Bioinformatics

Spring 2010

Instructor: Dr. Stuart Brown,

Associate Professor, NYUMC Dept. of Cell Biology

Schedule

Lectures: Wednesdays, Jan 20-May 5, 1-2:30 PM,

Location - varies- see each lecture listed below

Computer Lab: Wed, 3-5 PM,

Carlisle Computer Classroom (Ehrman Library)

Textbook:

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

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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.

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Spring 2010 Course Syllabus (G16.2604):

[NOTE: Lecture content posted here is subject to change up to minutes before it is actually presented in class]

Lecture 1. Introduction to the Course
Wed, Jan 20, Location: MSB 588

Lecture 1 PowerPoint slides
Exercise for Lecture 1

• Overview of the challenges of Bioinformatics in the era of Genomics

Lecture 2. UNIX Basics, Part I.
Wed, Jan 27, Location: MSB 588

Reading
Why Biologists Want to Program Computers by James Tisdall
Lecture 2 PowerPoint slides
Exercise for Lecture 2
Unix Homework

• Logging in to the class server
• UNIX filenames and file protections
• UNIX commands for working with directories
• File transfer with FTP

Lecture 3. UNIX Basics, Part II.
Wed, Feb 3, Location: Smilow 901a

Reading
How Perl Saved the Human Genome Project by Lincoln Stein
Emacs Reference Guide
Lecture 3 PowerPoint slides
Perl-1 PowerPoint
Exercise for Lecture 3
Perl Exercise 1

• Editing text files
• Additional UNIX commands
• Simple shell scripts & PERL
• How to become a UNIX power user

Lecture 4. Bioinformatics Databases
Wed, Feb 10, Location: Sackler Conf. Rm.

Lecture 4 PowerPoint slides
Perl 2 lecture ppt slides
Exercise 1 for Lecture 4
A Simple tutorial on the use of Entrez/PubMed (by Sandra Porter @ Geospiza Inc.)
Perl exercise #2

• Using ENTREZ to find and retrieve sequences and MEDLINE references
• download your own local data set
• Genome databases
• Other online genetic databases: mutations, SNPs, etc

Lecture 5. Sequence Alignment & Perl #3
Wed, Feb 17, Location: Sackler Conf. Rm.

Lecture 5 PowerPoint slides
Perl3 RegExpr PPT
Exercise for Lecture 5
# Reading:
O'Reilly BLAST book chap 4.
Similarity Searching on the Web

Lecture 6. Similarity Searching.
Wed, Feb 24, Location: Sackler Conf. Rm

Midterm assignment
Searching Databases by Similarity
Fun BLAST exercise
Optional addtional exercise on BLAST from NCBI

Reading:

Advanced Similarity Searching on the Web
Using Blast on the Web
Searching Sequence Databases A novel Src kinase in the C.elegans genome

Lecture 7. Multiple Alignment
Wed, March 3, Location: Sackler Conf. Rm.

Multiple alignment PPT slides

• Multiple Alignment: A Computational Challenge
• PILEUP
• CLUSTAL
• Editing Alignments, Consensus Sequences
• Producing Publication-Quality Printouts

Reading:
Multiple Alignment on the Web
Exercises
Multiple alignment exercise

Lecture 8. Computing Evolution: Phylogenetic Analysis
Wed, March 10, Location: Sackler Conf. Rm.

Phylogenetics PowerPoint slides
Comparative Genomics
Phylogenetics Exercise

Reading

Ks/Ka score detects evolution

• Sequence-based taxonomy: Overview and Assumptions
• From Multiple Alignment to Phylogeny
• Detecting selection in sequences

Lecture 9. Patterns and Sequence-Function Relationships
Wed, March 17, Location: Sackler Conf. Rm.

Lecture 9 PowerPoint slides
Pattern Exercise
Web motif & function Exercise
Protein structure tutorial with Cn3D

• Sequence Homology and Conserved Regions
• Conserved DNA sequences: Promoters, restriction sites
• Combinatorial complexity of simple patterns
• RNA Folding Patterns
• Protein Motifs (domains)
• Pattern recognition software

Lecture 10. Genomics I: SNPs and Haplotypes
Wed, March 24, Location: Sackler Conf. Rm.

Readings

• SNP/HapMap PowerPoint slides
  
• 1.42 Million SNPs
• Comparative Genomics of Regulatory Regions
  
  

Exercise

SNP and Haplotype Exercise

• Hapmap Tutorial - PPT by Lincoln Stein
• Users Guide to the Hapmap

Lecture 11. Genomics II: Analysis of Microarray Data
Wed, March 31, Location: Sackler Conf. Rm.

Microarray PowerPoint slides
Exrcises Array Express Tutorial
Microarray Exercise

Reading:
Gene Expression Data Analysis

• Basics of designing a microarray
• Image analysis
• Normalization
• Variability and replication
• Clustering
• Microarray Databases

Lecture 12. Genomics III: Next-Geration Sequencing
Wed, April 7, Location: Sackler Conf. Rm.

• New Sequencing Technologies
• Genome assembly
• ChIP-seq
• Mutation discovery in Cancer
• Metagenomics/Microbiome

Wed, April 14, Location: Sackler Conf. Rm.
Spillover if we need to more time on any topics, discusssion of work in progress on projects, or extra lecture on Next-Gen sequencing.

Wed April 21 (or TDB)
Poster/project presentations
4-6 PM - MSB Atrium



Examples of Posters for course projects

• Using bioinformatics to investigate a novel Cyclin A/Cdk 2-interacting protein, Khoo
• Gene Expression Profiles in Keratinocyte, Lee
• Genetic Structure of Atlantic Sturgeon using mtDNA, Kang