Welcome to Mathematical Foundations of Bioinformatics

By Marshall Hampton

About

This online book was primarily developed from lecture notes for the University of Minnesota Duluth course Math 5233: Mathematical Foundations of Bioinformatics.

CONTENTS

• Introduction
  • Computing (Useful Links)
  • Essentials of molecular biology
• Part 1: Sequence Alignment, Evolution, Entropy, and Information
  • Sequence alignment algorithms
  • Fast heuristic alignment and assembly methods
  • Models of DNA substitution and evolutionary distance
  • Empirical protein models, entropy, and scoring matrices
• Part 2: Populations and Phylogenies
  • Population genetics and the coalescent
  • Phylogenetics
• Part 3: Patterns
  • Statistical analysis of sequences
  • Simple pattern recognition: Regular expressions and position-specific scoring matrices
  • Hidden Markov Models
  • Forward, backward, and Baum-Welch algorithms
  • Artificial neural networks
  • RNA
  • Databases
  • Formal Ontologies
• Appendices

License

This work (text, mathematical images, and javascript applets) is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Biographical images are from Wikipedia and have their own (similar) licenses.