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Library of Congress Cataloging-in-Publication Data
Names: Baxevanis, Andreas D., editor. | Bader, Gary D., editor. | Wishart, David S., editor.
Title: Bioinformatics / edited by Andreas D. Baxevanis, Gary D. Bader, David S. Wishart.
Other titles: Bioinformatics (Baxevanis)
Description: Fourth edition. | Hoboken, NJ : Wiley, 2020. | Includes bibliographical references and index.
Identifiers: LCCN 2019030489 (print) | ISBN 9781119335580 (cloth) | ISBN 9781119335962 (adobe pdf) | ISBN 9781119335955 (epub)
Subjects: MESH: Computational Biology--methods | Sequence Analysis--methods | Base Sequence | Databases, Nucleic Acid | Databases, Protein
Classification: LCC QH324.2 (print) | LCC QH324.2 (ebook) | NLM QU 550.5.S4 | DDC 570.285–dc23
LC record available at https://lccn.loc.gov/2019030489
LC ebook record available at https://lccn.loc.gov/2019030490
Cover Design: Wiley
Cover Images: © David Wishart, background © Suebsiri/Getty Images
Foreword
As I review the material presented in the fourth edition of Bioinformatics I am moved in two ways, related to both the past and the future.
Looking to the past, I am moved by the amazing evolution that has occurred in our field since the first edition of this book appeared in 1998. Twenty-one years is a long, long time in any scientific field, but especially so in the agile field of bioinformatics. To use the well-trodden metaphor of the “biology moonshot,” the launchpad at the beginning of the twenty-first century was the determination of the human genome. Discovery is not the right word for what transpired – we knew it was there and what was needed. Synergy is perhaps a better word; synergy of technological development, experiment, computation, and policy. A truly collaborative effort to continuously share, in a reusable way, the collective efforts of many scientists. Bioinformatics was born from this synergy and has continued to grow and flourish based on these principles.
That growth is reflected in both the scope and depth of what is covered in these pages. These attributes are a reflection of the increased complexity of the biological systems that we study (moving from “simple” model organisms to the human condition) and the scales at which those studies take place. As a community we have professed multiscale modeling without much to show for it, but it would seem to be finally here. We now have the ability to connect the dots from molecular interactions, through the pathways to which those molecules belong to the cells they affect, to the interactions between those cells through to the effects they have on individuals within a population. Tools and methodologies that were novel in earlier editions of this book are now routine or obsolete, and newer, faster, and more accurate procedures are now with us. This will continue, and as such this book provides a valuable snapshot of the scope and depth of the field as it exists today.
Looking to the future, this book provides a foundation for what is to come. For me this is a field more aptly referred to (and perhaps a new subtitle for the next edition) as Biomedical Data Science. Sitting as I do now, as Dean of a School of Data Science which collaborates openly across all disciplines, I see rapid change akin to what happened to birth bioinformatics 20 or more years ago. It will not take 20 years for other disciplines to catch up; I predict it will take 2! The accomplishments outlined in this book can help define what other disciplines will accomplish with their own data in the years to come. Statistical methods, cloud computing, data analytics, notably deep learning, the management of large data, visualization, ethics policy, and the law surrounding data are generic. Bioinformatics has so much to offer, yet it will also be influenced by other fields in a way that has not happened before. Forty-five years in academia tells me that there is nothing to compare across campuses to what is happening today. This is both an opportunity and a threat. The editors and authors of this edition should be complimented for setting the stage for what is to come.
Philip E. Bourne, University of Virginia
Preface
In putting together this textbook, we hope that students from a range of fields – including biology, computer science, engineering, physics, mathematics, and statistics – benefit by having a convenient starting point for learning most of the core concepts and many useful practical skills in the field of bioinformatics, also known as computational biology.
Students interested in bioinformatics often ask about how should they acquire training in such an interdisciplinary field as this one. In an ideal world, students would become experts in all the fields mentioned above, but this is actually not necessary and realistically too much to ask. All that is required is to combine their scientific interests with a foundation in biology and any single quantitative field of their choosing. While the most common combination is to mix biology with computer science, incredible discoveries have been made through finding creative intersections with any number of quantitative fields. Indeed, many of these quantitative fields typically overlap a great deal, especially given their foundational use of mathematics and computer programming. These natural relationships between fields provide the foundation for integrating diverse expertise and insights, especially when in the context of performing bioinformatic analyses.
While bioinformatics is often considered an independent subfield of biology, it is likely that the next generation of biologists will not consider bioinformatics as being separate and will instead consider gaining bioinformatics and data science skills as naturally as they learn how to use a pipette. They will learn how to program a computer, likely starting in elementary school. Other data science knowledge areas, such as math, statistics, machine learning, data processing, and data visualization will also be part of any core curriculum. Indeed, the children of one of the editors recently learned how to construct bar plots and other data charts in kindergarten! The same editor is teaching programming in R (an important data science programming language) to all incoming biology graduate students at his university starting this year.
As bioinformatics and data science become more naturally integrated in biology, it is worth noting that these fields actively espouse a culture of open science. This culture is motivated by thinking about why we do science in the first place. We may be curious or like problem solving. We could also be motivated by the benefits to humanity that scientific advances bring, such as tangible health and economic benefits. Whatever the motivating factor, it is clear that the most efficient way to solve hard problems is to work together as a team, in a complementary fashion and without duplication of effort. The only way to make sure this works effectively is to efficiently share knowledge and coordinate work across disciplines and research groups. Presenting scientific results in a reproducible way, such as