Basant K. Tiwary - Bioinformatics and Computational Biology: A Primer for Biologists

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The goal of writing this book is to explain the theoretical foundation and mathematical concepts of bioinformatics and computational biology to a biologist who is new to this subject. This book is aimed at undergraduate and graduate students of any biological discipline like life sciences, genetics, medicine, agriculture, animal husbandry and bioengineering in addition to the students of bioinformatics and computational biology. Like any other technical subject, bioinformatics has its own language and terms. All terms are explained in simple language avoiding mathematical jargon. This textbook starts with basic theoretical concepts in bioinformatics building in a stepwise fashion leading to an optimum level where the application of bioinformatics in medicine, agriculture, animal husbandry and bioengineering is apparent. This work examines the underlying principles and methods in bioinformatics applied to answer real biological problems. The last four chapters are completely applied in nature although theoretical concepts discussed in earlier eight chapters are a prerequisite for understanding the applications. The exercises and multiple-choice questions at the end of each chapter will reinforce the understanding of the concepts discussed in the text. The worked-out answers to exercises in each chapter will provide a thorough understanding of the problems in bioinformatics and their stepwise solutions. Some useful references are added at the end of each chapter for further reading.

I am indebted to all my teachers who have shaped my understanding of interdisciplinary science. I thank my Ph.D. advisor, Prof. Arun K. Ray, who has given me the freedom to explore the interdisciplinary and experimental biological research at Bose Institute. I express my heartfelt gratitude to Prof. Wen-Hsiung Li, James Watson Professor at the University of Chicago to initiate me in the field of computational genomics during my stay in his lab as a visiting faculty. I am also grateful to all research workers across the world in the field of bioinformatics and computational biology for building the knowledge base of the book. I thank all my colleagues and students at the Department of Bioinformatics, Pondicherry University, for creating a wonderful teaching-learning environment. Special thanks to Dr. R. Krishna for reading and commenting on the chapter on structural bioinformatics. I also thank the team at Springer Nature for making this academic endeavour successful.

Biology has undergone a sea change in the last two decades and transformed itself into a true quantitative science akin to mathematics, physics and statistics. Although biology was fortunate enough to be enriched by great mathematicians like G.H. Hardy, R.A. Fisher, J.B.S. Haldane and Sewall Wright during the last century, it continued to remain largely a descriptive natural subject with less emphasis on quantitative methods until the end of last century. The advent of fast microcomputers and advanced molecular biology techniques such as PCR, microarray and next-generation sequencing has led to the emergence of high-throughput data in biology. Surprisingly, the generation of genomic data has surpassed astronomical data in terms of volume and became the most abundant available big data today. These drastic developments in generation of biological data has necessitated a parallel development of computational methods to analyse the data in a meaningful way and ultimately led to the emergence of a new discipline known as bioinformatics. Although biology and bioinformatics are currently being treated as separate disciplines, the time is not far away when a thin line of division between these two disciplines will gradually disappear in favour of a more holistic biology.

Bioinformatics and computational biology has been defined as distinct subjects initially albeit a significant overlap at the interface of two disciplines. The NIH Biomedical Information Science and Technology Initiative Consortium in the year 2000 proposed the working definitions of Bioinformatics and Computational Biology. Bioinformatics was defined as the research, development or application of computational tools and approaches for expanding the use of biological, medical, behavioural or health data, including those to acquire, store, organize, archive, analyse or visualize such data. On the other hand, computational biology was defined as the development and application of data-analytical and theoretical methods, mathematical modelling and computational simulation techniques to the study of biological, behavioural and social systems. In simple words, bioinformatics is the biological application of information technology with focus on data storage, whereas computational biology is an application of information technology in understanding biology with more emphasis on analytical algorithms. In other words, computational biology is a computational approach to analyse and understand biological processes. However, under current scenario, many areas in these two disciplines are overlapping, henceforth, we will use the term interchangeably in the rest of the book.