J. Hein

发表

Unified approach to alignment and phylogenies.

J. Hein, 1990, Methods in enzymology.

An evolutionary model for protein-coding regions with conserved RNA structure.

Irmtraud M. Meyer, J. S. Pedersen, J. Hein, 2004, Molecular biology and evolution.

A comparative method for finding and folding RNA secondary structures within protein-coding regions.

Irmtraud M. Meyer, J. S. Pedersen, J. Hein, 2004, Nucleic acids research.

Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars

Bjarne Knudsen, Jotun Hein, J. Hein, 2003 .

Statistical alignment: computational properties, homology testing and goodness-of-fit.

J. Hein, C. Wiuf, B. Knudsen, 2000, Journal of molecular biology.

Reconstructing evolution of sequences subject to recombination using parsimony.

J. Hein, 1990, Mathematical biosciences.

On the Complexity of Comparing Evolutionary Trees

Tao Jiang, Kaizhong Zhang, Lusheng Wang, 1996, Discret. Appl. Math..

A heuristic method to reconstruct the history of sequences subject to recombination

J. Hein, 1993, Journal of Molecular Evolution.

A simulation study of the reliability of recombination detection methods.

J. Hein, C. Wiuf, T. Christensen, 2001, Molecular biology and evolution.

Consequences of recombination on traditional phylogenetic analysis.

J. Hein, M. Schierup, 2000, Genetics.

GIBBS SAMPLER FOR STATISTICAL MULTIPLE ALIGNMENT

J. L. Jensen, J. Hein, 2005 .

Using biological networks to search for interacting loci in genome-wide association studies

J. Hein, T. Mailund, M. Schierup, 2009, European Journal of Human Genetics.

Recombination as a point process along sequences.

J. Hein, C. Wiuf, 1999, Theoretical population biology.

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

Jakob Skou Pedersen, Jotun Hein, J. S. Pedersen, 2003, Bioinform..

Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

Alexandre Z. Caldeira, A. Heger, J. Hein, 2008, Genome research.

Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony

Yun S. Song, Jotun Hein, Rune B. Lyngsø, 2008, RECOMB.

On the minimum number of recombination events in the evolutionary history of DNA sequences

Yun S. Song, J. Hein, 2004, Journal of mathematical biology.

Reconstructing pedigrees: a combinatorial perspective.

M. Steel, J. Hein, 2006, Journal of theoretical biology.

A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frames

Jotun Hein, J. Hein, Jens Støvlbæk, 1995, Journal of Molecular Evolution.

Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection

Paul A. Jenkins, J. Hein, O. Pybus, 2015, Genetics.

Coalescent inference using serially sampled, high-throughput sequencing data from intra-host HIV infection

Paul A. Jenkins, J. Hein, O. Pybus, 2015, bioRxiv.

genomic sequence alignment Uncertainty in homology inferences : Assessing and improving data

Andreas Heger, Jotun Hein, Gerton Lunter, 2008 .

Integrating prior knowledge to reverse-engineer simple biological systems Short-Project Report

J. Hein, Marton Munz, 2008 .

A Generative Angular Model of Protein Structure Evolution

K. Mardia, M. Sørensen, J. Hein, 2016, Molecular biology and evolution.

A tree · a window · a hill; generalization of nearest-neighbor interchange in phylogenetic optimization

David Sankoff, Jotun Hein, D. Sankoff, 1994 .

Technical Report : An n-free-passes CYK algorithm for error-correction and the prediction of non-canonical base-pairs in RNA secondary structure

Christian N. S. Pedersen, James W. J. Anderson, J. Hein, 2013 .

Integrative Genomics and Functional Explanation

J. Hein, G. Hellenthal, Joanna L Davies, 2009 .

From Global Studies of Biological Variation towards Functional Explanations of Phenotype

J. Hein, G. Hellenthal, Joanna L Davies, 2008 .

An optimal algorithm to reconstruct trees from additive distance data.

J. Hein, J J Hein, 1989, Bulletin of mathematical biology.

Algorithms for Haplotype Inference from Genotypes in the Presence of Recombination

T. Melham, J. Hein, Rune Lyngsoe, 2006 .

Algorithms for Haplotype Inference In the Presence of Recombination

T. Melham, J. Hein, Rune Lyngsoe, 2006 .

The Structure of the Computational Biosciences

J. Hein, 2007 .

Minimum Recombination Histories by Branch and Bound

Yun S. Song, Jotun Hein, Rune B. Lyngsø, 2005, WABI.

Ancestral Reconstruction for Association Mapping

J. Hein, R. Lyngsø, 2010 .

Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures

J. Hein, O. Pybus, B. Murrell, 2019, Molecular biology and evolution.

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases

C. Workman, J. Hein, Christian Degnbol Madsen, 2022, PLoS Comput. Biol..

Professor Jotun Hein " Comparative Virus Annotation "

J. Hein, 2005 .

Pleiotropic constraints promote the evolution of cooperation in cellular groups

Christian A. Yates, K. Foster, J. Hein, 2022, PLoS biology.

Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes

J. Hein, L. Ferretti, B. Singer, 2020, bioRxiv.

Search for Life in Catalytic Reaction Systems

J. Hein, R. Lyngsø, 2010 .

Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction

J. Hein, A. Ignatieva, P. Jenkins, 2021, bioRxiv.

An analysis of structural influences on selection in RNA genes.

Rune B. Lyngsø, J. Hein, R. Lyngsø, 2008, Molecular biology and evolution.

Identifiability of a simple biological system

J. Hein, 2022 .

Genomic Rearrangements Considered as Quantitative Traits

Richard M. Clark, G. Rätsch, R. Mott, 2016, bioRxiv.

Recoverability of Ancestral Recombination Graph Topologies

J. Hein, A. Ignatieva, Elizabeth Hayman, 2021, bioRxiv.

An investigation into irreducible autocatalytic sets and power law distributed catalysis

Leonard Hasenclever, J. Hein, W. Hordijk, 2014, Natural Computing.

Quantifying variances in comparative RNA secondary structure prediction

Adam M. Novak, James W. J. Anderson, J. Hein, 2013, BMC Bioinformatics.

Frnakenstein: multiple target inverse RNA folding

James W. J. Anderson, Rune B. Lyngsø, J. Hein, 2012, BMC Bioinformatics.

The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains

Jotun Hein, Philip C. Biggin, Márton Münz, 2012, PLoS Comput. Biol..

MCMC Integration over Evolutionary Histories of Metabolic Networks

J. Hein, 2008 .

Genomic alignment

Jotun Hein, J. Hein, Jens Støvlæk, 2004, Journal of Molecular Evolution.

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

Chris P. Ponting, Jotun Hein, Gerton Lunter, 2005, PLoS Comput. Biol..

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

Bjarne Knudsen, Jotun Hein, J. Hein, 1999, Bioinform..

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information

James W. J. Anderson, Jotun Hein, Rune B. Lyngsø, 2013, Bioinform..

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

Adam M. Novak, Rune B. Lyngsø, J. Hein, 2009, BMC Evolutionary Biology.

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

István Miklós, Adam M. Novak, Ádám Novák, 2008, Bioinform..

Comparative annotation of viral genomes with non-conserved gene structure

Thomas Mailund, Jotun Hein, Saskia de Groot, 2007, Bioinform..

Bayesian coestimation of phylogeny and sequence alignment

István Miklós, Jotun Hein, Alexei J. Drummond, 2005, BMC Bioinformatics.

Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model

István Miklós, Jotun Hein, Alexei J. Drummond, 2003, WABI.

Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes.

J. Hein, M. Schierup, M H Schierup, 2001, Genetics.

A tree reconstruction method that is economical in the number of pairwise comparisons used.

J. Hein, J Hein, 1989, Molecular biology and evolution.

Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split

J. Hein, A. Katzourakis, Patrick Gemmell, 2015, Retrovirology.

Reconstruction of Ancestral Metabolisms

Jotun Hein, Aziz Mithani, Jose Angel Riarola, 2009 .

Tree measures and the number of segregating sites in time-structured population samples

J. Hein, R. Forsberg, A. Drummond, 2005, BMC Genetics.

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

Jotun Hein, Aziz Mithani, Gail M. Preston, 2009, Bioinform..

Dynamic and Physical Clustering of Gene Expression during Epidermal Barrier Formation in Differentiating Keratinocytes

Jotun Hein, Martin S. Taylor, Gina Stolper, 2009, PloS one.

Modelling Leaf Shape Evolution

J. Hein, N. Jones, M. Tsiantis, 2011 .

Reconstructing the ancestral germ line methylation state of young repeats.

Rune B. Lyngsø, Thomas Lengauer, J. Hein, 2011, Molecular biology and evolution.

A nucleotide substitution model with nearest-neighbour interactions

Jotun Hein, Gerton Lunter, J. Hein, 2004, ISMB/ECCB.

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

Carsten Wiuf, Jotun Hein, Mikkel H. Schierup, 2004 .

A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given.

J Hein, J. Hein, 1989, Molecular biology and evolution.

An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees

Yun S. Song, István Miklós, Jotun Hein, 2003, J. Comput. Biol..

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs

István Miklós, Adam M. Novak, Ádám Novák, 2015, BMC Bioinformatics.

Approximate statistical alignment by iterative sampling of substitution matrices pdf

István Miklós, Jotun Hein, Adrienn Szabó, 2015, ArXiv.

Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.

Jotun Hein, Adam M. Novak, Joseph L Herman, 2014, Molecular biology and evolution.

Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and nonpathogenic lifestyles in Pseudomonas.

Jotun Hein, Aziz Mithani, Gail M Preston, 2011, Molecular biology and evolution.

Using hidden Markov models and observed evolution to annotate viral genomes

Jotun Hein, Stephen McCauley, J. Hein, 2006, Bioinform..

Systematic inference of regulation by protein kinases finds surprising level of transcription factor deactivation

C. Workman, J. Hein, Christian Degnbol Madsen, 2021 .

Inference of Structure, Function and Motion of an Ancestral Protein

Jotun Hein, Lee Pedersen, Mark Sansom, 2011 .

Evolutionary analysis of base-pairing interactions in DNA and RNA secondary structures

Ben Murrell, Jotun Hein, Michael Golden, 2018, bioRxiv.

Annotation of selection strengths in viral genomes

Thomas Mailund, Jotun Hein, Stephen McCauley, 2007, Bioinform..

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

Jotun Hein, Philip C. Biggin, Márton Münz, 2010, BMC Bioinformatics.

Evolution of Metabolic Networks

Eleni Giannoulatou, Jotun Hein, J. Hein, 2006 .

Recombination and the molecular clock.

J. Hein, M. Schierup, M H Schierup, 2000, Molecular biology and evolution.

A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease.

J. Hein, R. Forsberg, A. Bøtner, 2001, Virology.

Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder

Ahmad Salim Al-Sibahi, J. Hein, L. S. Moreta, 2022, ICLR.

Frnakenstein: multiple target inverse RNA folding

Jotun Hein, Elena Sizikova, James W. J. Anderson, 2012, BMC Bioinformatics.

A Simulation‐Based Approach to Statistical Alignment

Tal Pupko, Jotun Hein, Haim Ashkenazy, 2018, Systematic biology.

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

Paul Jenkins, Jotun Hein, Rune B. Lyngsø, 2006, WABI.

Genome Rearrangement in Mitochondria and Its Computational Biology

István Miklós, Jotun Hein, J. Hein, 2004, Comparative Genomics.

Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics

Yun S. Song, Jotun Hein, Rune B. Lyngsø, 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Constructing Minimal Ancestral Recombination Graphs

Yun S. Song, Jotun Hein, Yun S. Song, 2005, J. Comput. Biol..

The Icelandic Cancer Project – a population-wide approach to studying cancer

Jotun Hein, Violeta Calian, Thorunn Rafnar, 2004, Nature Reviews Cancer.

Stochastic models of sequence evolution including insertion—deletion events

István Miklós, Adam M. Novak, Jotun Hein, 2009, Statistical methods in medical research.

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

István Miklós, Jotun Hein, Adam M. Novak, 2008, BMC Bioinformatics.

Statistical Alignment: Recent Progress, New Applications, and Challenges

István Miklós, Alexei J. Drummond, Gerton Lunter, 2005 .

Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknown

J. Hein, C. Holmes, Joanna L. Davies, 2010, Genetic epidemiology.

Toroidal Diffusions and Protein Structure Evolution

Kanti V. Mardia, Michael Sørensen, Thomas Hamelryck, 2018, Applied Directional Statistics.

Erratum: The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

R. Mott, J. Hein, Xiangchao Gan, 2016, Nature Plants.

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

R. Mott, J. Hein, Xiangchao Gan, 2016, Nature Plants.

The ancestry of a sample of sequences subject to recombination.

J. Hein, C. Wiuf, J Hein, 1999, Genetics.

The coalescent with gene conversion.

J. Hein, C. Wiuf, J Hein, 2000, Genetics.

The Cardamine hirsuta genome highlights the pervasive role of transcription factors and tandem gene duplications in generating morphological diversity

Filatov, R. Mott, J. Hein, 2016 .

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

Gunnar Rätsch, André Kahles, Jotun Hein, 2017, Genetics.

Sex-specific aspects of endogenous retroviral insertion and deletion

J. Hein, A. Katzourakis, Patrick Gemmell, 2013, BMC Evolutionary Biology.

RNA Secondary Structures

Adam M. Novak, J. Hein, R. Lyngsø, 2010 .

Autocatalytic Sets and the Origin of Life

Mike A. Steel, Wim Hordijk, Jotun Hein, 2010, Entropy.

Quantifying variances in comparative RNA secondary structure prediction

Jotun Hein, Adam M. Novak, Zsuzsanna Sükösd, 2013, BMC Bioinformatics.

Evolving stochastic context--free grammars for RNA secondary structure prediction

James W. J. Anderson, Jotun Hein, Joe Staines, 2012, BMC Bioinformatics.

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

Jotun Hein, Gerton Lunter, Rahul Satija, 2010, Bioinform..

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

Lior Pachter, Jotun Hein, Rahul Satija, 2008, Bioinform..

Molecular evolution of selected families of human endogenous retroviruses

J. Hein, P. Villesen, Hugo Martins, 2011 .

The genetic diversity of European type PRRSV is similar to that of the North American type but is geographically skewed within Europe.

Roald Forsberg, Jotun Hein, Torben Storgaard, 2002, Virology.

A characterisation of the reconstructed birth-death process through time rescaling.

J. Hein, A. Ignatieva, P. Jenkins, 2019, Theoretical population biology.

Discussion: Recent Common Ancestors of all Present-Day Individuals

P. Donnelly, M. Slatkin, J. Hein, 1999, Advances in Applied Probability.

On the number of ancestors to a DNA sequence.

J. Hein, C. Wiuf, J Hein, 1997, Genetics.

Combinatorics of Polymer-Based Models of Early Metabolism

Mike Steel, Jotun Hein, Oliver Weller-Davies, 2021, SIAM J. Discret. Math..

Combinatorial results for network-based models of metabolic origins

Mike Steel, Jotun Hein, Oliver Weller-Davies, 2019, 1910.09051.

Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split

J. Hein, A. Katzourakis, Patrick Gemmell, 2015, Retrovirology.

Phylogenetics. - Charles Semple and Mike Steel. 2003. Oxford University Press, New York. xiii + 239 pp. ISBN 0-19-850942-1. $90.00.

Yun S. Song, J. Hein, 2004 .

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

Jotun Hein, Aziz Mithani, Gail M. Preston, 2009, Bioinform..

KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation

Jotun Hein, Anastasia Ignatieva, Paul A. Jenkins, 2020, bioRxiv.

Statistical Methods in Bioinformatics: An Introduction

Jotun Hein, Carsten Wiuf, J. Hein, 2002 .

The impact of COVID-19 certification mandates on the number of cases of and hospitalizations with COVID-19 in the UK: A difference-in-differences analysis

J. Hein, A. Prats-Uribe, D. Prieto-Alhambra, 2023, Frontiers in Public Health.

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

Jotun Hein, Aziz Mithani, Gail M. Preston, 2010, PLoS Comput. Biol..

The Exaptation of HERV-H: Evolutionary Analyses Reveal the Genomic Features of Highly Transcribed Elements

J. Hein, A. Katzourakis, Patrick Gemmell, 2019, Front. Immunol..

Human evolution: Pedigrees for all humanity

J. Hein, 2004, Nature.

Stochastic Turing Patterns

J. Hein, A. Rocco, 2006 .

A Novel Automated Screening Method for Combinatorially Generated Small Molecules

Jotun Hein, Pingshi Yu, Alistair J. Sterling, 2021, J. Chem. Inf. Model..

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

Jotun Hein, Aris Katzourakis, Patrick Gemmell, 2016, PLoS Comput. Biol..

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

J. Hein, Bjarne Knudsen, 2003, Nucleic Acids Res..

Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks

Yun S. Song, Jotun Hein, Yun S. Song, 2003, WABI.

On Recombination-Induced Multiple and Simultaneous Coalescent Events

Thomas Mailund, Jotun Hein, Rune B. Lyngsø, 2007, Genetics.

An evolutionary algorithm for stochastic context-free grammar design , with applications to RNA secondary structure prediction

James W. J. Anderson, Rune, J. Hein, 2011 .

Comparative annotation of viral genomes with non-conserved gene structure

J. Hein, S. Groot, Thomas Mailund, 2007, Bioinform..

Using biological networks to search for interacting loci in genome-wide association studies

J. Hein, T. Mailund, M. Schierup, 2009, European Journal of Human Genetics.

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

Adam M. Novak, J. Hein, I. Miklós, 2008, BMC Bioinformatics.

Tree measures and the number of segregating sites in time-structured population samples

J. Hein, R. Forsberg, A. Drummond, 2005, BMC Genetics.

Bayesian coestimation of phylogeny and sequence alignment

J. L. Jensen, J. Hein, I. Miklós, 2005, BMC Bioinformatics.

Aligning Covariance Models

Rune B. Lyngsø, J. Hein, Lu Gram, 2009 .

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

Jotun Hein, J. Hein, 2000, Pacific Symposium on Biocomputing.

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

J. Hein, G. Preston, Aziz Mithani, 2009, Bioinform..