CSci 166-80 / 297-80: Computational Biology
Dr. Liliana Florea
(firstname.lastname@example.org), CS Department. Office hours: Wed 4-6 pm (Phillips 714).
TA: Thang Nguyen (email@example.com). Office hours: 3-4 pm (Staughton 309).
Meeting time and venue: Tuesdays, 7:10 - 9:40 pm. Classroom: 2020 K Str, Rm. 15.
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.
CRN: 25032 (CS166-80); 25348 (CS297-80)
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 (1/16/07) Introduction to Computational Molecular Biology.
- Overview of course topics and objectives.
- Basic concepts in computational molecular biology.
- Lecture 2 (1/23/07) Biological Sequences. This class will meet in Tompkins 410.
- Types of biological sequences: DNA, RNA, proteins
- Sequence storage and retrieval
- Lab session on sequence data repositories (GenBank).
- Lecture 3 (1/30/07) Pairwise Sequence Alignments I.
- Definition of alignments
- Alignment scoring
- D.p. algorithms for optimal alignments (Needleman-Wunsch, Smith-Waterman)
- Lecture 4 (2/6/07) Pairwise Sequence Alignments II.
- Heuristics for fast and accurate alignment
- Hash indices, 'blast'
- 2/13/07 Class cancelled due to inclement weather. Makeup class day: 5/1/07
- Lecture 5 (2/20/07) Multiple Sequence Alignments.
- Orthologs and paralogs
- Progressive alignment methods (ClustalW)
- Iterative alignment methods (DiAlign)
- Lecture 6 (2/27/07) Gene Finding Methods I.
- What are genes? Review.
- Introduction to Hidden Markov Models
- Predictive methods: GenScan (HMM)
- Lecture 7 (3/6/07) Gene Finding Methods II.
- Comparative methods
- Combined methods
- Lecture 8 (3/20/07) Lab Session on Alignments and Gene Finding. This class will meet in Tompkins 410.
- Internet-based annotation of genes in genomic sequences.
- NCBI 'blast' tools.
- The UCSC Genome Browser.
- Lecture 9 (3/27/07) Mid-term Exam and Discussion of Final Projects.
- Lecture 10 (4/3/07) Methods for Identifying Regulatory Motifs. This class will meet in Tompkins 410.
- What are TFBS? Review.
- PWMs and information content
- (Optional) Gibbs sampling, EM methods
- Sequence conservation
- Lecture 11 (4/10/07) Molecular Evolution & Phylogenetics I.
- Models of sequence evolution (amino acid, nucleotide, codon levels)
- Synonymous/non-synonymous substitution rates
- Positive and negative selection
- Lecture 12 (4/17/06) Phylogenetics II.
- Building phylogenetic trees:
- maximum parsimony (MP) (Fitch)
- maximum likelihood (ML) (Feselstein)
- neighbor-joining (Saitou-Nei)
- Lecture 13 (4/24/07) Invited Lecture or Field Trip.
- Lecture 14 (5/1/07) Final Project Presentations.
Page last revised February 15th, 2007.