Algorithms in Bioinformatics

Overview

• Instructor: Alireza Fotuhi (ar.fotuhi at gmail.com) & Hesam Montazeri (hesam.montazeri at ut.ac.ir)
• Time & Location: Spring 2022 (online lectures)

Textbooks

• [BAL] Phillip Compeau and Pavel A. Pevzner, Bioinformatics Algorithms: An Active Learning Approach, 2015.
• [IBA] Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, 2004.
• [ITA] Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, Clifford Stein, Introduction to Algorithms, 2009.

Lecture Schedule

Module A: Background

Lecture	Reading Assignments	Homeworks
Lecture 1- Algorithms in Bioinformatics: Algorithms and Complexity	IBA, Ch. 2	HW1
Lecture 2- Algorithms in Bioinformatics: Algorithms and Complexity-continued	IBA, Ch. 2	HW2
Lecture 3- Introduction to p-values		HW3 HW4

Module B: Genomic Analysis

Lecture	Reading Assignments	Homeworks
Lecture 4- Next Generation Sequencing; read mapping; Suffix trees; BWT	BAL, Ch. 9
Lecture 5- read mapping-continued; De novo genome assembly	BAL, Ch. 9, 3
Lecture 6-7 De novo genome assembly-continued; sequence alignment	BAL, Ch. 3, 5	HW5 Project 1
Lecture 8-10 Hidden Markov Models	BAL, Ch. 10

Module C: RNA-Seq analysis

Lecture	Reading Assignments	Homeworks
Lecture 11- RNA sequencing; Splice aware alignment; Transcript quantification
Lecture 12- Differential expression analysis; clustering analysis; pathway enrichment
Lecture 13- Mathematical foundation of expectation-maximization and its applications to bioinformatics		HW6

Module D: Phylogenetic Analysis

Lecture	Reading Assignments	Homeworks
Lecture 14- introduction to phylogenetic analysis; clustering methods
Lecture 15-16 Parsimony; Likelihood methods
Lecture 17-Structure learning; Bayesian inference

Module E: Epigenetic Analysis