CS144: Introduction to Bioinformatics
Course Homepage: Fall 2007
General Course Information:
Dr. Liliana Florea,
Department of Computer Science (email@example.com)
Office Hours: Wednesdays, 4:00-6:00 pm, Phillips 714.
Class Time /Place: Mondays, 3:30-6:00 pm, Tompkins 411.
Pre-requisites: None, officially. Recommended background:
CSci 151 or
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 (9/10/07): Introduction
- What is bioinformatics?
- History of DNA discovery
- Topics in bioinformatics
- Applications of bioinformatics in biology and medicine
- Course goals
- Lecture 2 (9/17/07): Overview of Molecular Biology Concepts
- DNA and its components
- DNA replication, transcription, translation, protein synthesis
- DNA cloning technology: PCR, sequencing
- Sequence mutation and evolution; orthologs and paralogs
- Lecture 3 (9/24/07): Lab Session on Nucleotide and Protein Databases
- Sequence types and formats
- Public sequence databases
- Overview of GenBank resources
- Sequence retrieval and examples
- Lecture 4 (10/1/07): The Sequence Alignment Problem I
- 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 exercises
- Lecture 5 (10/8/07): The Sequence Alignment Problem II
- Applications of multiple sequence alignments
- Multiple sequence alignment
- Progressive versus iterative methods
- Lab exercises
- Lecture 6 (10/15/07) Methods in Gene Finding
- What is gene finding?
- Types of information used
- Prediction methods: Ab initio, comparative, combined
- Application to gene annotation
- Lecture 7 (10/22/07) Lab Session on Sequence Analysis and Gene Annotation
- Application: annotating a genomic sequence
- NCBI / GenBank / web resources
- Combining ab initio and comparative gene finding methods
- Lecture 8 (10/29/07) Molecular Evolution and Phylogenetics I
- The study of genetics
- Evolution: overview
- Models of sequence evolution
- Introduction to the MEGA software package
- Lecture 9 (11/5/07) Molecular Evolution and Phylogenetics II (Invited speaker: Dr. Sheri Church)
- Phylogenetic trees
- Phylogenetic networks
- Computer software and demos (MEGA)
- Lecture 10 (11/12/07) Comparative Genomics
- Genome re-arrangements
- Detecting functional sites via sequence conservation
- Web resources for comparative genomics
- Lecture 11 (11/19/07) Mid-term Exam and Final Project Progress Assessment
- Part I: Mid-term Exam.
- Part II: Final Projects - Progress Review, Feedback and Assistance - Lab Session
- Lecture 12 (11/26/07) Protein Analysis
- Biochemical properties of amino acids
- Protein secondary and tertiary structure
- Protein structure and function
- The protein folding problem
- Lecture 13 (12/3/07) Invited Lecture (Dr. Nathan Edwards, University of Maryland)
- Lecture 14 (12/10/07) Student Project Presentations
Page last revised August 15th, 2007.