Jotun Hein - RankMe

55 papers A* 1B 4C 5Misc 1Journal 41Unranked 2

Year	Rank	Type	Title / Venue / Authors
2022	A*	`conf`	Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder. ICLR Lys Sanz Moreta, Ola Rønning, Ahmad Salim Al-Sibahi, Jotun Hein, Douglas L. Theobald, Thomas Hamelryck
2022	J	`jnl`	Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases. PLoS Comput. Biol. Christian Degnbol Madsen, Jotun Hein, Christopher T. Workman
2021	J	`jnl`	A Novel Automated Screening Method for Combinatorially Generated Small Molecules. J. Chem. Inf. Model. Pingshi Yu, Alistair J. Sterling, Jotun Hein
2021	J	`jnl`	Combinatorics of Polymer-Based Models of Early Metabolism. SIAM J. Discret. Math. Oliver Weller-Davies, Mike A. Steel, Jotun Hein
2021	J	`jnl`	KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation. Bioinform. Anastasia Ignatieva, Rune B. Lyngsø, Paul A. Jenkins, Jotun Hein
2016	J	`jnl`	Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved. PLoS Comput. Biol. Patrick Gemmell, Jotun Hein, Aris Katzourakis
2015	J	`jnl`	Approximate statistical alignment by iterative sampling of substitution matrices. CoRR Joseph L. Herman, Adrienn Szabó, István Miklós, Jotun Hein
2015	J	`jnl`	Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC Bioinform. Joseph L. Herman, Ádám Novák, Rune B. Lyngsø, Adrienn Szabó, István Miklós, Jotun Hein
2014	J	`jnl`	An investigation into irreducible autocatalytic sets and power law distributed catalysis. Nat. Comput. Wim Hordijk, Leonard Hasenclever, Jie Gao, Dilyana Mincheva, Jotun Hein
2013	J	`jnl`	Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information. Bioinform. James W. J. Anderson, Pierre A. Haas, Leigh-Anne Mathieson, Vladimir Volynkin, Rune B. Lyngsø, Paula Tataru, Jotun Hein
2013	J	`jnl`	Quantifying variances in comparative RNA secondary structure prediction. BMC Bioinform. James W. J. Anderson, Ádám Novák, Zsuzsanna Sükösd, Michael Golden, Preeti Arunapuram, Ingolfur Edvardsson, Jotun Hein
2013	J	`jnl`	StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction. Bioinform. Preeti Arunapuram, Ingolfur Edvardsson, Michael Golden, James W. J. Anderson, Ádám Novák, Zsuzsanna Sükösd, Jotun Hein
2012	J	`jnl`	Evolving stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinform. James W. J. Anderson, Paula Tataru, Joe Staines, Jotun Hein, Rune B. Lyngsø
2012	J	`jnl`	Frnakenstein: multiple target inverse RNA folding. BMC Bioinform. Rune B. Lyngsø, James W. J. Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland, Jotun Hein
2012	J	`jnl`	The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains. PLoS Comput. Biol. Márton Münz, Jotun Hein, Philip C. Biggin
2010	J	`jnl`	A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny. PLoS Comput. Biol. Aziz Mithani, Gail M. Preston, Jotun Hein
2010	J	`jnl`	Autocatalytic Sets and the Origin of Life. Entropy Wim Hordijk, Jotun Hein, Mike A. Steel
2010	J	`jnl`	Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. BMC Bioinform. Márton Münz, Rune B. Lyngsø, Jotun Hein, Philip C. Biggin
2010	J	`jnl`	Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques. Bioinform. Rahul Satija, Jotun Hein, Gerton Lunter
2010	J	`jnl`	MCMC Network: Graphical Interface for Bayesian Analysis of Metabolic Networks. ERCIM News Eszter Friedman, István Miklós, Jotun Hein
2010	J	`jnl`	Reticular Alignment: A progressive corner-cutting method for multiple sequence alignment. BMC Bioinform. Adrienn Szabó, Ádám Novák, István Miklós, Jotun Hein
2009	J	`jnl`	A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinform. Aziz Mithani, Gail M. Preston, Jotun Hein
2009	J	`jnl`	Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinform. Aziz Mithani, Gail M. Preston, Jotun Hein
2008	B	`conf`	Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. RECOMB Rune B. Lyngsø, Yun S. Song, Jotun Hein
2008	J	`jnl`	Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinform. Rahul Satija, Lior Pachter, Jotun Hein
2008	J	`jnl`	How reliably can we predict the reliability of protein structure predictions? BMC Bioinform. István Miklós, Ádám Novák, Balázs Dombai, Jotun Hein
2008	J	`jnl`	Investigating selection on viruses: a statistical alignment approach. BMC Bioinform. Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein
2008	J	`jnl`	StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinform. Ádám Novák, István Miklós, Rune B. Lyngsø, Jotun Hein
2007	J	`jnl`	Annotation of selection strengths in viral genomes. Bioinform. Stephen McCauley, Saskia de Groot, Thomas Mailund, Jotun Hein
2007	J	`jnl`	Comparative annotation of viral genomes with non-conserved gene structure. Bioinform. Saskia de Groot, Thomas Mailund, Jotun Hein
2006	J	`jnl`	Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE ACM Trans. Comput. Biol. Bioinform. Yun S. Song, Rune B. Lyngsø, Jotun Hein
2006	J	`jnl`	GeneRecon - a coalescent based tool for fine-scale association mapping. Bioinform. Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Jesper N. Madsen, Jotun Hein, Leif Schauser
2006	J	`jnl`	Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model. PLoS Comput. Biol. Gerton Lunter, Chris P. Ponting, Jotun Hein
2006	C	`conf`	How Many Transcripts Does It Take to Reconstruct the Splice Graph? WABI Paul A. Jenkins, Rune B. Lyngsø, Jotun Hein
2006	J	`jnl`	Using hidden Markov models and observed evolution to annotate viral genomes. Bioinform. Stephen McCauley, Jotun Hein
2005	J	`jnl`	Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinform. Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein
2005	J	`jnl`	Constructing Minimal Ancestral Recombination Graphs. J. Comput. Biol. Yun S. Song, Jotun Hein
2005	C	`conf`	Minimum Recombination Histories by Branch and Bound. WABI Rune B. Lyngsø, Yun S. Song, Jotun Hein
2005	J	`jnl`	ParIS Genome Rearrangement server. Bioinform. István Miklós, Péter Ittzés, Jotun Hein
2004	—	`conf`	A nucleotide substitution model with nearest-neighbour interactions. ISMB/ECCB (Supplement of Bioinformatics) Gerton Lunter, Jotun Hein
2004	—	`book`	Gene Genealogies, Variation and Evolution - A Primer in Coalescent Theory. Jotun Hein, Mikkel H. Schierup, Carsten Wiuf
2004	—	`conf`	Genome Rearrangement in Mitochondria and Its Computational Biology. Comparative Genomics István Miklós, Jotun Hein
2003	C	`conf`	A Large Version of the Small Parsimony Problem. WABI Jakob Fredslund, Jotun Hein, Tejs Scharling
2003	J	`jnl`	An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. J. Comput. Biol. Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein
2003	C	`conf`	Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. WABI Gerton Lunter, István Miklós, Alexei J. Drummond, Jens Ledet Jensen, Jotun Hein
2003	J	`jnl`	Gene finding with a hidden Markov model of genome structure and evolution. Bioinform. Jakob Skou Pedersen, Jotun Hein
2003	C	`conf`	Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. WABI Yun S. Song, Jotun Hein
2003	J	`jnl`	Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. Bjarne Knudsen, Jotun Hein
2001	Misc	`conf`	An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. Pacific Symposium on Biocomputing Jotun Hein
2001	J	`jnl`	Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree. Appl. Math. Lett. Mike A. Steel, Jotun Hein
1999	J	`jnl`	RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinform. Bjarne Knudsen, Jotun Hein
1998	B	`conf`	Comparison of Coding DNA. CPM Christian N. S. Pedersen, Rune B. Lyngsø, Jotun Hein
1997	B	`ed.`	Combinatorial Pattern Matching, 8th Annual Symposium, CPM 97, Aarhus, Denmark, June 30 - July 2, 1997, Proceedings CPM Alberto Apostolico, Jotun Hein
1996	J	`jnl`	On the Complexity of Comparing Evolutionary Trees. Discret. Appl. Math. Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang
1995	B	`conf`	On the Complexity of Comparing Evolutionary Trees (Extended Abstract). CPM Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang