Preface

Many biological fields, including genetics, immunology, genomics, and epigenomics, can be readily integrated with bioinformatics and sequencing. In fact, sequencing is becoming an indispensable tool for biological and medical investigations, especially for the study of cancer, genetics, epigenetics, immunology, and developmental biology. Foreseeing the potential applications of sequencing technologies, we have initiated a sequence data analysis course at the Institute of Zoology, National Taiwan University to introduce sequencing technologies, genomics, epigenomics, bioinformatics, and biotechnologies to graduate and undergraduate students. At the same time, I started organizing the teaching materials to compose this book. Most of the materials were derived from my research at Academia Sinica and my teaching at National Taiwan University (NTU), National Central University (NCU), and National Yang Ming University (NYMU). Additionally, there are some from my previous work in the United States and Singapore.

Besides college students, this book is also written for people who already have some biological background, or with an interest in knowing more about DNA sequencing and its applications. With this effort, we hope to help develop sequence-associated knowledge among people from all walks of life, including researchers, professionals, and amateurs working in biology-related or -unrelated fields, with or without an ambition to apply sequencing technologies to biological or medical investigations. Extracting biological meaning from large quantities of sequence data is an art. We intend to help readers appreciate the various types of sequencing technologies, and learn how to use sequencing technologies to unravel the mystery of the biological system.

Sequence data analysis is not only an art, but also a tool to help researchers develop a constructive philosophy. When a diploma is awarded to a candidate, it may be treated by the recipient as a degree which can then help the graduate to find a better job, or achieve a higher social status. Some recipients may take it more seriously and use it for further, and possibly more advanced, studies. Similarly, sequence data analysis can be treated as either a course to be accomplished in class, or, alternatively, a process which will be a guide to the further understanding of the life of nanoscopic molecules within a cell. We gain many more experiences through the years of working in a lab, and, with those proficiencies, we build our philosophy. Sequencing and sequence data analysis can help us make sense of the activities which take place on a daily basis in the molecular world of our bodies, even though these activities are impalpable to the naked eye. Being able to “see” things that cannot “normally” be seen can help us build a philosophy, in which we travel between the macroscopic and molecular worlds.

A sincere attitude towards sequence data analysis is essential. Since omics sequence datasets are normally at large volumes, these data cannot be handled by traditional means, but by computer programs. Frequently we find bugs in computer programs which may produce erroneous or misleading results. A bug is a bug. No matter whether it is big or small, it has to be removed, so as to obtain the real molecular status of interest. Moreover, the author would like to emphasize the importance of practical exercise. Students are strongly encouraged to personally construct sequencing libraries, run sequencing, and analyze sequence libraries or related libraries whenever possible.

Although this book carries a mission, readers can treat it either as a novel, or a science fiction story. The development of sequencing technologies per se is science fiction, isn’t it? With limitations in man power and time, the contents of this edition may not be able to completely satisfy serious readers. Your opinions and suggestions are warmly welcomed!