CSci 166-80 / 297-80: Computational Biology
Dr. Liliana Florea
(firstname.lastname@example.org), CS Department.
Office Hours: Friday 2-4 pm
TA: Leming Zhou (email@example.com). Office hours: TBD.
Meeting time and venue: Tuesdays, 7:10 - 9:40 pm. Classroom: 414 Phillips.
CSci 212 or equivalent;
programming experience in C/C++ (preferred) or Java is a must;
CSci 177/144 or
permission from the instructor.
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.
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.
Page last revised April 7th, 2006.