PhD in Computing

42002 - Bioinformatics (BIO)

 

 

  • Type: Elective
  • Semester: S3
  • ECTS: 6
  • Teaching Points: 15
  • Offer: Annual
  • Responsible Unit: CS
  • Responsible: Gabriel Valiente
  • Language: English
  • Requirements: Basic knowledge on Algorithmics and Data structures.

 

GOALS
The main goal is the introduction of basic computer science skills for genomics, phylogenetics, and other research areas of computational biology.

 

 

 

CONTENTS
1. Biological introduction
2. Comparison methods for short sequences

 

  • Dot matrix
  • Dynamic algorithm: pairwise alignment
  • Multiple alignment
  • Hash algorithm

3. Comparison methods for large sequences

  • Suffix trees
  • Suffix arrays

4. Methods for matching patterns

  • Exact matching
  • Approximate matching
  • Sequence assembly

5. Phylogenetic reconstruction methods

  • Reconstruction of ultrametric trees
  • Reconstruction of additive trees
  • Reconstruction of non-additive trees
  • Reconstruction of perfect phylogenies

6. Taxonomic reconstruction methods

  • Compatibility of phylogenies
  • Consensus techniques for phylogenies
  • Combination techniques for phylogenies
  • Compatibility of taxonomies
  • Consensus techniques for taxonomies
  • Combination techniques for taxonomies
  • Current projects

 

DOCENT METHODOLOGY
Docent methodology is based on three aspects:
- Presence activities: teacher’s lectures, and in some cases, lectures by guest teachers.
- Supervised activities: based on article reading and solving example cases, all supervised by the teacher.
- Autonomous work.

 

 

 

EVALUATION METHODOLOGY
Solving problems along the course (50%) and a final exposition of an article, which will be set by the teacher, or a experimental algorithmic project (50%).

 

 

 

BIBLIOGRAPHY

 

  • G. Valiente, Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R.
Taylor & Francis/CRC Press, 2009
  • N. C. Jones, P. Pevzner. An introduction to bioinformatics algorithms. MIT Press, 2004.
  • A. M. Lesk. Introduction to bioinformatics (2nd edition). Oxford University Press, 2005
  • M. Waterman. Introduction to computational biology. Chapman and Hall, 1995
  • G. Navarro, M. Raffinot. Flexible pattern matching in strings. Cambridge University Press, 2002
  • D. Gusfield. Algorithms on strings, trees and sequences. Cambridge University Press, 1997
  • P. Pevzner. Computational molecular biology. MIT Press, 2000
  • D. Mount. Bioinformatics: Sequence and genome analysis. Cold Spring Harbor Laboratory Press, 2001

 

 

 

RESOURCES
Teachers’ lecture materials, bibliographical references and other materials can be found in the web page.

 


WEBSITE