Algorithmic bioinformatics
The efficiency of algorithms or of data representation is often the difference between feasible and infeasible data analysis. By improving our algorithms, we enable research that would not otherwise be possible. This project is concerned with the development of efficient algorithms and efficient implementation of software for bioinformatics problems.
Personnel
| Phone number | Name, Email, unit (building-room) |
|---|---|
| +45 8715 5564 | |
| +45 8715 5562 | |
| +45 8915 5559 | |
| +45 8715 5572 | |
| +45 8942 3175 | Tataru, Paula, paula@cs.au.dk, Bioinformatics Research Centre (BiRC) (-1110-428) |
Recent publications
- Kristensen, T. G., Nielsen, J., Pedersen, C. S., 18.2.2011, "Using Inverted Indices for Accelerating LINGO Calculations", Journal of Chemical Information and Modeling, vol. 51, nr. 3, s. 597-600. Journal article
- Nielsen, J., Kristensen, A. K., Mailund, T., Pedersen, C. S., 3.6.2011, "A sub-cubic time algorithm for computing the quartet distance between two general trees", Algorithms for Molecular Biology, vol. 6, nr. 15. Journal article
- Simonsen, M., Mailund, T., Pedersen, C. S., 2011, "Inference of Large Phylogenies Using Neighbour-Joining", Biomedical Engineering Systems and Technologies, vol. 127, nr. 5, s. 334-344. Journal article
- Nielsen, J., Sand, A., 2011, "Algorithms for a parallel implementation of Hidden Markov Models with a small state space", 2011 IEEE IPDPS Workshops & PhD Forum, IEEE Computer Society Press, s. 447-454. Article in proceedings
- Nielsen, J., 2011, "A Coarse-to-Fine Approach to Computing the k-best Viterbi Paths", Lecture Notes in Computer Science, vol. 6661, s. 376-387. Conference article
- Simonsen, M., Mailund, T., Pedersen, C. S., 2010, "Building Very Large Neighbour-Joining Trees", Fred, A., Filipe, J., Gamboa, H. (eds.), BIOINFORMATICS 2010, Institute for Systems and Technologies of Information, Control and Communication, s. 26. Article in proceedings
- Kristensen, T. G., 2010, "Transforming Tanimoto queries on real valued vectors to range queries in Euclidian space", Journal of Mathematical Chemistry, vol. 48, nr. 2, s. 287-289. Journal article
- Kristensen, T. G., Pedersen, C. S., 2010, "Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors", Moulton, V., Singh, M. (eds.), Algorithms in Bioinformatics, Springer, s. 28-39. Article in proceedings
- Pedersen, A. S., Brask, A. T., Pedersen, C. S., Mailund, T., 2010, "HMMlib: A C++ Library for General Hidden Markov Models Exploiting Modern CPUs", <em>Proceedings of the 2nd International Workshop on High Performance Computational Systems Biology (HiBi 2010)</em>. Article in proceedings