CS144: Introduction to Bioinformatics

Course Homepage: Fall 2007

General Course Information:

CRN: 64098

Instructor:
Dr. Liliana Florea, Department of Computer Science (florea@gwu.edu)

Office Hours: Wednesdays, 4:00-6:00 pm, Phillips 714.

Class Time /Place: Mondays, 3:30-6:00 pm, Tompkins 411.

Pre-requisites: None, officially. Recommended background: CSci 151 or CSci 212; BiSc 13- 14. (Spring).

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 (9/10/07): Introduction
  • What is bioinformatics?
  • History of DNA discovery
  • Topics in bioinformatics
  • Applications of bioinformatics in biology and medicine
  • Course goals
  
  
• Lecture 2 (9/17/07): Overview of Molecular Biology Concepts
  • DNA and its components
  • DNA replication, transcription, translation, protein synthesis
  • DNA cloning technology: PCR, sequencing
  • Sequence mutation and evolution; orthologs and paralogs
  
  
• Lecture 3 (9/24/07): Lab Session on Nucleotide and Protein Databases
  • Sequence types and formats
  • Public sequence databases
  • Overview of GenBank resources
  • Sequence retrieval and examples
  
  
• Lecture 4 (10/1/07): The Sequence Alignment Problem I
  • 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 exercises
  
  
• Lecture 5 (10/8/07): The Sequence Alignment Problem II
  • Applications of multiple sequence alignments
  • Multiple sequence alignment
  • Progressive versus iterative methods
  • Lab exercises
  
  
• Lecture 6 (10/15/07) Methods in Gene Finding
  • What is gene finding?
  • Types of information used
  • Prediction methods: Ab initio, comparative, combined
  • Application to gene annotation
  
  
• Lecture 7 (10/22/07) Lab Session on Sequence Analysis and Gene Annotation
  • Application: annotating a genomic sequence
  • NCBI / GenBank / web resources
  • Combining ab initio and comparative gene finding methods
  
  
• Lecture 8 (10/29/07) Molecular Evolution and Phylogenetics I
  • The study of genetics
  • Evolution: overview
  • Models of sequence evolution
  • Introduction to the MEGA software package
  
  
• Lecture 9 (11/5/07) Molecular Evolution and Phylogenetics II (Invited speaker: Dr. Sheri Church)
  • Phylogenetic trees
  • Phylogenetic networks
  • Computer software and demos (MEGA)
  
  
• Lecture 10 (11/12/07) Comparative Genomics
  • Genome re-arrangements
  • Detecting functional sites via sequence conservation
  • Web resources for comparative genomics
  
  
• Lecture 11 (11/19/07) Mid-term Exam and Final Project Progress Assessment
  • Part I: Mid-term Exam.
  • Part II: Final Projects - Progress Review, Feedback and Assistance - Lab Session
  
  
• Lecture 12 (11/26/07) Protein Analysis
  • Biochemical properties of amino acids
  • Protein secondary and tertiary structure
  • Protein structure and function
  • The protein folding problem
  
  
• Lecture 13 (12/3/07) Invited Lecture (Dr. Nathan Edwards, University of Maryland)
   
  
• Lecture 14 (12/10/07) Student Project Presentations