338 Nedderman Hall,
Monday and Wednesday, 12:00
1:00pm or by appointment
Monday and Wednesday, 3:30
Jung Hun Oh
107 Engineering Annex
phone number: 817
Mondays and Wednesdays: 11:30am
Biological sciences are undergoing a revolution in how they are practiced. In the last
decade, a vast amount of data (DNA sequences, protein sequences, etc.) has become
computational methods are playing a fundamental role in transforming this
data into scientific understanding.
Bioinformatics involves developing and applying computational methods for managing
and analyzing information about the sequence, structure a
nd function of biological
molecules and systems.
Topics will include understanding the evolutionary organization
of genes (genomics), the structure and function of gene products (proteomics), and the
dynamics for gene expression in biological processes (t
To provide students an understanding of the fundamental computational problems in
molecular biology and genomics, and a core set of widely used algorithms in
The proposed course is intended to help s
tudents have a working
knowledge of a variety of publicly available data and computational tools important in
bioinformatics, and a grasp of the underlying principles
of contemporary bioinformatics.
1. A background in biology is n
ot required, but students should be interested in
catching up quickly on relevant topics.
2. Half of the homework assignments is programming.
Students are free to choose
any language they are comfortable with.
For those who like Mat
lab, we have Matlab Bioinformatics Toolbox installed in
the public labs at Ransom Halls and Nedderman Halls.
Mount, D.W., "Bioinformatics : sequence and genome analysis". 2001,
Spring Harbor, N.Y.
: Cold Spring Harbor Laboratory
ress. xii, 564. ISBN:
(UTA library has electronic version of this book.)
"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic
Acids". R. Durbin, S. Ed
dy, A. Krogh, and G. Mi
Cambridge University Press,
"Discovering genomics, proteomics and bioinformatics", A. Malcolm Campbell,
Heyer, Benjamin Cummings, 2003.
"Biochemistry", L. Stryer,
H Freeman and Co.
Homework & Projects 60%
There will be about 5 homework assignments.
Mostly programming projects
Some written exercises
There will be two midterms.
Each exam will cov
er 50% o
f the class materials.
All assignments are due on the day of class time.
Hard copies with source
e should be turned in at class.
Source code is supposed to email to TA before that.
o emails or phone calls will be replied regarding to assignment within 24
hours of due time.
Late submission will be
deducted at 10% of each assign
All homework assign
ust be done
Cheating and plagia
will result in a default "F" grade for this course.
Code for programming assign
ments must NOT be developed in groups, nor should
Discussions with peers, or TA about
hes and techniques are encouraged, but not at a detail level of
Introduction to bioinformatics
Whirlwind tour of Chem/MolBio/BioChem
imer on probability theory
Tools for sequence alignment and database searches
Pairwise sequence alignment
Sequence database search
Multiple sequence alignment
iden Markov Models (HMM)
Protein structure and its prediction
Molecular modeling (mechanics & dynamics
Construction and use of microarrays
Statistical analysis of microarray data: clustering methods
Microarray analysis: dimensionality reduction
Overview: Mass spectrometry for proteomics