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2020 – today
- 2022
[j39]Christian Degnbol Madsen
, Jotun Hein, Christopher T. Workman:
Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases. PLoS Comput. Biol. 18(6) (2022)- [c12]Lys Sanz Moreta, Ola Rønning, Ahmad Salim Al-Sibahi, Jotun Hein, Douglas L. Theobald, Thomas Hamelryck:
Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder. ICLR 2022 - 2021
- [j38]Anastasia Ignatieva, Rune B. Lyngsø, Paul A. Jenkins, Jotun Hein:
KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation. Bioinform. 37(19): 3277-3284 (2021) - [j37]Pingshi Yu, Alistair J. Sterling, Jotun Hein:
A Novel Automated Screening Method for Combinatorially Generated Small Molecules. J. Chem. Inf. Model. 61(4): 1637-1646 (2021) - [j36]Oliver Weller-Davies, Mike A. Steel, Jotun Hein:
Combinatorics of Polymer-Based Models of Early Metabolism. SIAM J. Discret. Math. 35(4): 2304-2316 (2021)
2010 – 2019
- 2016
- [j35]Patrick Gemmell, Jotun Hein, Aris Katzourakis:
Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved. PLoS Comput. Biol. 12(6) (2016) - 2015
- [j34]Joseph L. Herman, Ádám Novák, Rune B. Lyngsø, Adrienn Szabó, István Miklós, Jotun Hein:
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinform. 16: 108:1-108:26 (2015) - [i2]Joseph L. Herman, Adrienn Szabó, István Miklós, Jotun Hein:
Approximate statistical alignment by iterative sampling of substitution matrices. CoRR abs/1501.04986 (2015) - 2014
- [j33]Wim Hordijk, Leonard Hasenclever, Jie Gao, Dilyana Mincheva, Jotun Hein:
An investigation into irreducible autocatalytic sets and power law distributed catalysis. Nat. Comput. 13(3): 287-296 (2014) - 2013
- [j32]Preeti Arunapuram, Ingolfur Edvardsson, Michael Golden, James W. J. Anderson, Ádám Novák, Zsuzsanna Sükösd, Jotun Hein:
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction. Bioinform. 29(5): 654-655 (2013) - [j31]James W. J. Anderson, Pierre A. Haas, Leigh-Anne Mathieson, Vladimir Volynkin, Rune B. Lyngsø, Paula Tataru, Jotun Hein:
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. Bioinform. 29(6): 704-710 (2013) - [j30]James W. J. Anderson, Ádám Novák, Zsuzsanna Sükösd, Michael Golden, Preeti Arunapuram, Ingolfur Edvardsson, Jotun Hein:
Quantifying variances in comparative RNA secondary structure prediction. BMC Bioinform. 14: 149 (2013) - 2012
- [j29]James W. J. Anderson, Paula Tataru, Joe Staines, Jotun Hein, Rune B. Lyngsø:
Evolving stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinform. 13: 78 (2012) - [j28]Rune B. Lyngsø, James W. J. Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland, Jotun Hein:
Frnakenstein: multiple target inverse RNA folding. BMC Bioinform. 13: 260 (2012) - [j27]Márton Münz, Jotun Hein, Philip C. Biggin:
The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains. PLoS Comput. Biol. 8(11) (2012) - 2010
- [j26]Rahul Satija, Jotun Hein, Gerton Lunter:
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques. Bioinform. 26(17): 2116-2120 (2010) - [j25]Márton Münz, Rune B. Lyngsø, Jotun Hein, Philip C. Biggin:
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. BMC Bioinform. 11: 188 (2010) - [j24]Adrienn Szabó, Ádám Novák, István Miklós, Jotun Hein:
Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment. BMC Bioinform. 11: 570 (2010) - [j23]Wim Hordijk, Jotun Hein, Mike A. Steel:
Autocatalytic Sets and the Origin of Life. Entropy 12(7): 1733-1742 (2010) - [j22]Aziz Mithani, Gail M. Preston, Jotun Hein:
A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny. PLoS Comput. Biol. 6(8) (2010) - [i1]Eszter Friedman, István Miklós, Jotun Hein:
MCMC Network: Graphical Interface for Bayesian Analysis of Metabolic Networks. ERCIM News 2010(82): 31-32 (2010)
2000 – 2009
- 2009
- [j21]Aziz Mithani, Gail M. Preston, Jotun Hein:
A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinform. 25(12): 1528-1535 (2009) - [j20]Aziz Mithani, Gail M. Preston, Jotun Hein:
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinform. 25(14): 1831-1832 (2009) - 2008
- [j19]Rahul Satija, Lior Pachter, Jotun Hein:
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinform. 24(10): 1236-1242 (2008) - [j18]Ádám Novák, István Miklós, Rune B. Lyngsø, Jotun Hein:
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinform. 24(20): 2403-2404 (2008) - [j17]Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein:
Investigating selection on viruses: a statistical alignment approach. BMC Bioinform. 9 (2008) - [j16]István Miklós, Ádám Novák, Balázs Dombai, Jotun Hein:
How reliably can we predict the reliability of protein structure predictions? BMC Bioinform. 9 (2008) - [c11]Rune B. Lyngsø, Yun S. Song, Jotun Hein:
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. RECOMB 2008: 463-477 - 2007
- [j15]Saskia de Groot, Thomas Mailund, Jotun Hein:
Comparative annotation of viral genomes with non-conserved gene structure. Bioinform. 23(9): 1080-1089 (2007) - [j14]Stephen McCauley, Saskia de Groot, Thomas Mailund, Jotun Hein:
Annotation of selection strengths in viral genomes. Bioinform. 23(22): 2978-2986 (2007) - 2006
- [j13]Stephen McCauley, Jotun Hein:
Using hidden Markov models and observed evolution to annotate viral genomes. Bioinform. 22(11): 1308-1316 (2006) - [j12]Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Jesper N. Madsen, Jotun Hein, Leif Schauser:
GeneRecon - a coalescent based tool for fine-scale association mapping. Bioinform. 22(18): 2317-2318 (2006) - [j11]Gerton Lunter, Chris P. Ponting, Jotun Hein:
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model. PLoS Comput. Biol. 2(1) (2006) - [j10]Yun S. Song, Rune B. Lyngsø, Jotun Hein:
Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE ACM Trans. Comput. Biol. Bioinform. 3(3): 239-251 (2006) - [c10]Paul A. Jenkins, Rune B. Lyngsø, Jotun Hein:
How Many Transcripts Does It Take to Reconstruct the Splice Graph? WABI 2006: 103-114 - 2005
- [j9]István Miklós, Péter Ittzés, Jotun Hein:
ParIS Genome Rearrangement server. Bioinform. 21(6): 817-820 (2005) - [j8]Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein:
Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinform. 6: 83 (2005) - [j7]Yun S. Song, Jotun Hein:
Constructing Minimal Ancestral Recombination Graphs. J. Comput. Biol. 12(2): 147-169 (2005) - [c9]Rune B. Lyngsø, Yun S. Song, Jotun Hein:
Minimum Recombination Histories by Branch and Bound. WABI 2005: 239-250 - 2004
- [b1]Jotun Hein, Mikkel H. Schierup, Carsten Wiuf:
Gene Genealogies, Variation and Evolution - A Primer in Coalescent Theory. Wiley 2004, ISBN 978-0-19-852996-5, pp. I-XIII, 1-276 - [c8]Gerton Lunter, Jotun Hein:
A nucleotide substitution model with nearest-neighbour interactions. ISMB/ECCB (Supplement of Bioinformatics) 2004: 216-223 - [c7]István Miklós, Jotun Hein:
Genome Rearrangement in Mitochondria and Its Computational Biology. Comparative Genomics 2004: 85-96 - 2003
- [j6]Jakob Skou Pedersen, Jotun Hein:
Gene finding with a hidden Markov model of genome structure and evolution. Bioinform. 19(2): 219-227 (2003) - [j5]Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein:
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. J. Comput. Biol. 10(6): 869-889 (2003) - [j4]Bjarne Knudsen, Jotun Hein:
Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 31(13): 3423-3428 (2003) - [c6]Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein:
Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. WABI 2003: 228-244 - [c5]Yun S. Song, Jotun Hein:
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. WABI 2003: 287-302 - [c4]Jakob Fredslund, Jotun Hein, Tejs Scharling:
A Large Version of the Small Parsimony Problem. WABI 2003: 417-432 - 2001
- [j3]Mike A. Steel, Jotun Hein:
Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree. Appl. Math. Lett. 14(6): 679-684 (2001) - [c3]Jotun Hein:
An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. Pacific Symposium on Biocomputing 2001: 179-190
1990 – 1999
- 1999
- [j2]Bjarne Knudsen, Jotun Hein:
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinform. 15(6): 446-454 (1999) - 1998
- [c2]Christian N. S. Pedersen, Rune B. Lyngsø, Jotun Hein:
Comparison of Coding DNA. CPM 1998: 153-173 - 1997
- [e1]Alberto Apostolico, Jotun Hein:
Combinatorial Pattern Matching, 8th Annual Symposium, CPM 97, Aarhus, Denmark, June 30 - July 2, 1997, Proceedings. Lecture Notes in Computer Science 1264, Springer 1997, ISBN 3-540-63220-4 [contents] - 1996
- [j1]Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang:
On the Complexity of Comparing Evolutionary Trees. Discret. Appl. Math. 71(1-3): 153-169 (1996) - 1995
- [c1]Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang:
On the Complexity of Comparing Evolutionary Trees (Extended Abstract). CPM 1995: 177-190
Coauthor Index
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