CS177: Introduction to Bioinformatics

Course Homepage: Spring 2006

General Course Information:

Instructors:
Dr. Liliana Florea, Department of Computer Science (florea@gwu.edu)
Dr. Sheri Church, Department of Biology (schurch@gwu.edu)

Office Hours:
Dr. Liliana Florea - Thur 4:00 -- 6:00 pm
Dr. Sheri Church - TBD

Class Time /Place: CS177/144: Mondays, 3:30 – 6:00 pm, Tompkins 405.

Pre-requisites: CSci 151 or CSci 212; BiSc 13- 14. (Spring). Permission from instructors.

Course Description: This course will provide a broad introduction to the area of bioinformatics. Topics include: biochemistry overview, databases, the alignment problem, sequence analysis methods, introductory phylogenetics, use of public databases, and proteins and protein structure-function.

Recommended textbook(s):
- D.W. Mount (2001) Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Lab Press.
- P.G. Higgs and T.K. Atwood (2005) Bioinformatics and Molecular Evolution. Blackwell Publishing.

Additional course material will be distributed in class and from the Blackboard course pages.

Lecture schedule:

• Lecture 1 (01/23/06): Introduction (Sheri Church & Liliana Florea)
  • What is bioinformatics?
  • History of DNA discovery
  • Topics in bioinformatics
  • Applications of bioinformatics in biology and medicine
  • Course goals
  
  
• Lecture 2 (01/30/06): Overview of Molecular Biology and Laboratory Technologies (Sheri Church)
  • DNA and its components
  • DNA replication, transcription, translation, protein synthesis
  • DNA cloning technology: PCR, sequencing
  • Inheritance, mutation, recombination
  • Technology overview: PCR, gels, sequencers, microarrays
  • New technology overview: PCR, gels, sequencers, microarrays, crystallography, mass spectrometry
  
  
• Lecture 3 (02/06/06): Lab Session on Nucleotide and Protein Databases (Liliana Florea)
  • Sequence types and formats
  • Public sequence databases
  • Overview of GenBank resources
  • Sequence retrieval and examples
  
  
• Lecture 4 (02/13/06): The Sequence Alignment Problem I (Liliana Florea)
  • Applications of pairwise sequence alignments
  • The pairwise sequence alignment problem (DNA, protein)
  • Local versus global alignments
  • Alignment scoring
  • Dynamic programming algorithms (Smith-Waterman, Needleman-Wunsch)
  • Lab exercise
  
  
• Lecture 5 (02/27/06): The Sequence Alignment Problem II (Liliana Florea)
  • Applications of multiple sequence alignments
  • Multiple sequence alignment
  • Progressive versus iterative methods
  • Lab exercise
  
  
• Lecture 6 (03/06/06) Methods in Gene Finding (Liliana Florea)
  • What is gene finding?
  • Types of information used
  • Prediction methods: Ab initio, comparative, combined
  • Application to gene annotation
  
  
• Lecture 7 (03/20/06) Lab Session on Sequence Analysis and Gene Annotation (Liliana Florea)
  • Application: annotating a genomic sequence
  • NCBI / GenBank / web resources
  • Combining ab initio and comparative gene finding methods
  
  
• Lecture 8 (03/27/06) Molecular Evolution (Sheri Church)
  • The study of genetics
  • Evolution: overview
  • Models of sequence evolution
  
  
• Lecture 9 (04/03/06) Phylogenetics I (Sheri Church)
  • Phylogenetic trees
  • Phylogenetic networks
  • Computer software and demos
  
  
• Lecture 10 (04/10/06) Phylogenetics II & Laboratory Session: Group Project on Evolutionary Biology (Sheri Church)
   
  
• Lecture 11 (04/17/06) Mid-term Exam and Final Project Progress Assessment (Liliana Florea & Sheri Church)
  • Part I: Mid-term Exam.
  • Part II: Final Projects - Progress Review, Feedback and Assistance – Lab Session (Liliana Florea & Sheri Church)
  
  
• Lecture 12 (04/24/06) Protein Analysis
  • Biochemical properties of amino acids
  • Protein secondary and tertiary structure
  • Protein structure and function
  • The protein folding problem
  
  
• Lecture 13 (05/01/06) Comparative Genomics (Sheri Church)
  • Genome re-arrangements
  • Detecting functional sites via sequence conservation
  • Evolutionary point mutation rates
  
  
• Lecture 14 (05/03/06) Student Project Presentations