Comparison of Coding DNA. - Christian N. S. Pedersen; Rune B. Lyngsø; Jotun Hein (CPM, 1998)

Finding Maximal Pairs with Bounded Gap. - Gerth Stølting Brodal; Rune B. Lyngsø; Christian N. S. Pedersen; Jens Stoye (CPM, 1999)

Metrics and Similarity Measures for Hidden Markov Models. - Rune B. Lyngsø; Christian N. S. Pedersen; Henrik Nielsen (ISMB, 1999)

Internal loops in RNA secondary structure prediction. - Rune B. Lyngsø; Michael Zuker; Christian N. S. Pedersen (RECOMB, 1999)

Fast evaluation of internal loops in RNA secondary structure prediction. - Rune B. Lyngsø; Michael Zuker; Christian N. S. Pedersen (Bioinform., 1999)

Pseudoknots in RNA secondary structures. - Rune B. Lyngsø; Christian N. S. Pedersen (RECOMB, 2000)

RNA Pseudoknot Prediction in Energy-Based Models. - Rune B. Lyngsø; Christian N. S. Pedersen (J. Comput. Biol., 2000)

Complexity of Comparing Hidden Markov Models. - Rune B. Lyngsø; Christian N. S. Pedersen (ISAAC, 2001)

Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar. - Arun K. Jagota; Rune B. Lyngsø; Christian N. S. Pedersen (WABI, 2001)

Solving the String Statistics Problem in Time O(n log n). - Gerth Stølting Brodal; Rune B. Lyngsø; Anna Östlin; Christian N. S. Pedersen (ICALP, 2002)

The consensus string problem and the complexity of comparing hidden Markov models. - Rune B. Lyngsø; Christian N. S. Pedersen (J. Comput. Syst. Sci., 2002)

Complexity of Pseudoknot Prediction in Simple Models. - Rune B. Lyngsø (ICALP, 2004)

Minimum Recombination Histories by Branch and Bound. - Rune B. Lyngsø; Yun S. Song; Jotun Hein (WABI, 2005)

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. - Jakob Hull Havgaard; Rune B. Lyngsø; Gary D. Stormo; Jan Gorodkin (Bioinform., 2005)

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. - Jakob Hull Havgaard; Rune B. Lyngsø; Jan Gorodkin (Nucleic Acids Res., 2005)

How Many Transcripts Does It Take to Reconstruct the Splice Graph? - Paul A. Jenkins; Rune B. Lyngsø; Jotun Hein (WABI, 2006)

Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. - Yun S. Song; Rune B. Lyngsø; Jotun Hein (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. - Rune B. Lyngsø; Yun S. Song; Jotun Hein (RECOMB, 2008)

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. - Ádám Novák; István Miklós; Rune B. Lyngsø; Jotun Hein (Bioinform., 2008)

RNA Secondary Structure Boltzmann Distribution. - Rune B. Lyngsø (Encyclopedia of Algorithms, 2008)

RNA Secondary Structure Prediction by Minimum Free Energy. - Rune B. Lyngsø (Encyclopedia of Algorithms, 2008)

RNA Secondary Structure Prediction Including Pseudoknots. - Rune B. Lyngsø (Encyclopedia of Algorithms, 2008)

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. - Márton Münz; Rune B. Lyngsø; Jotun Hein; Philip C. Biggin (BMC Bioinform., 2010)

Synthesising graphics card programs from DSLs. - Luke Cartey; Rune B. Lyngsø; Oege de Moor (PLDI, 2012)

Evolving stochastic context-free grammars for RNA secondary structure prediction. - James W. J. Anderson; Paula Tataru; Joe Staines; Jotun Hein; Rune B. Lyngsø (BMC Bioinform., 2012)

Frnakenstein: multiple target inverse RNA folding. - Rune B. Lyngsø; James W. J. Anderson; Elena Sizikova; Amarendra Badugu; Tomas Hyland; Jotun Hein (BMC Bioinform., 2012)

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. - James W. J. Anderson; Pierre A. Haas; Leigh-Anne Mathieson; Vladimir Volynkin; Rune B. Lyngsø; Paula Tataru; Jotun Hein (Bioinform., 2013)

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. - Joseph L. Herman; Ádám Novák; Rune B. Lyngsø; Adrienn Szabó; István Miklós; Jotun Hein (BMC Bioinform., 2015)

RNA Secondary Structure Boltzmann Distribution. - Rune B. Lyngsø (Encyclopedia of Algorithms, 2016)

RNA Secondary Structure Prediction by Minimum Free Energy. - Rune B. Lyngsø (Encyclopedia of Algorithms, 2016)

RNA Secondary Structure Prediction Including Pseudoknots. - Rune B. Lyngsø (Encyclopedia of Algorithms, 2016)

KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation. - Anastasia Ignatieva; Rune B. Lyngsø; Paul A. Jenkins; Jotun Hein (Bioinform., 2021)