Lawrence Technological University
College of Arts and Science
Department of Mathematics and Computer Sciences

Introduction to Bioinformatics, MCS 5603, Spring 2015

Handouts | Lecture Notes

Credit Hours3
Dates Monday, January 12, 2015 - Monday, May 4, 2015
Times5:45-7:00pm, Mondays, Wednesdays
Class RoomS326
Instructor John M. Miller M.D.
Office Hours Before class, by email or Blackboard discussion board, and by appointment
Phone(248) 204-3560
Web Page
also see the LTU Blackboard Pages for this course
Objective This course will offer the student an timely introduction to the emerging field of bioinformatics, including hands-on experience with its algorithms. Both recent advances in computer science for the biologist and recent advances in biology for the computer scientist will be discussed.
Textbook Exploring Bioinformatics: A Project Based Approach 2nd Ed. by Caroline St. Clair and Jonathan Visick, Jones and Bartlett 2015, ISBN 978-1-284-03424-0
1 Introduction 01/12 01/14
2 Chapter 1 St. Clair & Visick, Web Resources and NCBI eUtilities 01/19 01/21
3 Homework Assignment 1: Automating with the NCBI eUtilities 01/26 01/28
4 Chapter 2 St. Clair & Visick, Manipulating Nucleotides as Strings 02/02 02/04
5 Homework Assignment 2: Chapter 2 St. Clair & Visick, Putting your skills into practice, Problems 1-5 02/09 02/11
6 Chapter 3 St. Clair & Visick, Alignments and Algorithms 02/16 02/18
7 Chapter 3 St. Clair & Visick, continued 02/23 02/25
8 Homework Assignment 3: Chapter 3 St. Clair & Visick, Putting your skills into practice, Problem 5 03/02 03/04
9 HIPAA and the Common Rule 03/16 03/18
10 Homework Assignment 4: De-identification of datasets 03/23 03/25
11 Chapter 6 St. Clair & Visick, Edit Distance and Phylogeny 03/30 04/01
12 Homework Assignment 5: Chapter 6 St. Clair & Visick, Putting your skills into practice, Problem 1 04/06 04/08
13 Chapter 7 St. Clair & Visick, Tree Building in Molecular Phylogenetics 04/13 04/15
14 Homework Assignment 6: Chapter 7 St. Clair & Visick, Putting your skills into practice, Problems 1, 2 04/20 04/22
15 Finding a novel gene for study using BLAST (Results to be presented as a final exam project) 04/27 04/29
Homework Assignments 1, 2, 3, 4, 5, 6 15% of grade for each of the best 5
Final Exam Presentation, Monday, 5/4/15 5:30-7:20pm 25% of grade
Grade Scale
Fbelow 60 (below 70 for graduate students)
General Policies Assignments and projects are to be individual efforts unless prior approval is obtained from the instructor. The student's personal academic honor code statement is to be provided with their work or kept on file in the case of a graduate student.
Late Assignments Late assignments will be given half credit for one week and no credit thereafter.
Academic Integrity Course participation will always be conducted according to the high standards of honesty and integrity discussed in the University's Academic Honor Code and Student Code of Conduct. See
Options For those with some specific interest, on request, the instructor will substitute individualized projects for the assignments
Supplemental Texts and Readings
  • Class Handouts Web page
  • Notes of the class discussions
  • The Processes of Life: An Introduction to Molecular Biology by Lawrence E. Hunter, MIT Press 2009, ISBN 978-0-262-01305-5
  • A Computer Scientist's Guide to Cell Biology by William W. Cohen, Springer 2007, ISBN 978-0-387-48278-1
  • Beautiful Evidence, by Edward Tufte, Graphics Press 2006, ISBN 0-9613921-7-7
  • Web site for Beautiful Evidence and all Tufte's books
  • Bioinformatics and Functional Genomics 2nd Edition by Jonathan Pevsner, Wiley-Blackwell, ISBN 978-0-470-08585-1
  • A Ruby Language Companion for Exploring Bioinformatics

This is a dynamic document generally finalized after midterm feedback. Please refer to the master copy at

Revised February 23, 2015