On the Complexity of Comparing Evolutionary Trees (Extended Abstract). - Jotun Hein; Tao Jiang 001; Lusheng Wang 001; Kaizhong Zhang (CPM, 1995)

On the Complexity of Comparing Evolutionary Trees. - Jotun Hein; Tao Jiang 001; Lusheng Wang 001; Kaizhong Zhang (Discret. Appl. Math., 1996)

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

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. - Bjarne Knudsen; Jotun Hein (Bioinform., 1999)

An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. - Jotun Hein (Pacific Symposium on Biocomputing, 2001)

Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree. - Mike A. Steel; Jotun Hein (Appl. Math. Lett., 2001)

A Large Version of the Small Parsimony Problem. - Jakob Fredslund; Jotun Hein; Tejs Scharling (WABI, 2003)

Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. - Gerton Lunter; István Miklós; Alexei J. Drummond; Jens Ledet Jensen; Jotun Hein (WABI, 2003)

Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. - Yun S. Song; Jotun Hein (WABI, 2003)

Gene finding with a hidden Markov model of genome structure and evolution. - Jakob Skou Pedersen; Jotun Hein (Bioinform., 2003)

An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. - Gerton Lunter; István Miklós; Yun S. Song; Jotun Hein (J. Comput. Biol., 2003)

Pfold: RNA secondary structure prediction using stochastic context-free grammars. - Bjarne Knudsen; Jotun Hein (Nucleic Acids Res., 2003)

Gene Genealogies, Variation and Evolution - A Primer in Coalescent Theory. - Jotun Hein; Mikkel H. Schierup; Carsten Wiuf (Wiley, 2004)

A nucleotide substitution model with nearest-neighbour interactions. - Gerton Lunter; Jotun Hein (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Genome Rearrangement in Mitochondria and Its Computational Biology. - István Miklós; Jotun Hein (Comparative Genomics, 2004)

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

ParIS Genome Rearrangement server. - István Miklós; Péter Ittzés; Jotun Hein (Bioinform., 2005)

Bayesian coestimation of phylogeny and sequence alignment. - Gerton Lunter; István Miklós; Alexei J. Drummond; Jens Ledet Jensen; Jotun Hein (BMC Bioinform., 2005)

Constructing Minimal Ancestral Recombination Graphs. - Yun S. Song; Jotun Hein (J. Comput. Biol., 2005)

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

GeneRecon - a coalescent based tool for fine-scale association mapping. - Thomas Mailund; Mikkel H. Schierup; Christian N. S. Pedersen; Jesper N. Madsen; Jotun Hein; Leif Schauser (Bioinform., 2006)

Using hidden Markov models and observed evolution to annotate viral genomes. - Stephen McCauley; Jotun Hein (Bioinform., 2006)

Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model. - Gerton Lunter; Chris P. Ponting; Jotun Hein (PLoS Comput. Biol., 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)

Comparative annotation of viral genomes with non-conserved gene structure. - Saskia de Groot; Thomas Mailund; Jotun Hein (Bioinform., 2007)

Annotation of selection strengths in viral genomes. - Stephen McCauley; Saskia de Groot; Thomas Mailund; Jotun Hein (Bioinform., 2007)

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)

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. - Rahul Satija; Lior Pachter; Jotun Hein (Bioinform., 2008)

Investigating selection on viruses: a statistical alignment approach. - Saskia de Groot; Thomas Mailund; Gerton Lunter; Jotun Hein (BMC Bioinform., 2008)

How reliably can we predict the reliability of protein structure predictions? - István Miklós; Ádám Novák; Balázs Dombai; Jotun Hein (BMC Bioinform., 2008)

A stochastic model for the evolution of metabolic networks with neighbor dependence. - Aziz Mithani; Gail M. Preston; Jotun Hein (Bioinform., 2009)

Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. - Aziz Mithani; Gail M. Preston; Jotun Hein (Bioinform., 2009)

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques. - Rahul Satija; Jotun Hein; Gerton Lunter (Bioinform., 2010)

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)

Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment. - Adrienn Szabó; Ádám Novák; István Miklós; Jotun Hein (BMC Bioinform., 2010)

Autocatalytic Sets and the Origin of Life. - Wim Hordijk; Jotun Hein; Mike A. Steel (Entropy, 2010)

MCMC Network: Graphical Interface for Bayesian Analysis of Metabolic Networks. - Eszter Friedman; István Miklós; Jotun Hein (ERCIM News, 2010)

A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny. - Aziz Mithani; Gail M. Preston; Jotun Hein (PLoS Comput. Biol., 2010)

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)

The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains. - Márton Münz; Jotun Hein; Philip C. Biggin (PLoS Comput. Biol., 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)

StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction. - Preeti Arunapuram; Ingolfur Edvardsson; Michael Golden; James W. J. Anderson; Ádám Novák; Zsuzsanna Sükösd; Jotun Hein (Bioinform., 2013)

Quantifying variances in comparative RNA secondary structure prediction. - James W. J. Anderson; Ádám Novák; Zsuzsanna Sükösd; Michael Golden; Preeti Arunapuram; Ingolfur Edvardsson; Jotun Hein (BMC Bioinform., 2013)

An investigation into irreducible autocatalytic sets and power law distributed catalysis. - Wim Hordijk; Leonard Hasenclever; Jie Gao; Dilyana Mincheva; Jotun Hein (Nat. Comput., 2014)

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)

Approximate statistical alignment by iterative sampling of substitution matrices. - Joseph L. Herman; Adrienn Szabó; István Miklós; Jotun Hein (CoRR, 2015)

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved. - Patrick Gemmell; Jotun Hein; Aris Katzourakis (PLoS Comput. Biol., 2016)

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

A Novel Automated Screening Method for Combinatorially Generated Small Molecules. - Pingshi Yu; Alistair J. Sterling; Jotun Hein (J. Chem. Inf. Model., 2021)

Combinatorics of Polymer-Based Models of Early Metabolism. - Oliver Weller-Davies; Mike A. Steel; Jotun Hein (SIAM J. Discret. Math., 2021)

Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder. - Lys Sanz Moreta; Ola Rønning; Ahmad Salim Al-Sibahi; Jotun Hein; Douglas L. Theobald; Thomas Hamelryck (ICLR, 2022)

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases. - Christian Degnbol Madsen; Jotun Hein; Christopher T. Workman (PLoS Comput. Biol., 2022)