CS466: Introduction to Bioinformatics Instructor: Jian Peng Assistant Professor of Computer Science Email: jianpeng@illinois.edu Office: 2118 Siebel Center Office Hour: 11:00AM - 11:59AM M/W Teaching Assistant: Wei Qian PhD Student of Computer Science Email: weiqian3@illinois.edu Office: 1218 Siebel Center Office Hour: 1:00PM - 2:00PM T/R Location: 0216 Siebel Center Time: 09:00AM - 9:50AM, M/W/F Forum: piazza

Course Objectives

Introduction to bioinformatics:

• Basic problems in computational biology
• Statistics and machine learning for data analysis
• Algorithms for data processing

Learning to do research:

• Course project experience
• Hands-on practice with real datasets
• Propose and perform independent research

Prerequisites

• Programming skills (equivalent to CS 225) for doing the mini-project.
• Knowledge of basic probability and statistics for understanding several lectures.
• No biology background is necessary.

Introductory materials

Molecular Biology for Computer Scientists by Larry Hunter.

An Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner.

Grading Scheme

3-credit students:

• Five problem sets (30%)
• Midterm (25%)
• Final (25%)
• Team-based mini-project and report (20%)

4-credit students:

• Five problem sets (20%)
• Midterm (25%)
• Final (25%)
• Mini-project + individual report (30%)

Assignments

Problem Set 1

• Release Date: 02/02/2018
• Due Data: 02/09/2018
• File: piazza

Exams

Midterm

• Date: 03/14/2018
• Time: 8:15 AM - 9:45 AM
• Location: 0216 SC

Final

• Date: 05/10/2018
• Time: 1:30pm-4:30pm
• Location: 0216 SC

Course Mini-Project

Topics

Computational techniques:

• Comparing algorithms
• Efficient implementation of algorithms that scale on large datasets
• New probabilistic models for biological data

Biological problems:

• Comparative analysis
• Interesting data analysis
• New computational biological problems

Team size

• One or two (4-credit students)
• Up to four (3-credit students)

* Make clear your contribution in the project report

Implementation

• Put your code/data on Github
• Get your hands dirty and work on real-world datasets

Assignments Policy

• Please see the University Policy on Academic Integrity, especially the section on plagiarism.
• Late submission within 3 days (72 hours) is worth 80% credit.
• A student may request an extension of 3 days at most once in the semester.

Schedule

Date	Presenter	Slides
01/19/2018	Jian Peng	Introduction [slides]
01/22/2018	Jian Peng	Molecular Biology [slides]
01/24/2018	Jian Peng	Probability and Statistics [slides]
01/26/2018	Jian Peng	Probability and Statistics II [slides]
01/29/2018	Jian Peng	Sequence [slides]
01/31/2018	Jian Peng	Sequence II [slides]
02/02/2018	Jian Peng	Alignment [slides]
02/05/2018	Jian Peng	Alignment II [slides]
02/07/2018	Jian Peng	Alignment III [slides]
02/09/2018	Jian Peng	Pattern [slides]
02/12/2018	Jian Peng	Pattern II [slides]
02/14/2018	Jian Peng	Pattern III [slides]
02/16/2018	Jian Peng	Review [slides]
02/19/2018	Jian Peng	BLAST [slides]
02/21/2018	Jian Peng	BLAST II [slides]
02/23/2018	Jian Peng	BLAST III [slides]
02/26/2018	Jian Peng	BLAST IV [slides]
02/28/2018	Jian Peng	BLAST V [slides]
03/02/2018	Jian Peng	BLAST VI [slides]
03/05/2018	Jian Peng	Assembly [slides]
03/07/2018	Jian Peng	Assembly II [slides]
03/09/2018	Jian Peng	Assembly III [slides]
03/12/2018	Wei Qian	Review I [slides]
03/26/2018	Jian Peng	HMM [slides]
03/28/2018	Jian Peng	HMM II [slides]
03/30/2018	Jian Peng	HMM III [slides]
04/02/2018	Jian Peng	HMM IV [slides]
04/04/2018	Jian Peng	HMM V [slides]
04/06/2018	Jian Peng	Motif Finding [slides]
04/09/2018	Jian Peng	Motif Finding II [slides]
04/11/2018	Jian Peng	Clustering [slides]
04/13/2018	Wei Qian	Review II [slides]
04/16/2018	Jian Peng	Clustering II [slides]
04/18/2018	Jian Peng	Clustering III [slides]
04/20/2018	Jian Peng	Classification I [slides]
04/23/2018	Jian Peng	Classification II [slides]
04/25/2018	Jian Peng	Classification and Regression [slides]
04/27/2018	Jian Peng	Regression II [slides]
04/30/2018	Jian Peng	Final Review [slides]