Bioinformatics Syllabus


Bioinformatics

Spring 2012

Instructor: Dr. Stuart Brown,

Associate Professor, NYUMC Center for Health Informatics & Bioinformatics

Schedule

Lectures/Lab: Tuesesdays, Jan 24-May 1, 1-4:30 PM,

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 Genome 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 which 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 knowledge of computer programming or computer hardware is necessary.


Spring 2012 Course Syllabus (G16.2604):

[NOTE: Lectures & exercises posted here are subject to change up to minutes before they are actually presented in class]

Lecture 1. Introduction to the Course: Bionformatics Algorithms & Data Structures
Tues, Jan 24

Lecture 1 PowerPoint slides

Exercise for Lecture 1 

Lecture 2. Bioinformatics Databases, UNIX Basics (part 1)
Tues, Jan 30

Reading

Why Biologists Want to Program Computers by James Tisdall

A Simple video on the use of Entrez/PubMed

Entrez Tutorial 

Unix Exercise 


Lecture 3. Alignment, UNIX Basics (part 2)
Tues, Feb 7

Alignment PowerPoint slides

Unix II PowerPoint slides

Unix text editing exercise for Lecture 3

Alignment exercise


Reading

How Perl Saved the Human Genome Project by Lincoln Stein

Emacs Reference Guide


Lecture 4. Similarity Searching (BLAST), Perl (part 1)
Tues, Feb 14

Lecture 4 PowerPoint slides

Perl 2 lecture ppt slides

Perl-1 PowerPoint

Perl Exercise 1


Searching Databases by Similarity

O'Reilly BLAST book chap 4.

Similarity Searching on the Web

Fun BLAST exercise

Optional addtional exercise on BLAST from NCBI


Exercise 1 for Lecture 4


Lecture 5. Advanced Alignment methods, Perl (part 2)
Tues, Feb 21

Lecture 5 PowerPoint slides

Perl exercise #2


Reading:

Advanced Similarity Searching on the Web

Searching Sequence Databases A novel Src kinase in the C.elegans genome


Lecture 6.  Patterns and Sequence-Function Relationships, Perl (part 3)
Tues, Feb 28

Lecture 6 PowerPoint slides 

Pattern Exercise

Web motif & function Exercise

Protein structure tutorial with Cn3D


Perl3 RegExpr PPT 

Perl Exercise #3 will be graded for a Midterm. 


Lecture 7. Multiple Alignment,
Tues, March 6

Reading:

Multiple Alignment on the Web

Exercises

Multiple alignment exercise  

[Extra week to work on Perl Ex #3]


Lecture 8.  Computing Evolution: Phylogenetic Analysis
Tues, March 13 

Phylogenetics PowerPoint slides

Comparative Genomics

Phylogenetics Exercise

Marine Mammals phylogenetics exercise (Fun!) 

Reading

Ks/Ka score detects evolution

INSERT SOME SORT OF more objective MIDTERM EXAM HERE


Lecture 9. Genomics I: SNPs and Haplotypes
Tues, March 20

Readings

Exercise


Lecture 10. Genomics II: Analysis of Microarray Data
Tues, March 27

Microarray PowerPoint slides

Exrcises Array Express Tutorial

Microarray Exercise


Reading:

Gene Expression Data Analysis


Lecture 11. Genomics III: Next-Geration Sequencing (part 1): Sequence Alignment & Variation
Tues, April 3 

Next-Generation Sequencing PowerPoint slides