Jotun Hein

According to our database, Jotun Hein authored at least 54 papers between 1995 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2022

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases.

Christian Degnbol Madsen, Jotun Hein, Christopher T. Workman

PLoS Comput. Biol., 2022

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

Proceedings of the Tenth International Conference on Learning Representations, 2022

2021

Combinatorics of Polymer-Based Models of Early Metabolism.

Oliver Weller-Davies, Mike A. Steel, Jotun Hein

SIAM J. Discret. Math., 2021

A Novel Automated Screening Method for Combinatorially Generated Small Molecules.

Pingshi Yu, Alistair J. Sterling, Jotun Hein

J. Chem. Inf. Model., 2021

KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation.

Anastasia Ignatieva, Rune B. Lyngsø, Paul A. Jenkins, Jotun Hein

Bioinform., 2021

2016

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved.

Patrick Gemmell, Jotun Hein, Aris Katzourakis

PLoS Comput. Biol., 2016

2015

Approximate statistical alignment by iterative sampling of substitution matrices.

Joseph L. Herman, Adrienn Szabó, István Miklós, Jotun Hein

CoRR, 2015

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

2014

An investigation into irreducible autocatalytic sets and power law distributed catalysis.

Wim Hordijk, Leonard Hasenclever, Jie Gao, Dilyana Mincheva, Jotun Hein

Nat. Comput., 2014

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

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

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

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

Frnakenstein: multiple target inverse RNA folding.

Rune B. Lyngsø, James W. J. Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland, Jotun Hein

BMC Bioinform., 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

2010

A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny.

Aziz Mithani, Gail M. Preston, Jotun Hein

PLoS Comput. Biol., 2010

MCMC Network: Graphical Interface for Bayesian Analysis of Metabolic Networks.

Eszter Friedman, István Miklós, Jotun Hein

ERCIM News, 2010

Autocatalytic Sets and the Origin of Life.

Wim Hordijk, Jotun Hein, Mike A. Steel

Entropy, 2010

Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment.

Adrienn Szabó, Ádám Novák, István Miklós, Jotun Hein

BMC 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

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.

Rahul Satija, Jotun Hein, Gerton Lunter

Bioinform., 2010

2009

Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison.

Aziz Mithani, Gail M. Preston, Jotun Hein

Bioinform., 2009

A stochastic model for the evolution of metabolic networks with neighbor dependence.

Aziz Mithani, Gail M. Preston, Jotun Hein

Bioinform., 2009

2008

How reliably can we predict the reliability of protein structure predictions?

István Miklós, Ádám Novák, Balázs Dombai, Jotun Hein

BMC Bioinform., 2008

Investigating selection on viruses: a statistical alignment approach.

Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein

BMC Bioinform., 2008

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Rahul Satija, Lior Pachter, Jotun Hein

Bioinform., 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

Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony.

Rune B. Lyngsø, Yun S. Song, Jotun Hein

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Annotation of selection strengths in viral genomes.

Stephen McCauley, Saskia de Groot, Thomas Mailund, Jotun Hein

Bioinform., 2007

Comparative annotation of viral genomes with non-conserved gene structure.

Saskia de Groot, Thomas Mailund, Jotun Hein

Bioinform., 2007

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

Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model.

Gerton Lunter, Chris P. Ponting, Jotun Hein

PLoS Comput. Biol., 2006

Using hidden Markov models and observed evolution to annotate viral genomes.

Stephen McCauley, Jotun Hein

Bioinform., 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

How Many Transcripts Does It Take to Reconstruct the Splice Graph?

Paul A. Jenkins, Rune B. Lyngsø, Jotun Hein

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2005

Constructing Minimal Ancestral Recombination Graphs.

Yun S. Song, Jotun Hein

J. Comput. Biol., 2005

Bayesian coestimation of phylogeny and sequence alignment.

Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein

BMC Bioinform., 2005

ParIS Genome Rearrangement server.

István Miklós, Péter Ittzés, Jotun Hein

Bioinform., 2005

Minimum Recombination Histories by Branch and Bound.

Rune B. Lyngsø, Yun S. Song, Jotun Hein

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

2004

Genome Rearrangement in Mitochondria and Its Computational Biology.

István Miklós, Jotun Hein

Proceedings of the Comparative Genomics, 2004

A nucleotide substitution model with nearest-neighbour interactions.

Gerton Lunter, Jotun Hein

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Gene Genealogies, Variation and Evolution - A Primer in Coalescent Theory.

Jotun Hein, Mikkel H. Schierup, Carsten Wiuf

Wiley, ISBN: 978-0-19-852996-5, 2004

2003

Pfold: RNA secondary structure prediction using stochastic context-free grammars.

Bjarne Knudsen, Jotun Hein

Nucleic Acids Res., 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

Gene finding with a hidden Markov model of genome structure and evolution.

Jakob Skou Pedersen, Jotun Hein

Bioinform., 2003

Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks.

Yun S. Song, Jotun Hein

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model.

Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

A Large Version of the Small Parsimony Problem.

Jakob Fredslund, Jotun Hein, Tejs Scharling

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

2001

Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree.

Mike A. Steel, Jotun Hein

Appl. Math. Lett., 2001

An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree.

Jotun Hein

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

1999

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history.

Bjarne Knudsen, Jotun Hein

Bioinform., 1999

1998

Comparison of Coding DNA.

Christian N. S. Pedersen, Rune B. Lyngsø, Jotun Hein

Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998

1996

On the Complexity of Comparing Evolutionary Trees.

Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang

Discret. Appl. Math., 1996

1995

On the Complexity of Comparing Evolutionary Trees (Extended Abstract).

Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang

Proceedings of the Combinatorial Pattern Matching, 6th Annual Symposium, 1995