Syllabus

vivaciousefficientBiotechnology

Oct 1, 2013 (3 years and 8 months ago)

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MICR /BNFO 653


Advanced Molecular Genetics Bioinformatics & Computational
Genomics

Time
: Thursday,
2
:
0
0
-
4
:
45
,

Spring
.

Place
: Trani Center

104
, 1000 West Cary Street

Course
Director
: Ping Xu
,
Email:
pxu@vcu.edu



Course
Objectives
:

T
his is an introductory course in bioinformatics, or the application of computational
technology to the analysis of biological sequence data. It is targeted to introductory
molecular biologists with sufficient background in biochemistry, molec
ular biology and
genetics.

The specific objectives of the course are:


1. Provide a working knowledge of UNIX and X
-
windows.

2. To provide practical experience with sequence software analysis strategies.

3. To provide gene expression array analysis strate
gies.

4. To provide an introduction to molecular modeling

5. To provide a survey of important concepts in bioinformatics.

Grading Policies:

1. A grade (A
-
F) will be assigned to each student.

2. You are expected to attend all classes.

3. You will be grad
ed on homework problems.

Course Schedule:

1.
Jan.
19


Introduction and Overview UNIX/X
-
windows/Batch/Web Browser

Xu/Davis
,
BCCL


2. Jan. 2
6

DNA Sequenc
ing

and Genomics
,

Xu
,
BCCL


3
.
Feb
.
2

Database

search and Sequence analysis

Xu
,
BCCL


4. Feb.
9

Synthe
tic Biology

Fong
,
BCCL


5
. Feb. 1
6

Evolution/Phylogeny Pileup with ClustalX, PAUP

Rivera
,
BCCL


6. Feb.
2
3

Genome
-
Wide Association (GWA) study for human diseases

Riley
,
BCCL


7.
March

1

Human Microbiome

Xu/Sheth
,
BCCL


8. Mar.
8

Microarray platforms and l
ow level analysis Commercial Affymetrix

Arrays

Miles

,
BCCL


Mar
1
2
-
16

Spring Break


9. Mar.
2
2

Unsupervised learning methods and microarray data

Ge
,
BCCL


10.
Mar
.

29

Macromolecular Graphics/Visualization Molecular Mechanics, Molecule Concepts

Kellogg
,
Bi
otech Park 212


11. Apr.

5

Macromolecular Graphics/Visualization Molecular Mechanics, Molecule Concepts

Kellogg
,
Biotech Park 212


12
.

Apr.
1
2

Pattern Recognition and Gene Finding

Elhai
,
BCCL


1
3
.

Apr.
19

Protein
-
protein interaction network

Uetz
,
BCCL


14
.

Apr. 2
6

Network Analysis for Biological Sciences

Bonchev
,
BCCL


Instructors and emails:

Ping Xu, pxu@vcu.edu, Philips Institute

Danail Bonchev, dgbonchev@vcu.edu, Mathematical Sciences

James M Davis, jmdavis1@vcu.edu, CSBC

Jeffrey Elhai, elhaij@vcu.ed
u, CSBC

Stephen Fong, ssfong@vcu.edu, Chemical and Life Science Engineering

Xiuchun Ge, xge2@vcu.edu, Philips Institute

Glen Kellogg, gekellog@vcu.edu, Medical Chemistry

Michael Miles, mfmiles@vcu.edu, Pharmacology and Toxicology

Nihar Sheth, nsheth@v
cu.edu, CSBC

Brien Riley, bpriley@vcu.edu, Psychiatry and Human Genetics

Maria C Rivera, mcrivera@vcu.edu, Biology

Peter Uetz, peter@uetz.us, CSBC