L519: Bioinformatics: theory & application (3CR)
Fall Semester 2005
Lecture : Monday/Wednesday 11:15am-12:05pm Ballantine Hall (BH) #245
Office Hour: Monday/Wednesday
9:00am-10:00am, Eigenmall 1008
Lab : Fri 16:00-17:15 Informatics Building #109
Instructor: Haixu Tang
AI : Junguk Hur
Description: We aim to introduce the broad frontiers of bioinformatics topics from fundamental algorithms to practical tools. The first week of this course will introduce necessary backgrounds in molecular biology and computer science to understand the content of the entire course. The important themes that will be covered by this course include
- DNA and protein sequence comparison;
- Genome
mapping and sequencing;
- SNPs and
variations
- Gene
finding and genome annotation;
- Discovery
of DNA regulatory elements
- Non-coding
RNA finding
- Data
analysis in DNA microarray
- Protein
structure comparison and prediction
-
Integrative genomics
Many
practical bioinformatics software will be discussed in a special designed lab
section of this course (meeting on every Thursday, time to be determined with
Assistant Instructor), including BLAST, FASTA, ClustalW, T-COFFEE, Phred/Phrap, GenScan, GeneMark, MEME, Gibbs Sampler, Mfold, RSEARCH, SAM, Predator, Threader, DALI, etc.
This course is designed for the entry level bioinformatics graduate students. Graduate students with either biology or phisical/computer science backgrounds who are interested in bioinformatics research are also welcome to take this course.
Textbook: David Mount: Bioinformatics, Sequence and
Genome Analysis (Second Edition) , Cold Spring Harbor Laboratory Press,
2004. 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, Neil Jones
and Pavel Pevzner An introduction to
bioinformatics algorithms , MIT press, 2004.
Assignments: We will have 6 take-home
assignments and 1 class project.
Grading: Combined
assignments (30%), One mid-term exam (20%), Final exam (25%), Class Project (20%), Attendence
(5%).
Office hour: Professor Haixu Tang: Monday/Wednesday
9:00am-10:00am, Eigenmann #1008, or upon appointment
AI Junguk Hur: Monday 2:00-3:00pm, Tuesday 11:00am-Noon, Eigenmann #1009, or upon appointment
Prerequisites:
No particular
knowledge required, except high school level chemistry/biology and most
important common sense.
Group Assignment: The class will be divided into several small groups for mini projects. Group Assignment. Project Evaluation Form
Projects : Some of the project topics are now available for preview. More topics and detailed instruction will be posted soon.
1. Genome Size (John Kenneth Colbourne <jcolbour@cgb.indiana.edu>)
2. Text Mining (Luis M. Rocha <rocha@indiana.edu>)
3. Viral Genome Analysis (Michael Lynch <milynch@indiana.edu>)
4. Effect of Biases on Genome Sequence, Male-biased gene-expression (Matthew Hahn <mwh@indiana.edu>)
5. Regulatory Genomics (Mehmet Dalkilic <dalkilic@indiana.edu>)
Sub1. Integrating and visualizing gene networks.
Sub2: Inferring gene relationships by finding condensed subgraph from integrated gene network.
Sub3: Statistical analysis of single nucleotide polymorphisms (SNPs)
Project Topic Selection Status : Check this EXCEL file for current assignment of project topics.
We will try to keep this up-to-date.
Preliminary syllabus [This may change!]:
| Week |
Date |
Contents |
Lecture
notes |
| 1 |
8/29 Mon. |
Introduction to the
class and to molecular biology |
BIO Chapter 1 |
| 8/31 Wed. |
Introduction to
algorithm |
Notes | |
| 9/2 Fri. |
Lab1: Pubmed and
Genbank (Homework 1) |
||
| 2 |
9.5 Mon. |
||
| 9/7 Wed. |
Sequence comparison:
string and pattern matching |
Notes | |
| 9/9 Fri. |
Lab2: Swissprot and
PDB CGI programming |
||
| 3 |
9/12 Mon. |
Sequence alignment I:
dynamic programming |
BIO Chapter 3 Notes |
| 9/14 Wed. |
Sequence alignment II: local alignment and protein motif | ||
|
9/16 Fri. |
Lab3: Smith-waterman
algorithm (Homework 1 due) |
||
| 4 |
9/19 Mon. |
Sequence database searching
(Homework 2, SEQ, NetBLAST) |
BIO Chapter 4,6 Notes |
| 9/21 Wed. |
Multiple sequence alignment
|
BIO Chapter 5 Notes | |
|
9/23 Fri. |
Lab4: PSI-Blast, PROSITE | ||
| 5 |
9/26 Mon. |
Genome sequencing and
assembly I |
BIO Chapter 11 Notes |
| 9/28 Wed. |
Genome sequencing and
assembly II |
||
|
9/30 Fri. |
Lab5: ClustalW and T-Coffee | ||
| 6 |
10/3 Mon. |
Gene finding I
|
BIO Chapter 11 Notes |
| 10/5 Wed. |
Guest Lecture: Prof. Michael Lynch (Biology)
|
||
|
10/7 Fri. |
Lab6: Phred/Phrap |
||
| 7 |
10/10 Mon. |
Gene finding II
|
|
| 10/12 Wed. |
Midterm exam | ||
| 8 |
10/17 Mon. |
Gene finding III
|
|
| 10/19 Wed. |
Gene finding IV
(Class project) |
||
|
10/22 Fri. |
Lab7: Gene Prediction Program (GenScan, TwinScan) (Homework 3 due) |
||
| 8 |
10/24 Mon. |
Transcriptomics and
DNA microarray (Homework 4) |
BIO chapter 13 Notes |
| 10/26 Wed. |
Guest lecture: Professor Mehmet Dalkilic (Class project) |
||
|
10/29 Fri. |
Lab8: SMD, Cluster, TreeView |
||
| 10 |
10/31 Mon |
DNA regulatory element discovery
|
BIO chapter 9 Notes |
| 11/2 Wed. |
Genome variation and SNP |
BIO chapter 11 Notes | |
|
11/5 Fri. |
Lab9: MEME, Gibbs, Logo |
||
| 11 |
11/7 Mon. |
RNA
folding |
BIO Chapter 8 Notes |
| 11/9 Wed. |
non-coding RNA finding | ||
|
11/12 Fri. |
Lab10: TRANSFAC, BLASTZ, EST_GENOME | ||
| 12 |
11/14 Mon. |
Protein 3D structure comparison | |
| 11/16 Wed. |
Protein structure
prediction (Homework 5 due, Homework 6) |
||
|
11/19 Fri. |
Lab11: dbSNP, group presentation | ||
| 13 |
11/21 Mon. |
Guest lecture: Professor Luis Rocha | |
| 11/23 Wed. |
Homework 6, Q1_Seqs | ||
| 14 |
11/28 Mon. |
Phylogenetic analysis I | |
| 11/30 Wed. |
Phylogenetic analysis II | ||
|
12/2 Fri. |
Lab12: MFOLD, Vienna RNA package, Rfam |
||
| 15 |
12/5 Mon. |
Mass spectrometry in
proteomics |
|
| 12/7 Wed. |
Intergrative
genomics |
||
| 16 |
12/9 Fri. |
Final exam |
|
| 17 | 12/16 Fri | Final report due |
Last updated : December 5, 2005