| 2012 | PLDI | Synthesising graphics card programs from DSLs. | Luke Cartey, Rune B. Lyngs, Oege de Moor |
| 2008 | RECOMB | Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. | Rune B. Lyngs, Yun S. Song, Jotun Hein |
| 2006 | WABI | How Many Transcripts Does It Take to Reconstruct the Splice Graph? | Paul A. Jenkins, Rune B. Lyngs, Jotun Hein |
| 2005 | WABI | Minimum Recombination Histories by Branch and Bound. | Rune B. Lyngs, Yun S. Song, Jotun Hein |
| 2004 | ICALP | Complexity of Pseudoknot Prediction in Simple Models. | Rune B. Lyngs |
| 2002 | ICALP | Solving the String Statistics Problem in Time O(n log n). | Gerth Stlting Brodal, Rune B. Lyngs, Anna stlin, Christian N. S. Pedersen |
| 2001 | ISAAC | Complexity of Comparing Hidden Markov Models. | Rune B. Lyngs, Christian N. S. Pedersen |
| 2001 | WABI | Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar. | Arun K. Jagota, Rune B. Lyngs, Christian N. S. Pedersen |
| 2000 | RECOMB | Pseudoknots in RNA secondary structures. | Rune B. Lyngs, Christian N. S. Pedersen |
| 1999 | CPM | Finding Maximal Pairs with Bounded Gap. | Gerth Stlting Brodal, Rune B. Lyngs, Christian N. S. Pedersen, Jens Stoye |
| 1999 | ISMB | Metrics and Similarity Measures for Hidden Markov Models. | Rune B. Lyngs, Christian N. S. Pedersen, Henrik Nielsen |
| 1999 | RECOMB | Internal loops in RNA secondary structure prediction. | Rune B. Lyngs, Michael Zuker, Christian N. S. Pedersen |
| 1998 | CPM | Comparison of Coding DNA. | Christian N. S. Pedersen, Rune B. Lyngs, Jotun Hein |