CS612: Algorithms in Bioinformatics

Spring 2025

Instructor

Name: Nurit Haspel
email: nurith@cs.umb.edu
Office: M03-201-04
Office hours: Mo, We 2:30–3:50PM

Class meetings

Mo, We 4:00-3:45 in Y04-4140

Course Description

This course will introduce students to bioinformatics - the area concerning the development and application of computational methods to address key problems in biology. It will introduce the students to a variety of methods and skills required to conduct research in this highly rising field. The emphasis of the course is structural bioinformatics with focus on various computational methods to simulate, analyze and model protein structure, dynamics and function. Other subjects such as systems biology, genomics and interaction networks will be introduced as well. The course is designed first and foremost for computer scientists but is also open to biology majors with adequate computational/mathematical background.

See the course syllabus for a detailed list of topics.

Prerequisites: CS210 or equivalent knowledge in data structures and programming, MATH 260 (Linear algebra).

Homework assignments

Assignment (PDF) Posted/Given on Due Date Handouts Solution
Homework #1 Feb. 13, 2023 Feb. 21, 2023, on Gradescope   Solution
Code
Homework #2 Feb. 26, 2025 Mar. 10, 2025 (updated!), on Gradescope Skeleton code Solution

 

Class notes

Week

Topic

Book Chapters

Session Dates

Session Info

Slides/notes

1

Introduction

Monday,
January 27

Intro to Molecular Biology
and Bioinformatics

Introduction

Wednesday,
January 29

Same

Same as last time

2

Introduction
Sequence alignment

Monday,
February 3

Intro
Start sequence alignment

Sequence

Wednesday,
February 5

Sequence Alignment

DP notes

3

Sequence alignment

Monday,
February 10

Sequence alignment
MSA

Python environment

Wednesday,
February 12

MSA
Biopython exercise

4

MSA
Protein Structure

Monday,
February 17

President's day

Wednesday,
February 19

MSA
Intro to Protein Structure

Structure

Structure notes

5

Protein Structure

Monday,
February 24

Protein Structure

Wednesday,
February 26

Protein Structure
Visualization

6

Databases
Visualization

Monday,
March 3

Databases

Databases

Databases notes

Wednesday,
March 5

 Visualization

Visualization
Visualization notes
PDB Python environment

7

Protein Folding

Monday,
March 10

Protein Folding

 Folding

Folding notes

Recommended Textbooks

Structural Bioinformatics, edited by Jenny Gu and Phillip E. Bourne, Willey Blackwell, 2nd edition.

Introduction to Bioinformatics, Arthur M. Lesk, Oxford, 3rd or 4th edition.

Online material

All material for this course will be kept online at http://www.cs.umb.edu/~nurith/cs612.

Written work

There will be about 5 written homeworks and a final presentation. See the syllabus for more details.

Grade Composition

Honesty

You must do your own work in this course. You are encouraged to discuss problems/projects with classmates, or to ask for help with debugging. When you do share ideas or get help you must acknowledge that help in writing. However IT IS NOT ALLOWED TO USE ANOTHER STUDENTS CODE IN ANY WAY WHILE DOING YOUR HOMEWORK, even if you acknowledge that.

Working from home

All the software you need to work from home is available for free. See resources below and class notes for links (the links on this page will be periodically updated).

Resources