CSE5370 Bioinformatics Syllabus

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Oct 1, 2013 (3 years and 6 months ago)

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CSE5370


Bioinformatics Syllabus

Fall 2004













Instructor:












Jean Gao













Email:












gao@cse.uta.edu













Office:











338 Nedderman Hall,


phone: 817
-
272
-
3628













Office Hours:











Monday and Wednesday, 12:00
-

1:00pm or by appointment













Course Information:



Monday and Wednesday, 3:30
-

4:50pm.


Course Website:
http://crystal.uta.edu/~gao/
CSE5370
/Syllabus.html














TA:










Jung Hun Oh













Email:












joh@cse.uta.edu












Office:










107 Engineering Annex
-
West,


phone number: 817
-
272
-
1240












Office Hours:










Mondays and Wednesdays: 11:30am
-

12:30pm


Course Description:


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
available, and

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
ranscriptomics).

Objectives:





To provide students an understanding of the fundamental computational problems in
molecular biology and genomics, and a core set of widely used algorithms in
computational biology.

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.

Prerequisites:


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.

Textbook:












Mount, D.W., "Bioinformatics : sequence and genome analysis". 2001,

Cold
Spring Harbor, N.Y.
: Cold Spring Harbor Laboratory
P
ress. xii, 564. ISBN:
0879696087.















(UTA library has electronic version of this book.)

References:


















--



"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic
Acids". R. Durbin, S. Ed
dy, A. Krogh, and G. Mi
tchison.
Cambridge University Press,
1998















--


"Discovering genomics, proteomics and bioinformatics", A. Malcolm Campbell,
and Laurie
Heyer, Benjamin Cummings, 2003.
ISBN: 0
-
8053
-
4722
-
4.













--


"Biochemistry", L. Stryer,


5th ed,

W
H Freeman and Co.


Grading:











Homework & Projects 60%


















--

There will be about 5 homework assignments.


















--

Mostly programming projects


















--

Some written exercises











Exam












































































































40%


















--

There will be two midterms.


















--

Each exam will cov
er 50% o
f the class materials.







Homework Policy:

















--

All assignments are due on the day of class time.


Hard copies with source
cod
e should be turned in at class.
Source code is supposed to email to TA before that.

















--


N
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
ment score
for every

24 hours.


Academic Misconduct:











All homework assign
ments m
ust be done
individually
.

Cheating and plagia
rism
will result in a default "F" grade for this course.











Code for programming assign
ments must NOT be developed in groups, nor should
be shared.

Discussions with peers, or TA about











approac
hes and techniques are encouraged, but not at a detail level of
implementation.


















Tentative Topics:









1. Introduction













--

Introduction to bioinformatics













--

Whirlwind tour of Chem/MolBio/BioChem













--

Pr
imer on probability theory










2. Genomics













--

Tools for sequence alignment and database searches













--

Pairwise sequence alignment













--

Sequence database search













--

Multiple sequence alignment













--

H
iden Markov Models (HMM)













--

Gene Finding










3. Proteomics













--

Protein structure and its prediction













--

Structure alignment













--

Phylogenetic inference













--

Molecular modeling (mechanics & dynamics
)













--

Protein threading











4. Transcriptomics












--

Construction and use of microarrays












--

Statistical analysis of microarray data: clustering methods












--

Microarray analysis: dimensionality reduction












--

Overview: Mass spectrometry for proteomics