Syllabus

skirlorangeBiotechnology

Oct 1, 2013 (3 years and 10 months ago)

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Instructor:

Dr. Stuart Brown
,
Associate Professor, NYUMC Center for Health
Informatics & Bioinformatics

Schedule

Lectures/Lab:

Previously held on Tue
sdays,
1
-
4:30 PM (subject to change based on
course registrant’s availability)

Location
-

NYUMC Center for Bioinformatics: Verizon Bldg, 227 E 30th St., 7th fl conf
room.


Textbooks:

Understanding Bioinformatics

by Marketa Zvelebil and Jeremy Baum

Beginning Perl for Bioinformatics

by James Tisdall


Also Recommended:

Bioinformatics, A Practical Guide to the Analysis of Genes and Proteins

by A.D. Baxevanis and B.F. Ouellettee

(free online for NYU students: http://www3.interscience.wiley.com/cgi
-
bin/booktoc/104086862)


Bioinformatics: Sequence and Ge
nome Analysis

by David W. Mount


Essentials of Medical Genomics

by Stuart M. Brown


Bioinformatics for Dummies

by Jean
-
Michel Claverie & Cedric Notredame


Blast

by Ian Korf, Mark Yandell, and Joseph Bedell


This is a practical course in Bioinformatics
that
will emphasize how to use the computer
as a tool for biomedical research. Prerequsites include a thorough understanding of
theoretical and practical aspects of molecular biology, and some University level
mathematics and statistics, but no prior knowl
edge of computer programming or
computer hardware is necessary.


Bioinformatics

Stuart M. Brown, NYU Center for Health Informatics & Bioinformatics

Fall 2012 Course Syllabus (G16.2604)


Lecture 1. Introduction to the Course: Bio
i
nformatics Algorithms &
Data Structures


Lecture 2. Bioinformatics Databases, UNIX Basics (part 1)


Lecture 3. Alignment, UNIX Basics (part 2)



Lecture 4. Similarity Searching (BLAST), Intro to Perl

Lecture 5. Advanced Alignment methods, Perl (#2)


Lecture 6. Multiple Alignme
nt, Perl #3


[Midterm]

Lecture 7. Computing Evolution: Phylogenetic Analysis

Tues, March 6

Lecture 9.

SNPs and Haplotypes



Lecture 10. Analysis of Microarray Data & Introduction to the "R" programming
language for bio
-
statistical computing



Lecture 11.
Next
-
Ge
ne
ration Sequencing (part 1): Sequence Alignment & Variation


Lecture 12. Galaxy Genomics Toolkit



Lecture 13.
Next
-
Ge
ne
ration Sequencing (part 3
): ChIP
-
seq



Lecture 14. Next
-
Ge
ne
ration Sequencin
g (part 4
): RNA
-
seq



Lecture 15. Microbial Genomes & Metagenomics



Final Projects