Rune Lyngsoe
Dr Rune Lyngsø
Postdoctoral Researcher
lyngsoe at stats.ox.ac.uk
+44 (1865) 285365 (Direct)
+44 (1865) 272595 (Fax)
Biographical Sketch
After obtaining a Ph.D. from the University of Aarhus in 2000 I have been working as post-doc, first in the group of David Haussler at the University of California at Santa Cruz, and since then in the group of Jotun Hein. As part of my Ph.D. programme I spent most of 1998 visiting the group of Michael Zuker at Washington University.
Research interests
Algorithmic and complexity aspects of computational problems, in particular with applications in bioinformatics.
In particular RNA structure and its effect on sequence evolution, recombination in population models, stochastic models of formal languages and models for sequence evolution inference have been objects of this interest.
About my research
The focus of my research is the computational aspects of problems. This mostly means developing efficient methods for solving problems and in many cases convert these into useful software. However, at times the search for efficient solutions ends up with categorising the problem as hard. One example of this has been my ongoing work on RNA secondary structure. This started with the discovery of a more efficient algorithm for the standard prediction problem, followed by NP hardness results for predicting pseudoknots. Lately, the familiarity gained with the standard thermodynamic model for RNA secondary structure has even led to the proposal of a hypothesis of how it constrains evolution of the underlying sequence.
Other work involves fundamental problems relating to hidden Markov models and stochastic context free grammars. Again this work spans both development of new, efficient algorithms and classification of some problems as hard. Inferring recombinations in population sequence data is known to be a hard problem, and consequently my work in this area has focused on developing heuristic methods. With the focus on computational aspects, there is no unified biological theme to my research, and I have made various smaller contributions in other areas.
Selected publications
Mimouni NK, Lyngsoe RB, Griffiths-Jones S, Hein J (2008) An Analysis of Structural Influences on Selection in RNA Genes. Molecular Biology and Evolution
Lyngsoe, RB (2004) Complexity of Pseudoknot Prediction in Simple Models. ICALP
Lyngsoe, RB, Song YS, Hein J (2008) Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony. RECOMB
Miklos, I, Nóvak A, Satija R, Lyngsoe, RB, Hein J (2009) Stochastic Models of Sequence Evolution including Insertion-Deletion events. Statistical Methods in Medical Research
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