Lectures: Mondays, Jan 26-May 4, 10-11:30 PM,
Location - Coles 105
Computer Lab: Mondays, 12-2 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
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 2009 Course Syllabus (G16.2604):
[NOTE: Lecture content posted here is subject to change up to minutes before
it is actually presented in class]
Wed, Jan 21
Carlisle Computer Classroom (Ehrman Library)
Lecture 1. Introduction to the course
Lecture 1 PowerPoint slides
Exercise for Lecture 1
- Overview of the challenges of Molecular Biology Computing
- The Biologist in the Age of Information and the Computer Savvy Biologist
- Genomics
Mon, Jan 26
Lecture 2. UNIX Basics, Part I.
Reading
Why Biologists Want to Program Computers by James Tisdall
Lecture 2 PowerPoint slides
Exercise for Lecture 2
- Logging in to the RCR server
- UNIX filenames and file protections
- UNIX commands for working with directories
- File transfer with FTP
Mon, Feb 2
Lecture 3. UNIX Basics, Part II.
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
Mon, Feb 9
Coles 101
Lecture 4. Finding Sequences by Name, Accession#, Keyword, or by Association
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
Mon, Feb 16
President's Day: NO CLASS
Mon, Feb 23
Lecture 5. Sequence Alignment & Perl #3
Lecture 5 PowerPoint slides
Perl3 RegExpr PPT
<>
Exercise for Lecture 5
Perl exercise #3 - MIDTERM EXAM
Reading:
O'Reilly BLAST book chap 4.
Similarity Searching on the Web
Mon, March 2
Lecture 6. Similarity Searching
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
Mon, March 9
Lecture 7. Multiple Alignment
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
Mon, March 16
Review of Perl midterm assignment
Lecture 8. Computing Evolution: Phylogenetic Analysis
Alumni Auditorium A
Phylogenetics PowerPoint slides
Comparative Genomics
Phylogenetics Exercise
Reading
Ks/Ka score detects evolution
- Sequence-based taxonomy: Overview and Assumptions
- From Multiple Alignment to Phylogeny
- Neighbor Joining
- Maximum Likelyhood vs. Parsimony
- Computer Tools for phylogenetic analysis
- DISTANCES
- GROWTREE
- PAUP
- PHYLIP
Mon, March 23
Lecture 9. Patterns and Sequence-Function Relationships
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)
- GCG pattern recognition tools: FINDPATTERNS, MOTIFS, PROFILESCAN, MEME
- Other pattern recognition software
Mon, April 6
Lecture 11. Genomics II: Analysis of Microarray Data
Lecture 10 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
Mon, April 13
Lecture 12. Genomics III: Next-Geration Sequencing
Examples of Posters for course projects
pril 20 (or TDB)
Poster/project presentations
4-6 PM - MSB Atrium