Up to Research, Theory group at Nada, KTH.
Computational biology
Researchers
Ph.D. students
Former Ph.D. students
Open positions
If you are interested in a PhD position in
computational biology, please contact Jens Lagergren for more information.
Short description (a longer can be found here)
We currently focus on genome evolution and
gene regulation. In genome evolution, the goal is to find
the genome level events that
lead to the currently existing species. Examples of such events are duplications of
genes, lateral transfers, and inversions of a segment of a genome.
Recent publications
- Towards Identifying Lateral Gene Transfer Events.
- L. Addario-Berry, M. Hallett, J. Lagergren
- Proc. 8th Pacific Symp. on Biocomputing (PSB 2003), January 2003.
- Combining Polynomial Running Time and Fast Convergence for the
Disk-Covering Method
- J. Lagergren.
- J. Comput. Syst. Sci. (invited, special issue on computational
biology), to appear, 2002.
- Efficient Algorithms for Lateral Gene Transfer Problems.
- M.T. Hallett and J. Lagergren.
- In RECOMB´01, pages 149-156.
- Fitting Point on the Real Line and its Application to RH Mapping
- J. Håstad, L. Ivansson, and J. Lagergren
- Journal of Algorithms, to appear.
- Hunting for Functionally Analogous Genes.
- M.T. Hallett and J.Lagergren.
- In FSTTCS´00.
- New algorithms for the duplication-loss model.
- M.T. Hallett and J.Lagergren.
- In RECOMB´00, pages 138-146.
- Algorithms for Biological Sequence Alignment
- Lars Arvestad
- PhD thesis, December 1999.
(WWW)
- On the approximability of the Steiner tree problem in phylogeny
- D. Fernandez-Baca, J. Lagergren
- Discrete Applied Mathematics Special Issue on Computational
Molecular Biology, 88 (1), pages 127-143, 1999
- Fitting Point on the Real Line and its Application to RH Mapping
- J. Håstad, L. Ivansson, and J. Lagergren
- ESA 98, pages 465-476, LNCS 1461, 1998.
PostScript
- A 7/3 Approximation Algorithm for Fitting Points on the Real Line
and its Application to RH Mapping
- L. Ivansson and J. Lagergren
- NADA report TRITA-NA-9807, 1998.
- Adapting to Nature---Some Improvements on Alignment Algorithms in Computational Biology
- L. Arvestad
- Licentiat Thesis, 1997, TRITA-NA-9707, Royal Institute of Technology
(PostScript, 441 kB)
- Aligning coding DNA in the presence of frame-shifts errors
- L. Arvestad
- CPM 97, LNCS 1264, pp 180-190
(PostScript, 132 kB)
- Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences
- L. Arvestad and W. J. Bruno
- Journal of Molecular Evolution, 1997, 45 (6): 696-703
- A polynomial time algorithm for near-perfect phylogeny.
- D. Fernandez-Baca and J. Lagergren.
- 23rd ICALP, pages 670-680, LNCS 1099, 1996.
- Hypothesis testing in perfect phylogeny for a bounded number of characters.
- J. Lagergren.
- 13th STACS, pages 605--616, LNCS 1046, 1996.
Up to Research, Theory group at Nada, KTH.
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Latest change October 17, 2002
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