(This course is listed also in the Department of Information Technology and Bioinformatics Laboratory, University of Turku, under the name “Fundamentals of Bioinformatics – Sequence analysis”)
Research at the border of Molecular Biology and Information Technology has witnessed in recent years an exciting development, with remarkable benefits for both areas. On one hand, biological data is being produced at an astounding rate nowadays, supported by the ever increasing advances in biotechnology, and IT-related tools are necessary to handle the data, interpret them, visualize various parameters, etc. Moreover, many combinatorial problems related to these biological data need IT-specific approaches. On the other hand, the biological systems have huge capabilities for information storing, data manipulation, pattern recognition, parallelism, and energy efficiency, that makes them interesting for computer scientists.
Biocomputing is often used as a catch-all term covering all this area at the intersection of Biology and Computation, although many other terms are used to name the same area. We distinguish and introduce in this course four (non-disjoint) sub-fields:
- Computational Biology – this includes efforts to solve biological problems with computational tools (such as modeling, algorithms, heuristics)
- Bioinformatics – this includes management of biological databases, data mining and data modeling, as well as IT-tools for data visualization
- DNA computing and nano-engineering – this includes models and experiments to use DNA (and other) molecules to perform computations
- Computations in living organisms – this is concerned with constructing computational components in living cells, as well as with studying computational processes taking place daily in living organisms
This course gives an introduction to the field and presents a number of typical problems and questions, as well as some basic models and tools used to address them. The course is intended primarily for graduate and advanced undergraduate students in Computer Science, Molecular Biology and Biochemistry. Students with other background are also welcome.
- Notions of Molecular Biology and Biotechnology
- Physical Mapping
- DNA sequencing
- Investigation of similarities between DNA
- Construction of phylogenetic trees
- Bioinformatics databases and tools
- DNA computing – theory, experiments, perspectives
- R. Dubin, S. Eddy, A. Krogh, G. Mitchison, Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 1999.
- D. Gusfield, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, 1997.
- A.M. Lesk, Introduction to Bioinformatics, Oxford University Press, 2002.
- P. Pevzner, Computational Molecular Biology : An Algorithmic Approach, MIT Press, 2000.
- J. Setubal, J. Meidanis, Introduction to Computational Molecular Biology, PWS Publishing Company, 1997.
- R. Shamir, Lecture Notes on “Algorithms in Molecular Biology“, University of Tel Aviv, 2002.
- M. Waterman, Introduction to Computational Biology: Maps, Sequences and Genomes, CRC Press, 1995.
- G. Paun, G. Rozenberg, A. Salomaa, DNA-Computing – new computing paradigms, Springer, 1998.
Credits: 3 CU.
Components: 28h lectures, several exercise sessions.
Time schedule: The course starts on September 6, 2004. Lectures are given every week on Mondays and Wednesdays 14-16, in room 3101, DataCity A, 3rd floor.
Prerequisites: No background on Biology is required, as this will be provided throughout the course, when needed. Only basic notions of Math and Computer Science are needed (e.g., very basic notions of strings, graphs, matrices), the rest will be introduced in the course.
Registration: The participants to this course must register using our Web-based system. Please follow instructions at https://www.cs.abo.fi/anmalan. You will be asked for the user name/password you normally use to login in your home university servers (be it Abo Akademi or Turun Yliopisto).
Lecturer: Ion PETRE, Department of Computer Science, Abo Akademi, http://www.abo.fi/~ipetre/.
- Presentation of the field and outline of the course
- Notions of Biochemistry and Molecular Biology
- Elements of Biotechnology
- Elements of computability and complexity
- DNA computing
- A glimpse at nano-scale engineering
- Sequence comparison
- Bioinformatics databases and tools – guest lecturer Dr. Jarno Tuimala, Center for Scientific Computing (CSC), Helsinki
- Physical mapping
- Sequence assembly
- Gene prediction
- Genome rearrangements
- Exercise set 1, due October 13, 2004. Answers here. Detailed solutions here (author: Sandra Munoz, email@example.com)
- Exercise set 2, due October 25, 2004. Answers here. Detailed solutions here (authors: Leticia Rios Peris, firstname.lastname@example.org, Consuelo Richart Zanón, email@example.com)
- Exercise set 3, due November 1, 2004. Answers here. Detailed solutions here (author: Evgeni Tsivtsivadze, firstname.lastname@example.org)
- First exam: November 22, 2004, DataCity 3102, 12-16
- Second exam: December 13, 2004, DataCity 3102, 12-16
Acknowledgment: Many thanks to Prof. Ron Shamir, University of Tel Aviv, who kindly agreed that we use in this course parts of his lecture notes and exercises on “Algorithms in Molecular Biology“.
This course has a follow-up in the Spring semester 2005: Computational processes in living cells.
Back to Ion Petre’s homepage.
Last updated: November, 2004.