CS612: Algorithms in Bioinformatics

Spring 2023

Instructor

Name: Nurit Haspel
email: nurith@cs.umb.edu
Office: M03-201-04
Office hours: Mo, We 1:00–2:20PM

Class meetings

Mo, We 2:30-3:45 in Y04-4120

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. 3, 2023 Feb. 16, 2023, on Gradescope   Solution
Homework #2 Feb. 17, 2023 Mar. 3, 2023, on Gradescope
Updated!		   Solution
Homework #3 Mar. 7, 2023 Mar. 30, 2023 (extended!) set1.txt
set2.txt		 Solution
Homework #4 Apr. 1, 2023 Apr. 24, 2023 (updated!) hw4.R Solution
Homework #5 Apr. 25, 2023 May 9, 2023
Term project Mar. 22, 2023 May 22, 2023 Sequences

 

Class notes

Week

Topic

Book Chapters

Session Dates

Session Info

Slides/notes

1

Introduction

Monday,
January 23

Intro to Molecular Biology
and Bioinformatics

Introduction

Wednesday,
January 25

Same

Same as last time

2

Introduction
Sequence alignment

Monday,
January 30

Intro
Start sequence alignment

Sequence

Wednesday,
February 1

Sequence Alignment

DP notes

3

Sequence alignment

Monday,
February 6

Sequence alignment
MSA

Wednesday,
February 8

Intro to Protein Structure

Structure

Structure notes

4

Protein Structure

Monday,
February 13

Protein Structure

Wednesday,
February 15

Biological Databases

Databases

Databases notes

5

Visualization, Folding

Monday,
February 22

Presidents' day

Wednesday,
February 28

Protein Structure
Visualization
Databases

Visualization

Visualization notes

6

Folding

Monday,
February 27

Protein Folding

Folding

Folding notes

Wednesday,
March 1

Folding methods

 Folding methods

7

Folding
Methods

Monday,
March 6

Computational Folding

Wednesday,
March 8

Folding methods notes

8

Folding Methods
Distance measures

Monday,
March 20

Folding methods

Wednesday,
March 28

 Distance Measures Distance Measure

Distance notes

9

Distance
Simulations

Monday,
March 27

Distance
Simulations

Same as last week

Wednesday,
March 29

Simulations
Simulations notes

10

Manipulation

Monday,
April 3

Simulations
Manipulations

Structural Manipulation
Manipulation Notes

Wednesday,
April 5

 Geometric Hashing
Motif Detection

11

Manipulation
Structural Alignment

Monday,
April 10

Quaternions
Structural Alignment

Structural Alignment
Structural Alignment notes

Wednesday,
April 12

12

Alignment
Docking

Monday,
April 17

Patriot's day
No class

Wednesday,
April 19

 Start Docking

Docking
Docking notes

13

Docking

Monday,
April 24

Surface Representation
Docking

Wednesday,
April 26

 Docking

14

Sampling
Dimensionality Reduction

Monday,
May 1

Sampling

Sampling
Sampling notes

Wednesday,
May 3

 Sampling, Dimensionality Reduction Dimensionality Reduction

15

Dimensionality Reduction

Monday,
May 8

PCA
Isomap

Same

Wednesday,
May 10

 ? Dimensionality Reduction

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