CS177: Introduction to Bioinformatics
Course Homepage: Spring 2006
General Course Information:
Dr. Liliana Florea,
Department of Computer Science (firstname.lastname@example.org)
Dr. Sheri Church,
Department of Biology (email@example.com)
Dr. Liliana Florea - Thur 4:00 -- 6:00 pm
Dr. Sheri Church - TBD
Class Time /Place: CS177/144: Mondays, 3:30 – 6:00 pm, Tompkins 405.
CSci 151 or
Permission from instructors.
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.
- 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.
Additional course material will be distributed in class and from the
Blackboard course pages.
- Lecture 1 (01/23/06): Introduction (Sheri Church & Liliana Florea)
- What is bioinformatics?
- History of DNA discovery
- Topics in bioinformatics
- Applications of bioinformatics in biology and medicine
- Course goals
- Lecture 2 (01/30/06): Overview of Molecular Biology and Laboratory Technologies
- DNA and its components
- DNA replication, transcription, translation, protein synthesis
- DNA cloning technology: PCR, sequencing
- Inheritance, mutation, recombination
- Technology overview: PCR, gels, sequencers, microarrays
- New technology overview: PCR, gels, sequencers, microarrays, crystallography,
- Lecture 3 (02/06/06): Lab Session on Nucleotide and Protein Databases (Liliana Florea)
- Sequence types and formats
- Public sequence databases
- Overview of GenBank resources
- Sequence retrieval and examples
- Lecture 4 (02/13/06): The Sequence Alignment Problem I (Liliana Florea)
- 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 exercise
- Lecture 5 (02/27/06): The Sequence Alignment Problem II (Liliana Florea)
- Applications of multiple sequence alignments
- Multiple sequence alignment
- Progressive versus iterative methods
- Lab exercise
- Lecture 6 (03/06/06) Methods in Gene Finding (Liliana Florea)
- What is gene finding?
- Types of information used
- Prediction methods: Ab initio, comparative, combined
- Application to gene annotation
- Lecture 7 (03/20/06) Lab Session on Sequence Analysis and Gene Annotation (Liliana Florea)
- Application: annotating a genomic sequence
- NCBI / GenBank / web resources
- Combining ab initio and comparative gene finding methods
- Lecture 8 (03/27/06) Molecular Evolution (Sheri Church)
- The study of genetics
- Evolution: overview
- Models of sequence evolution
- Lecture 9 (04/03/06) Phylogenetics I (Sheri Church)
- Phylogenetic trees
- Phylogenetic networks
- Computer software and demos
- Lecture 10 (04/10/06) Phylogenetics II & Laboratory Session: Group Project on Evolutionary Biology
- Lecture 11 (04/17/06) 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 (04/24/06) Protein Analysis
- Biochemical properties of amino acids
- Protein secondary and tertiary structure
- Protein structure and function
- The protein folding problem
- Lecture 13 (05/01/06) Comparative Genomics (Sheri Church)
- Genome re-arrangements
- Detecting functional sites via sequence conservation
- Evolutionary point mutation rates
- Lecture 14 (05/03/06) Student Project Presentations
Page last revised January 22nd, 2006.