Bio/Recursion

Bio/Recursion introduces topics in programming, computer science, and bioinformatics via examples in the R programming language. While often associated with statistics, Bio/Recursion employs R's algorithmic capabilities to implement and visualize several fascinating methods, ranging from DNA alignment to drawing fractal trees.

Recursion (self-reference) provides a central theme, with topics spanning searching, sorting, data structures, proofs, fractals, and important bio-informatics algorithms. Along the way, over 100 color illustrations and 150 code blocks illuminate the text, and dozens of exercises challenge the readers' imagination.

Chapters:

1. Programming in R
2. Recursive Structures
3. Searching and Sorting
4. Induction and Stacks
5. Hash Tables, Memoization, and Dynamic Programming
6. Alignment
7. Fast Alignment and Local Alignment
8. Hidden Markov Models
9. Recursive Drawing and L-Systems

Shawn T. O'Neil earned a BS in computer science from Northern Michigan University, and later an MS and PhD in the same subject from the University of Notre Dame. His past and current research focuses on bioinformatics. O'Neil has developed and taught several courses at both Notre Dame and Oregon State University, where he currently works at the Center for Genome Research and Biocomputing.