Lahore University of Management Sciences

BIO 331 Computational Biology II

Instructor
Room No.
Office Hours
Email
Telephone
Secretary/TA
TA Office Hours
Course URL (if any)

Fall 2013

Dr Aziz Mithani and Dr Safee Ullah Chaudhary

9-419A and 9-420A
12:00-13:00
aziz.mithani@lums.edu.pk and safeeullah@lums.edu.pk
8397 and 8352
Ashar J Malik and Roop Omar

Course Basics
Credit Hours
Lecture(s)
Recitation (per week)
Lab (if any ) per week
Tutorial (per week)

Course Distribution
Core
Elective
Open for Student Category
Closed for Student Category

3
Nbr of Lec(s) Per Week
Nbr of Rec (s) Per
Week
Nbr of Session(s) Per
Week
Nbr of Tut(s) Per
Week

Duration
Duration

1 hr 15 mins

Duration

1 hr 30 mins

Duration

Yes
Any

COURSE DESCRIPTION
The primary focus of the course is to understand theoretical foundation of some of the most widely used computational biology techniques. The
principles and methods for pair-wise and multiple sequence analysis using hidden Markov models, phylogenetic analysis, protein structure
modelling and prediction are extensively covered. In addition systems biology is introduced at a glance with a significant amount of time spent on
microarray analysis. The tutorials will provide hands-on training of programming in Python and Perl with the aim of developing problem solving
skills in computational biology research using scripting languages
COURSE PREREQUISITE(S)

BIO 213
MATH 230 (Probability and Statistics)

COURSE OBJECTIVES

To understand theory behind of some of the most widely used computational biology techniques.
To provide in depth knowledge of sequence and evolutionary analyses.
To provide hands-on training of programming in Python and Perl for computational biology.

Learning Outcomes
After the course, the student should:
Understand the inner working of some of the most widely used computational biology techniques.

Be able to apply the techniques to biological data.

Be able to solve moderate complexity problems related to bioinformatics using Python and Perl.

Lahore University of Management Sciences

Grading Breakup and Policy
Assignment(s): 30%
Home Work:
Quiz(s): 10%
Class Participation: 5%
Attendance:
Midterm Examination: 25%
Project:
Final Examination: 30%

Examination Detail

Midterm
Exam

Yes/No: Yes
Combine Separate: Combine
Duration: 2 hrs
Preferred Date:
Exam Specifications:

Final Exam

Yes/No: Yes
Combine Separate: Combine
Duration: 2 hrs
Exam Specifications:

COURSE OVERVIEW
Week/
Lecture/
Topics
Module
Introduction, Sequence Comparison and
1
Markov Chains
2
Markov and Hidden Markov Models
3
Pairwise alignment using HMM
4
Profile HMM - Multiple sequence alignment
5
Literature Based Discussion
6
Molecular Evolution I
7
Molecular Evolution II
8
Genes in Population - Forward in Time
9
Genes in Population - Backward in Time
10
Testing Evolutionary Hypothesis
11
Literature Based Discussion
12
RNA Structure Prediction using HMM
13
Protein Secondary Structures Prediction
Solving Structures using X-ray Crystallography
14
and NMR
15
Homology Modelling I
16
Homology Modelling II
17
Threading and ab initio Structue Prediction
18
Modelling Protein Ligand Interactions
19
Literature Based Discussion
20
Introduction to Systems Biology
21
Microarrays - Introduction
22
Microarrays - Image Processing
23
Microarrays - Normalisation

Recommended
Readings

Objectives/
Application

Lahore University of Management Sciences

24
25
26
27

Microarrays - Differential Expression

Microarrays - Clustering
Microarrays - Classification
Literature Based Discussion

Textbook(s)/Supplementary Readings

Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme
Mitchison. Cambridge University Press, 1998.
nd

Inferring Phylogenies, 2 Ediition, Joseph Felsenstein. Sinauer Associates, 2003.

Introduction to Computational Biology. An Evolutionary Approach. Bernhard Haubold, Thomas Wiehe. Birkhauser,Verlag 2006.

Microarray Bioinformatics. Dov Sketel. Cambridge University Press. 2003

Python for Bioinformatics (Chapman and Hall/CRC Mathematical and Computational Biology Series ed. Etheridge et. al.), Sebastian Bassi,
Taylor and Francis Group, LLC, 2010.

Computational Biochemistry and Biophysics, Becker O et al., Marcel Dekker, Inc. 2001.

Beginner's Introduction to Perl. http://www.perl.com/pub/2000/10/begperl1.html