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2 Οκτ 2013 (πριν από 3 χρόνια και 6 μήνες)

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BIOINFORMATICS & COMPARATIVE GENOMICS

BIOL 4005


006/BIOL 5005


006/CSCE 4930


003/CSCE 5933


002


Instructor:
Qunfeng Dong (qunfeng.dong@unt.edu)

Lectures:
TR 11:00 am
-

12:20 pm, PEB220

Office hours
: F noon
-
1 pm LIFE A358

Recommended Textbook
:
Understanding Bioinformatics.

http://www.garlandscience.com/textbooks/0815340249.asp?type=toc


Course Objective:

If you are able to have your genomes of interest sequenced
(thi
s is becoming a reality now for biologists due to the rapid advent of DNA
sequencing

technologies), what interesting biological questions can you think of
to address with the

genome sequences? Do you know which computational tools
or database resources are

suitable for analyzing the sequence data? Do you
understand the computational principles

behind these tools? If you are curious
about the answers to any of these questions, you

are welcome to join us in this
class where we will study molecular evolution t
heories,

bioinformatics algorithms,
and the application of these subjects in the context of

comparative genomics
(e.g., genome annotation, gene expression and biological network

analysis).

If
you are a biology student, you have not completed your

training
unless you
learn
bioinformatics. Are you prepared to

analyze the vast amount of data produced by
various high

throughput

technologies? This course will help you to

understand
bioinformatics tools and databases, and find out

how to apply them to genomic
res
earch.

If you are a computer science student, you don’t want to miss

out on
the tremendous opportunities in the research and job

markets that are provided
by the on
-
going genome revolution.

You will learn bioinformatics algorithms and
find out how to

devel
op suitable tools that benefit scientists.


Prerequisites:
Ideally, in order to excel in bioinformatics, one should have an in
-
depth

understanding of molecular biology, genetics, evolution, computer science
data structures

& algorithms, and statistics; but

in reality, nobody can claim that
they are experts in all of

the previously mentioned subjects (even the instructor
would not be qualified for this

course if such prerequisites were strictly imposed).
The most important prerequisite

for this course is that you have a serious
desire to learn.
You will be given a basic

background in biology, computer
science, and statistics in this class.
Y
ou should also be prepared to take care of
the more

detailed readings on your own.


Grading:
There

will be no closed
-
book exams. Grades will be based on in
-
class

discussions

(10%)
, homework assignments

(50%)
, and final projects

(40%)
. If
you make a conscious effort,

you should be able to do well in this class.


Computer Account:
Please obtain an accoun
t on Talon (email
hpc
-
admin@unt.edu
),

which is a Linux
-
based computer cluster at UNT
(
http://citc.unt.edu/hpc/content/talon
).




Week Topic
s

----------------------------------

1.

Introduction to
Linux

2.

Introduction to
Perl

3.

Introduction to R

4.

Introduction to MySQL


5.

Genome biology

overview

6.

Next
-
generation DNA sequencing technologies

7.

Bioinformatics databases

8.

Sequence comparison

9.

Genome assembly

10.

Genome annotation

11.

Transcriptome analysis

12.


M
otif

analysis

13.


Molecular evolution

14.


Team project presentation

15.


Final presentation