Introduction to Bioinformatics

Recommended Prerequisites

- Cell and molecular biology.

Teaching Methods

The course is divided into expository and laboratory classes. The first is dedicated to present the content in a more theoretical approach, without failing to include the active participation of students. The aim is to develop their’s reasoning ability and integration of knowledge and stimulate their critical thinking. Practical classes will enable the student to explore the acquired concepts. Those will follow a problem oriented approach by launching challenges that require knowledge integration, and wherever possible, the use of working groups and discussion.

Learning Outcomes

The main aim of this course is provide the main sources of data and tools used available in bioinformatics as a user. In particular it is expected that students develop the skills listed below:

- Become familiar with the terminology used in bioinformatics;

- Identify and use the main sources of biomedical data and bioinformatic tools;

- Recognize biological entities and use them to navigate between databases;

- Understand the different types of search and alignment algorithms on gene sequences;

- Be able to carry out advanced genetic alignments;

- Be able to determine the protein structure and function of its starting sequence;

- Get a macroscopic view of the biological system by matching information from different fields.

Work Placement(s)

No

Syllabus

1. Introduction and Key Concepts
     a. Background (biology, statistics, computer science)
     b. Challenges in Bioinformatics
     c. Application areas of bioinformatics
2. Sources of biomedical information
     a. Literature
     b. General
     c. Domain/specie specific
     d. Online tools
     e. Programmatic access to data
3. Analysis of sequences
     a. Data Storage Formats
     b. Tools for sequence alignment
     c. Tools for genome organization
     d. Multiple Sequences Alignment (amino acid and nucleic acid).
     e. Sequences search
     f. Detection of genes
4. Sequence, structure and function
     a. From primary structure to secondary structure
     b. Tertiary structure
     c. Identification of protein structure and function
     d. Research and determination of motifs and domains
5. Biological Networks
     a. Protein interaction networks
     d. Time series and regulatory networks

Head Lecturer(s)

Joel Perdiz Arrais

Assessment Methods

Assessment
Laboratory work or Field work: 30.0%
Exam: 70.0%

Bibliography

Discovering genomics, proteomics, and bioinformatics, 2nd Edition,  A. Malcolm Campbell, Laurie J. Heyer, Benjamin Cummings; 2006

 

An introduction to bioinformatics algorithms, Neil C. Jones, Pavel Pevzner, MIT Press, 2004

 

Bioinformatics computing, Bryan P. Bergeron, Prentice Hall PTR, 2003