CS177 / CS144: Introduction to Bioinformatics

Course Homepage: Spring 2005

General Course Information:

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

Office Hours:
Dr. Liliana Florea - Tue 3:00 -- 6:00 pm
Dr. Sheri Church - Thur 1:00 -- 2:30 pm, Fri 11:00 am -- 12:30 pm.

Class Time /Place: CS177 / CS144: Mondays, 3:30 – 6:00 pm, Tompkins 405.

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

Course grading and policies (doc)

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, proteins and protein structure-function, introductory phylogenetics, and use of public databases.

Textbook: D.W. Mount (2001) “Bioinformatics: Sequence and Genome Analysis”. Cold Spring Harbor Lab Press.
Additional course material will be distributed in class and from the Blackboard course pages.

Lecture schedule:

• Lecture 1 (01/24/05): Introduction (Sheri Church & Liliana Florea)
  • What is bioinformatics?
  • History of DNA discovery
  • Topics in bioinformatics
  • Applications of bioinformatics in biology and medicine
  • The future: bioinformatics careers
  • Course goals
  
  
• Lecture 2 (01/31/05): 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
  • Old technology overview: microscopy, etc.
  • New technology overview: PCR, gels, sequencers, microarrays, crystallography, mass spectrometry
  
  
• Lecture 3 (02/07/05): The Sequence Alignment Problem (Liliana Florea)
  • The pairwise sequence alignment problem
  • Alignment scoring
  • Dynamic programming algorithm
  • Heuristics for fast alignments
  • Multiple sequence alignment
  • Applications of alignments
  
  
• Lecture 4 (02/14/05) Lab Session on Nucleotide and Protein Databases (Liliana Florea)
  • Sequence types and public sequence databases
  • Sequence retrieval and examples
  • Software packages for sequence management and manipulation (MEGA 3.0)
  
  
• Lecture 5 (02/28/05) Methods in Gene Finding (Liliana Florea)
  • Types of information used
  • Ab initio prediction methods
  • Comparative methods
  • Combined methods
  • Application to gene annotation
  
  
• Lecture 6 (03/07/05) Lab Session on Sequence Analysis (Liliana Florea)
  • Application: annotating a genomic sequence
  • NCBI / GenBank / web resources
  • Combining ab initio and comparative gene finding methods
  
  
• Lecture 7 (03/21/05) Phylogenetics I (Sheri Church)
  • The study of genetics
  • Evolution: overview
  • Taxonomy and phylogenetics
  • Cladistic vs Phenetic analyses
  • Models of sequence evolution
  
  
• Lecture 8 (03/28/05) Phylogenetics II (Sheri Church)
  • Phylogenetic trees
  • Phylogenetic networks
  • Computer software and demos
  
  
• Lecture 9 (04/04/05) Laboratory Session: Group Project on Evolutionary Biology (Sheri Church)
   
  
• Lecture 10 (04/11/05) Comparative Genomics (Sheri Church)
  • Genome re-arrangements
  • Detecting functional sites via sequence conservation
  • Evolutionary point mutation rates (Ka/Ks)
  • Application: study of HIV strains
  
  
• Lecture 11 (04/18/05) 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 (04/25/05) Protein Analysis (Liliana Florea)
  • Review of protein structure and function
  • Review of experimental techniques to determine structure
  • The protein folding problem
  • How folding energy is computed
  • Implications of folding
  
  
• Lecture 13 (05/02/05) Computational Problems in Emerging Biotechnologies (invited speaker: Dr. Nathan Edwards, University of Maryland)
  • Proteomics through mass spectrometry
  
  
• Lecture 14 (05/04/05) Student Project Presentations