Lectures: Monday, Jan 28-May 5, 1-2:30 PM,
Location - varies (Alumni Audiorium B, Schwartz F, Coles 101) - see below
Computer Lab: Monday, 2:30-5 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
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 2008 Course Syllabus (G16.2604):
[NOTE: Lecture content posted here is subject to change up to minutes before
it is actually presented in class]
Mon, Jan 28
Alumni Hall B
Lecture 1. Introduction to the course, Unix and Perl
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
- Using the Molecular Biology Computing Tools at NYU Medical Center
- UNIX, Mac/Windows software, and Web Browsers as Platforms for Sequence Analysis
- Genomics
Mon, Feb 4
Alumni Hall B
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 11
Schwartz F
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 18
President's Day: NO CLASS
Mon, Feb 25
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, March 3
Schwartz F
Lecture 5. Database Searching by Similarity
Exercise for Lecture 5
Lecture 5 PowerPoint slides
Reading:
O'Reilly BLAST book chap 4.
Similarity Searching on the Web
- Worldwide databases
- Similarity vs. homology
- BLAST vs FASTA
- Interpretation of results
- Translation, Filtering, and other options
- Run your own BLAST software
Mon, March 10 (abbreviated)
Coles 101
Lecture 6. Advanced Similarity and Multiple Alignment
Advanced Concepts in Similarity Searching
Perl3 RegExpr PPT
Fun BLAST exercise
Optional addtional exercise on BLAST from NCBI
Perl exercise #3 - MIDTERM EXAM
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 10
Coles 101
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
Easy alignment exercise
Harder exercise for Lecture 7
Mon, March 17
Coles 101
Review of Perl midterm assignment
Lecture 8. Computing Evolution: Phylogenetic Analysis
Alumni Auditorium A
Phylogenetics PowerPoint slides
Comparative Genomics
Phylogenetics Exercise
A more fun Phylogenetics Exercise
- 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 24
Coles 101
Lecture 9. Patterns and Sequence-Function Relationships
Lecture 9 PowerPoint slides
Exercise 1 for Lecture 8
Exercise 2 for Lecture 8
Web motif & function Exercise
- 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, March 31
Lecture 10. Genomics I: Analysis of Microarray Data
Coles 101
Lecture 10 PowerPoint slides
Microarray Exercise
Reading:
Gene Expression Data Analysis
- Basics of designing a microarray
- Image analysis
- Normalization
- Variability and replication
- Clustering
- Microarray Databases
Mon, April 7
Lecture 11. Genomics II: SNPs and Haplotypes
Alumni Hall B
Readings
Exercise
Mon, April 14
Lecture 12. Using R for Bioinformatics
Alumni Hall B
R Bioinformatics - PowerPoint slides
R Bioinformatics - Word doc
Exercise
R Exercise (Jinhua Wang)
Mon, April 21
Coles 101
Lecture 13. Genomics III: Genome Tiling arrays
Examples of Posters for course projects
[deleted]
Alternate Interfaces & Other Bioinformatics programs
Alumni Aud. A
A short PowerPoint for Lecture #10.
Reading:
Get Your Bioinformatics on the Web
Lecture 10 Web Pages
Instructions to install WebTermX
Exercise for Lecture 10 (SeqLab Tutorial)
SeqWeb Tutorial
- SeqWeb: a Web interface to GCG
- SeqLab: an X-Windows interface to GCG
- EMBOSS - a free GCG-like bioinformatics suite with command-line and X-windows interface
[changed]
Computer Tools for Sequencing Projects, PCR and Restriction
Mapping
Lec8 PowerPoint slides
Map and PCR primer Exercise
A fun exercise in plasmid design
- Practical and theoretical problems in sequencing and assembly of contigs
- The GCG FRAGMENT ASSEMBLY tools for managing sequencing projects
- Using Mac/Windows desktop MolBio programs
- The challenges of whole genome sequencing
- Restriction Mapping WITH GCG: MAP, MAPPLOT, MAPSORT
- Web-based tools for restriction mapping
- PCR primer design
- GCG tools: PRIME and FINDPATTERNS
- Primer design tools on the web
- DNA sequencing and fragments assembly tools
- Sequencher
- Phred, Phrap, and Consed
- TIGR Assembler, CAP4 and other tools
May 5 (or TDB)
Poster/project presentations
4-6 PM - MSB Atrium