Bioinformatics And Functional Genomics, 3rd edition


Welcome to the website for Bioinformatics and Functional Genomics (3rd edition, Wiley-Blackwell, 2015). This site features a complete bioinformatics teaching curriculum: PowerPoints for an entire course taught at the Johns Hopkins School of Medicine, and web site links organized by chapter in the new textbook, Bioinformatics and Functional Genomics. A separate resource (at the Wiley Higher Education site) is available to instructors.

Features of the textbook

This book is organized into three parts. In part I (Chapters 1-7), we introduce the field of bioinformatics. Topics include access to sequence (and other) data, pairwise sequence alignment, BLAST and other methods of searching databases, multiple sequence alignment, and phylogeny. In part II (Chapters 8-14), we discuss functional genomics, moving from DNA (including next-generation sequencing) to RNA (including RNAseq) to protein. Part III (Chapters 15-21) describes the tree of life from a genomics perspective, including chapters on viruses, bacteria and archaea, and the eukaryotes. Practically, I have used this textbook in teaching two courses: an introduction to bioinformatics (Chapters 1-14) and a course on genomics in which we survey the tree of life (Chapters 15-21).

About this website

This site includes Web Documents and WebLinks that are referred to in each chapter. For example, Chapter 7 describes how phylogenetic trees are made. You can use the Web Documents to obtain the raw sequence data that go into making a particular tree, and to see the outputs from a variety of software packages that produce phylogenetic trees. Additionally I provide PowerPoints that teachers may use and modify (for teaching purposes only). In some cases there are audiovisual files from lectures at Johns Hopkins.

Solutions To Problems

Solutions to problems in Chapters 2-7

Solutions to problems in Chapters 8-14

Solutions to problems in Chapters 15-21


If you have any questions, drop me an email at