-established panel of research scientists, the book provides an up-to-date collection of methods used regularly in the authors’ own research programs.
