CSci 166-80 / 297-80: Computational Biology

Spring 2006

Instructor: Dr. Liliana Florea (florea@gwu.edu), CS Department. Office Hours: Friday 2-4 pm

TA: Leming Zhou (lmzhou@gwu.edu). Office hours: TBD.

Meeting time and venue: Tuesdays, 7:10 - 9:40 pm. Classroom: 414 Phillips.

Pre-requisites: CSci 151, CSci 212 or equivalent; programming experience in C/C++ (preferred) or Java is a must; CSci 177/144 or permission from the instructor.

Course Description: This course will provide an overview of algorithms for computational biology. Topics may include algorithms for: DNA and protein sequence alignments; gene annotation; identification of gene regulatory regions; models of sequence evolution; phylogenetic analyses; comparative genomics; microarray and/or proteomics data analysis. (Flyer)

Textbook:
Neil C. Jones and Pavel A. Pevzner (2004). "An Introduction to Bioinformatics Algorithms (Computational Biology)". The MIT Press. ISBN: 0262101068.

Additional reading and course materials will be distributed in class and/or from the course Blackboard pages.
 

Tentative Lecture Schedule:

• Lecture 1 (1/17/06) Introduction to Computational Molecular Biology.
  • Overview of course topics and objectives.
  • Basic concepts in computational molecular biology.
  
  
• Lecture 2 (1/24/06) Biological Sequences. This class will meet in Tompkins 405.
  • Types of biological sequences: DNA, RNA, proteins
  • Sequence storage and retrieval
  • Lab session on sequence data repositories (GenBank).
  
  
• Lecture 3 (1/31/06) Pairwise Sequence Alignments I.
  • Definition of alignments
  • Alignment scoring
  • D.p. algorithms for optimal alignments (Needleman-Wunsch, Smith-Waterman)
  
  
• Lecture 4 (2/7/06) Pairwise Sequence Alignments II.
  • Heuristics for fast and accurate alignment
  • Hash indices, 'blast'
  • Advanced topics (optional): suffix trees, spaced seeds
  
  
• Lecture 5 (2/14/06) Multiple Sequence Alignments.
  • Orthologs and paralogs
  • Progressive alignment methods (ClustalW)
  • Iterative alignment methods (DiAlign)
  
  
• Lecture 6 (2/21/06) Gene Finding Methods I.
  • What are genes? Review.
  • Introduction to Hidden Markov Models
  • Predictive methods: GenScan (HMM)
  
  
• Lecture 7 (2/28/06) Gene Finding Methods II.
  • Comparative methods: Sim4 (greedy alignment)
  • Combined methods: TwinScan (pair HMMs)
  
  
• Lecture 8 (3/7/06) Lab Session on Alignments and Gene Finding. This class will meet in Tompkins 405.
  • Internet-based annotation of genes in genomic sequences.
  • NCBI 'blast' tools.
  • The UCSC Genome Browser.
  
  
• Lecture 9 (3/21/06) Methods for Identifying Regulatory Motifs. This class will meet in Tompkins 405.
  • What are TFBS? Review.
  • PWMs and information content
  • (Optional) Gibbs sampling, ML methods
  • Sequence conservation
  
  
• Lecture 10 (3/28/06) Mid-term Exam and Discussion of Final Projects.
  
  
• Lecture 11 (4/4/06) Phylogenetics I.
  • Building phylogenetic trees:
    • maximum parsimony (MP) (Fitch)
    • maximum likelihood (ML) (Feselstein)
    • neighbor-joining (Saitou-Nei)
  
  
• Lecture 12 (4/11/06) Phylogenetics II.
  • Models of sequence evolution
  • Synonymous/non-synonymous substitution rates
  • Statistical tests for positive and negative selection
  
  
• Lecture 13 (4/18/06) Field Trip. Visit to the J. Craig Venter Institute, April 19th.
  
  
• Lecture 14 (4/25/06) Final Project Presentations.