I529:  Bioinformatics in Molecular Biology and Genetics: Practical Applications (3CR)

Spring Semester 2009
Lecture: MW 4-4:50pm

Lab: F 4-5pm

Office Hour: M 2-3pm
Instructor: Haixu Tang (INFO 225)
AI: Kwangmin Choi: kwchoi@indiana.edu


Description: We aim to introduce a broad range of, from fundamantal and advanced, applications of bioinformatics methods and tools to solve problems in genomics and molecular biology. Prior to this class, the students should have learned basic methods and theories in bioinformatics, e.g. by taking I519. In this class, we will focus on how to apply them to solving biological problems in real life. Some advanced computational techniques that are widely applied in bioinformatics, e.g. Hidden Markov model (HMM), Bayesian Network (BN), will be discussed in details in the class. The important themes that will be covered by this course include

- Sequence modeling and classification
- Genome annotation
- Motif finding
- Genome comparison
- Protein families
- Non-coding RNAs
- MicroRNAs and their targets
- Functional prediction
- Phylogenetics
- Mass spectrometry and proteomics

This class will have a separate lab section, in which the students will be taught in how to solve biological problems in a step-by-step fashion. The programs that will be covered in the lab of this class include

- Sequence modeling using Markov chains: seq++;
- Pair HMM: SLAM, TwinScan, QRNA;
- HMM: Genscan;
- Profile HMM: Hmmer, Pfam;
- Stochastic Context Free Grammer (SCFG): COVE;
- Non-coding RNA search: Rsearch;
- Phylogenetics: PHYLIP, PAML;

Students will be instructed to write scripts (Perl and PHP preferrable) and/or programs that make use of the current implementation of sophisticated algorithms, such as HMM, BN, SVM, etc., to solve biological problems.

This course is designed for the advanced level bioinformatics graduate students after they take I519. Graduate students with either biology or phisical/computer science backgrounds who are interested in bioinformatics applications in molecular biology are also welcome to take this course.


Textbook: : Richard Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , Cambridge University Press, 1999, (BSA)
Some of the topics from the course can not be found in this book. We will distribute complementary lecture notes and reading materials along the course for these topics. We also recommend the students to read the book, Nello Cristianini and Matthew W. Hahn,
Introduction to Computational Genomics: A Case Studies Approach ,Cambridge University Press, 2006
Assignments: We will have 5 take-home assignments and 1 class project.

Grading: Combined assignments (30%), One mid-term exam (20%), Final exam (25%), Class Project (20%), Attendence (5%).

  I519 or equivalent knowledge in bioinformatics required.

Group Assignment: The class will be divided into several small groups for mini projects.
The group assignment is going to be determined in the first class.

Tentative syllabus [This is subject to minor changes!]:


Lecture notes
1/12 Mon.
Introduction to the class

BSA 1.1 - 1.2
The primer of Perl
Hypertext Preprocessor PHP
-- we will use it for the web site design in this class.

1/14 Wed.
Probabilistic modeling
BSA 1.4, Chapter 11

1/16 Fri.
Lab1: Web site design using PHP and mySQL
(Homework 1)

1/19 Mon.
No class (Martin Luther King Jr. Day)

1/21 Wed.
Probabilistic sequence modeling I: frequency and profiles

1/23 Fri.
Lab2: Alignment algorithms: Smith-Waterman, FASTA and Blast

1/26 Mon.
Probabilistic sequence modeling I: frequency and profiles

1/28 Wed.
Probabilistic sequencing modeling II: Markov chain BSA Chapter 4

1/30 Fri.

Lab3: Modeling biological sequences using seq++ ; blocks and related tools; Sequence weblogo

2/2 Mon.
Probabilistic sequencing modeling II: Markov chain
Homework 2)

2/4 Wed.
Hidden Markov Model I: Model structure
BSA Chapter 3

2/6 Fri.

Group Discussion (HW1)

2/9 Mon.
Hidden Markov Model I: Model structure

2/11 Wed.
Hidden Markov Model II: Generalized HMM

2/13 Fri.

Lab4: GeneMark.HMM & Genscan
2/16 Mon.

HMM III: Parameter estimation
Homework 3)

BSA Chapter 3

2/18 Wed.
HMM III: parameter estimation

2/20 Fri.

Group discussion (HW2)

2/23 Mon.
EM algorithm I

2/25 Wed.
EM algorithm II

2/27 Fri.

Lab5: MEME


3/2 Mon.

Pair HMM I

3/4 Wed.


3/6 Fri.


3/9 Mon.
Q & A
(Homework 4)
BSA Chapter 4

3/11 Wed.

Spring recess
11 3/23 Mon.
Profile HMM I
BSA Chapter 5

3/25 Wed.
Profile HMM II

3/27 Fri.

Lab7: Pfam & Hmmer

3/30 Mon.
Profile HMM III

4/1 Wed.
Advance probabilistic graphic models I

4/3 Fri.

Group Discussion (HW 3)
4/6 Mon.
Gibbs sampling I
Homework 5

4/8 Wed.
Gibbs sampling II

4/10 Fri.

Lab8: ClustalW, Treeview/ATV

4/13 Mon.
Phylogenetics: Distance-based methods I
BSA Chapter 7

4/15 Wed.
Phylogenetics: Distance-based methods II
BSA Chapter 7

4/17 Fri.
Lab9: Phylip
(Group discussion HW4)

4/20 Mon.
Phylogenetics: character-based methods I BSA 7

4/22 Wed.
Phylogenetics: character-based method II

4/24 Fri.

Lab10: PAML

4/27 Mon.
Phylogenetics: Maximal likelihood (ML) method

4/29 Wed.
Project presentation (continue on 4/25, Friday)
17 5/4 Mon Final Exam

5/8 Fri. Final project report due

Last updated : 1/5/2009