CS466: Introduction to Bioinformatics Instructor: Jian Peng Assistant Professor of Computer Science Email: jianpeng@illinois.edu Office Hour Zoom: TBD Office Hour: 2:00PM - 3:00PM Thursday Teaching Assistant: Wei Qian PhD Student of Computer Science Email: weiqian3@illinois.edu Office Hour Zoom: Meeting ID Office Hour: 11:00AM - 12:00PM Thursday Teaching Assistant: Xiaoming Zhao PhD Student of Computer Science Email: xz23@illinois.edu Office Hour Zoom: Meeting ID Office Hour: 4:00PM - 5:00PM Tuesday Lecture Zoom: Meeting ID Time: 12:30PM - 1:45PM, T/R 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

• Five problem sets + one programming assigment (50%)
• Midterm (25%)
• Final (25%)

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 without costing credits at most once in the semester.

Schedule

Date	Presenter	Slides
01/21/2020	Jian Peng	Introduction [slides]
01/23/2020	Jian Peng	Molecular Biology [slides]
01/28/2020	Mohammed El-Kebir	Sequence Alignment I [slides][notes]
01/30/2020	Mohammed El-Kebir	Sequence Alignment II [slides][notes]
02/04/2020	Mohammed El-Kebir	Sequence Alignment III [slides][notes]
02/06/2020	Mohammed El-Kebir	Sequence Alignment IV [slides][notes]
02/11/2020	Jian Peng	Sequence Alignment Review [slides]
02/13/2020	Wesley Wei Qian	Probability and Statistics [slides]
02/18/2020	Jian Peng	Pattern Matching [slides]
02/20/2020	Jian Peng	Pattern Matching II[slides]
02/25/2020	Jian Peng	Pattern Matching III[slides]
02/25/2020	Mohammed El-Kebir	Pattern Matching IV[slides]
03/03/2020	Jian Peng	Blast I [slides]
03/05/2020	Jian Peng	Blast II [slides]
03/10/2020	Wesley Wei Qian	Midterm Review [slides]
03/24/2020	Wesley Wei Qian	Blast III [slides]
03/26/2020	Wesley Wei Qian	Sequence Assembly I [slides]
03/31/2020	Jian Peng	Sequence Assembly II [slides]
04/02/2020	Jian Peng	Sequence Assembly III & HMM I [slides]
04/07/2020	Jian Peng	HMM II [slides]
04/09/2020	Jian Peng	HMM III & Gene Finding [slides]
04/14/2020	Jian Peng	Classification I [slides]
04/16/2020	Jian Peng	Classification II & Regression [slides]
04/21/2020	Jian Peng	Clustering [slides]
04/23/2020	Xiaoming Zhao	Homework Review
04/28/2020	Wesley Wei Qian	Final Review [slides]

Assignments

Please use entry code 9G8B82 for submitting homework on Gradescope.

Release Date	Due Time	Assignments	Solutions
02/11/2020	23:59:59, 02/18/2020	Assignment 1	Solution 1
02/25/2020	23:59:59, 03/03/2020	Assignment 2	Solution 2
04/03/2020	23:59:59, 04/14/2020	Assignment 3	Solution 3
04/18/2020	23:59:59, 04/27/2020	Assignment 4	Solution 4
05/01/2020	23:59:59, 05/14/2020	Assignment 5 - (a)
05/01/2020	23:59:59, 05/14/2020	Assignment 5 - (b)