| 2022 | ICLR | Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder. | Lys Sanz Moreta, Ola Rnning, Ahmad Salim Al-Sibahi, Jotun Hein, Douglas L. Theobald, Thomas Hamelryck |
| 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 | ISMB | A nucleotide substitution model with nearest-neighbour interactions. | Gerton Lunter, Jotun Hein |
| 2004 | RECOMB | Genome Rearrangement in Mitochondria and Its Computational Biology. | Istvn Mikls, Jotun Hein |
| 2003 | WABI | A Large Version of the Small Parsimony Problem. | Jakob Fredslund, Jotun Hein, Tejs Scharling |
| 2003 | WABI | Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. | Gerton Lunter, Istvn Mikls, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein |
| 2003 | WABI | Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. | Yun S. Song, Jotun Hein |
| 2001 | PSB | An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. | Jotun Hein |
| 1998 | CPM | Comparison of Coding DNA. | Christian N. S. Pedersen, Rune B. Lyngs, Jotun Hein |
| 1995 | CPM | On the Complexity of Comparing Evolutionary Trees (Extended Abstract). | Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang |