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J. Hein · SciRah

Researcher profile · Semantic Scholar

J. Hein

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J. Hein — researcher profile on SciRah

h-index: 41
Works: 162
Citations: 7,388

Most-cited papers

Autocatalytic Sets and the Origin of Life
W. Hordijk, J. Hein, M. Steel
2010Entropy160 citations Open access
Semantic Scholar
Uncertainty in homology inferences: assessing and improving genomic sequence alignment.
G. Lunter, A. Rocco, N. Mimouni, A. Heger +2 more
2008Genome Research159 citations Open access
Semantic Scholar
Using biological networks to search for interacting loci in genome-wide association studies
M. Emily, T. Mailund, J. Hein, L. Schauser +1 more
2009European Journal of Human Genetics150 citations Open access
Semantic Scholar
The Cardamine hirsuta genome offers insight into the evolution of morphological diversity
Xiang-Chao Gan, A. Hay, M. Kwantes, G. Haberer +27 more
2016Nature Plants105 citations Open access
Semantic Scholar
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees
Adam M. Novak, I. Miklós, Rune B. Lyngsø, J. Hein
2008Bioinform.105 citations Open access
Semantic Scholar
The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains
Márton Münz, J. Hein, P. Biggin
2012PLoS Comput. Biol.83 citations Open access
Semantic Scholar
Frnakenstein: multiple target inverse RNA folding
Rune B. Lyngsø, James W. J. Anderson, E. Sizikova, Amarendra Badugu +2 more
2012BMC Bioinformatics81 citations Open access
Semantic Scholar
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
Aziz Mithani, G. Preston, J. Hein
2009Bioinform.70 citations Open access
Semantic Scholar
Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction
Anastasia Ignatieva, J. Hein, P. A. Jenkins
2021bioRxiv46 citations Open access
Semantic Scholar
Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.
Joseph L. Herman, Christopher J Challis, Adam M. Novak, J. Hein +1 more
2014Molecular biology and evolution46 citations Open access
Semantic Scholar
Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and nonpathogenic lifestyles in Pseudomonas.
Aziz Mithani, J. Hein, G. Preston
2011Molecular biology and evolution46 citations Open access
Semantic Scholar
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
R. Satija, Adam M. Novak, I. Miklós, Rune B. Lyngsø +1 more
2009BMC Evolutionary Biology37 citations Open access
Semantic Scholar
Evolving stochastic context--free grammars for RNA secondary structure prediction
James Wj Anderson, P. Tataru, J. Staines, J. Hein +1 more
2012BMC Bioinformatics35 citations Open access
Semantic Scholar
Dynamic and Physical Clustering of Gene Expression during Epidermal Barrier Formation in Differentiating Keratinocytes
Jennifer M. Taylor, T. Street, L. Hao, R. Copley +7 more
2009PLoS ONE34 citations Open access
Semantic Scholar
A stochastic model for the evolution of metabolic networks with neighbor dependence
Aziz Mithani, G. Preston, J. Hein
2009Bioinform.33 citations Open access
Semantic Scholar
KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation
Anastasia Ignatieva, Rune B. Lyngsø, P. A. Jenkins, J. Hein
2020bioRxiv29 citations Open access
Semantic Scholar
Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved
Patrick Gemmell, J. Hein, A. Katzourakis
2016PLoS Comput. Biol.29 citations Open access
Semantic Scholar
Stochastic models of sequence evolution including insertion—deletion events
I. Miklós, Adam M. Novak, R. Satija, Rune B. Lyngsø +1 more
2009Statistical Methods in Medical Research28 citations
Semantic Scholar
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
Márton Münz, Rune B. Lyngsø, J. Hein, P. Biggin
2010BMC Bioinformatics27 citations Open access
Semantic Scholar
A Generative Angular Model of Protein Structure Evolution
M. Golden, Eduardo García-Portugués, Michael Sørensen, K. Mardia +2 more
2016Molecular biology and evolution25 citations Open access
Semantic Scholar
Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
Joseph L. Herman, Adam M. Novak, Rune B. Lyngsø, Adrienn Szabó +2 more
2015BMC Bioinformatics25 citations Open access
Semantic Scholar
The Exaptation of HERV-H: Evolutionary Analyses Reveal the Genomic Features of Highly Transcribed Elements
Patrick Gemmell, J. Hein, A. Katzourakis
2019Frontiers in Immunology22 citations Open access
Semantic Scholar
A Bayesian Approach to the Evolution of Metabolic Networks on a Phylogeny
Aziz Mithani, G. Preston, J. Hein
2010PLoS Comput. Biol.21 citations Open access
Semantic Scholar
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
Adrienn Szabó, Adam M. Novak, I. Miklós, J. Hein
2010BMC Bioinformatics20 citations Open access
Semantic Scholar
Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split
Patrick Gemmell, J. Hein, A. Katzourakis
2015Retrovirology18 citations Open access
Semantic Scholar
An investigation into irreducible autocatalytic sets and power law distributed catalysis
W. Hordijk, Leonard Hasenclever, Jie Gao, Dilyana Mincheva +1 more
2014Natural Computing18 citations
Semantic Scholar
On Recombination-Induced Multiple and Simultaneous Coalescent Events
Joanna L. Davies, F. Simančík, Rune B. Lyngsø, T. Mailund +1 more
2007Genetics16 citations Open access
Semantic Scholar
Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits
Martha Imprialou, A. Kahles, Joshua G. Steffen, E. J. Osborne +18 more
2017Genetics15 citations Open access
Semantic Scholar
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction
Preeti Arunapuram, Ingolfur Edvardsson, M. Golden, James W. J. Anderson +3 more
2013Bioinform.15 citations Open access
Semantic Scholar
Pleiotropic constraints promote the evolution of cooperation in cellular groups
Michael A. Bentley, C. Yates, J. Hein, G. Preston +1 more
2022PLoS Biology14 citations Open access
Semantic Scholar
How reliably can we predict the reliability of protein structure predictions?
I. Miklós, Adam M. Novak, Balázs Dombai, J. Hein
2008BMC Bioinformatics13 citations Open access
Semantic Scholar
Recoverability of Ancestral Recombination Graph Topologies
Ella Hayman, Anastasia Ignatieva, J. Hein
2021bioRxiv12 citations Open access
Semantic Scholar
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information
James W. J. Anderson, Pierre A. Haas, L. Mathieson, V. Volynkin +3 more
2013Bioinform.12 citations Open access
Semantic Scholar
An analysis of structural influences on selection in RNA genes.
N. Mimouni, Rune B. Lyngsø, S. Griffiths-Jones, J. Hein
2008Molecular biology and evolution12 citations Open access
Semantic Scholar
Investigating selection on viruses: a statistical alignment approach
Saskia de Groot, T. Mailund, G. Lunter, J. Hein
2008BMC Bioinformatics12 citations Open access
Semantic Scholar
Ancestral protein sequence reconstruction using a tree-structured Ornstein-Uhlenbeck variational autoencoder
L. S. Moreta, Ola Rønning, Ahmad Salim Al-Sibahi, J. Hein +2 more
2022International Conference on Learning Representations11 citations
Semantic Scholar
Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection
Kevin Dialdestoro, J. Sibbesen, L. Maretty, J. Raghwani +5 more
2015Genetics11 citations Open access
Semantic Scholar
Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures
M. Golden, B. Murrell, Darren P. Martin, O. Pybus +1 more
2019Molecular biology and evolution10 citations Open access
Semantic Scholar
A characterisation of the reconstructed birth-death process through time rescaling.
Anastasia Ignatieva, J. Hein, P. A. Jenkins
2019Theoretical Population Biology10 citations Open access
Semantic Scholar
Quantifying variances in comparative RNA secondary structure prediction
James W. J. Anderson, Adam M. Novak, Zsuzsanna Sükösd, M. Golden +3 more
2013BMC Bioinformatics10 citations Open access
Semantic Scholar
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony
Rune B. Lyngsø, Yun S. Song, J. Hein
2008Annual International Conference on Research in Computational Molecular Biology10 citations
Semantic Scholar
Genetics and population analysis GeneRecon — a coalescent based tool for fine-scale association mapping
T. Mailund, M. Schierup, Christian N. S. Pedersen, Jesper N. Madsen +2 more
200610 citations
Semantic Scholar
A Simulation‐Based Approach to Statistical Alignment
Eli Levy Karin, H. Ashkenazy, J. Hein, T. Pupko
2018Systematic Biology8 citations
Semantic Scholar
Erratum: The Cardamine hirsuta genome offers insight into the evolution of morphological diversity
Xiang-Chao Gan, A. Hay, M. Kwantes, G. Haberer +27 more
2016Nature Plants6 citations Open access
Semantic Scholar
Evolution of Metabolic Networks
E. Giannoulatou, J. Hein
20065 citations
Semantic Scholar
Toroidal Diffusions and Protein Structure Evolution
Eduardo García-Portugués, M. Golden, Michael Sørensen, K. Mardia +2 more
2018Applied Directional Statistics3 citations Open access
Semantic Scholar
Sex-specific aspects of endogenous retroviral insertion and deletion
Patrick Gemmell, J. Hein, A. Katzourakis
2013BMC Evolutionary Biology3 citations Open access
Semantic Scholar
How Many Transcripts Does It Take to Reconstruct the Splice Graph?
P. A. Jenkins, Rune B. Lyngsø, J. Hein
2006Workshop on Algorithms in Bioinformatics3 citations
Semantic Scholar
INVESTIGATION OF ONGOING RECOMBINATION THROUGH GENEALOGICAL RECONSTRUCTION FOR SARS-CoV-2
J. Hein, P. A. Jenkins
20212 citations
Semantic Scholar
Complexity results for autocatalytic network models.
Oliver Weller-Davies, M. Steel, J. Hein
2020Mathematical Biosciences2 citations
Semantic Scholar

Frequent co-authors

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Rune B. Lyngsø×13
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Adam M. Novak×9
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I. Miklós×6
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T. Mailund — researcher profile on SciRah

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James W. J. Anderson×4

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Aziz Mithani×4

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Anastasia Ignatieva×4

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Patrick Gemmell×4

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Patrick Gemmell — researcher profile on SciRah