Bioinformatics and Functional Genomics, Second Edition

Preface to the First Edition

ORIGINS OF THIS BOOK

This book emerged from lecture notes I prepared several years ago for an introductory bioinformatics and genomics course at the Johns Hopkins School of Medicine. The first class consisted of about 70 graduate students and several hundred auditors, including postdoctoral fellows, technicians, undergraduates, and faculty. Those who attended the course came from a broad variety of fields—students of genetics, neuroscience, immunology or cell biology, clinicians interested in particular diseases, statisticians and computer scientists, virologists and microbiologists. They had a common interest in wanting to understand how they could apply the tools of computer science to solve biological problems. This is the domain of bioinformatics, which I define most simply as the interface of computer science and molecular biology. This emerging field relies on the use of computer algorithms and computer databases to study proteins, genes, and genomes. Functional genomics is the study of gene function using genome-wide experimental and computational approaches.

COMPARISON

At its essence, the field of bioinformatics is about comparisons. In the first third of the book we learn how to extract DNA or protein sequences from the databases, and then to compare them to each other in a pairwise fashion or by searching an entire database. For the student who has a gene of particular interest, a natural question is to ask “what other genes (or proteins) ...