CS177 / CS144: Introduction to Bioinformatics
Course Homepage: Spring 2005
General Course Information:
Dr. Sheri Church,
Department of Biology (firstname.lastname@example.org)
Dr. Liliana Florea,
Department of Computer Science (email@example.com)
Co-instructor: Dr. Rahul Simha
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.
CSci 151 or
BiSc 13-14. (Spring).
Permission from instructors.
Course grading and policies (doc)
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 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
- 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,
- 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
- 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
- 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
Page last revised April 29th, 2005.