Jotun’s Google Scholar page

2021

• Yu, P., Sterling, A.J. & Hein, J. (2021). A Novel Automated Screening Method for Combinatorially Generated Small Molecules. Journal of Chemical Information and Modeling (61:4)
• Weller-Davies, O., Steel, M. & Hein, J. (2021). Combinatorics of polymer models of early metabolism. arXiv (preprint, arXiv:2104.05867)
• Ignatieva, A., Hein, J. & Jenkins, P.A. (2021). Ongoing recombination in SARS-CoV-2 revealed through genealogical reconstruction. bioRxiv (preprint)

2020

• Golden, M., Murrell, B., Martin, D., Pybus, O.G., Hein, J. (2020). Evolutionary analyses of base-pairing interactions in DNA and RNA secondary structures. Molecular biology and evolution (37:2)
• Weller-Davies, O., Steel, M. & Hein, J. (2020). Complexity results for autocatalytic network models. Mathematical biosciences (325)
• Ignatieva, A., Hein, J. & Jenkins, P.A. (2020). A characterisation of the reconstructed birth–death process through time rescaling. Theoretical Population Biology (134)
• Yu, P., Sterling, A.J. & Hein, J. (2020). A Novel Automated Screening Method For Combinatorial Small Molecules. ChemRxiv (preprint)
• Ignatieva, A., Lyngsø, R., Jenkins, P.A., Hein, J. (2020). KwARG: Parsimonious reconstruction of ancestral recombination graphs with recurrent mutation. arXiv (preprint, arXiv:2012.09562)
• Singer, B., Di Nardo, A., Hein, J., Ferretti, L. (2020). Comparing Phylogeographies: Incompatible Geographical Histories in Pathogens’ Genomes. bioRxiv (preprint)

2019

• Levy Karin, E., Ashkenazy, H., Hein, J., Pupko, T. (2019). A simulation-based approach to statistical alignment. Systematic Biology (68:2)
• Gemmell, P., Hein, J. & Katzourakis, A. (2019). The exaptation of HERV-H: Evolutionary analyses reveal the genomic features of highly transcribed elements. Frontiers in immunology (10)
• Weller-Davies, O., Steel, M. & Hein, J. (2019). Combinatorial results for network-based models of metabolic origins. arXiv (preprint, arXiv:1910.09051)

2018

• García-Portugués, E., Golden, M., Sørensen, M., Mardia, K,V., Hamelryck, T., Hein, J. (2018). Toroidal diffusions and protein structure evolution. Applied Directional Statistics: Modern Methods and Case Studies (pp 77-110)

2017

• Golden, M., García-Portugués, E., Sørensen, M., Mardia, K. V., Hamelryck, T., & Hein, J. (2017). A generative angular model of protein structure evolution. Molecular Biology and Evolution (34:8) msx137.
• Imprialou, M., Kahles, A., Steffen, J,G., Osborne, E,J., Gan, X., Lempe, J., Bhomra, A., Belfield, E., Visscher, A., Greenhalgh, R., Harberd, N,P., Goram, R., Hein, J., Robert-Seilaniantz, A., Jones, J., Stegle, O., Kover, P., Tsiantis, M., Nordborg, M., Rätsch, G., Clark, R.M., Mott, R (2017). Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits. Genetics (205:4)

2016

• Review of Recombinatorics by Gusfield with Kelly, Emms, Atkins, Hein (2016). SIAM Review.
• Review of Mathematical Phylogenetics by Mike Steel with Ferreti, Emms, Cronjager, Hein (2016).  In press.
• Gemmell, P., Hein, J. & Katzourakis, A.. Phylogenetic Analysis Reveals That ERVs” Die Young” but HERV-H Is Unusually Conserved. PLoS Comput Biol 12.6 (2016): e1004964.
• Dialdestoro, K., Sibbesen, J.A., Maretty, L., Raghwani, J., Gall, A., Kellam, P., Pybus, O.G., Hein, J. and Jenkins, P.A., 2016. Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection. Genetics, 202(4), pp.1449-1472.

2015

• Herman, J.L., Novák, A., Lyngsø, R., Szabó, A., Miklós, I., Hein, J. (2015). Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs. BMC bioinformatics, 16(1), p.1.
• Herman, J.L., Szabó, A., Miklós, I., Hein, J. (2015). Approximate statistical alignment by iterative sampling of substitution matrices.
• Gemmell, P., Hein, J. & Katzourakis, A. (2015) Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split. Retrovirology 12:52

2014

• Herman, J., Challis, C., Novak, A., Hein, J., Schmidler, S. (2014)  Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure.  Mol Biol Evol 31(9), 2251-2260
• Sainudiin, R, Thatte, B. & Veber, A. (2014)  Ancestries of a recombining diploid population.  UCDMS Research Report.  In press.
• Hordijk, W., Hasenclever, L., Gao, J., Minchever, D. & Hein, J. (2014)  An investigation into irreducible autocatalytic sets and power law distributed catalysis. Nat Comput 13. 287-296  

2013

• Arunapuram, P., Edvardsson, I., Golden, M., Anderson, J., Novak, A., Sukosd, Z. & Hein, J. (2013)  StatAlign 2.0: Combining statistical alignment and RNA secondary structure prediction.  Bioinformatics 29(5), 654-655
• Anderson, J., Haas, P., Mathieson, L.A., Volykin, V., Lyngsø, R., Tataru, P. & Hein, J. (2013)  Oxford: Kinetic folding of RNA using stochastic context-free grammars and evolutionary information.  Bioinformatics 29(6), 704-710
• Sukosd, Z., Knudsen, B., Anderson, J.W.J., Novak, A., Kjems, J. & Pedersen, C. (2013)  Characterising RNA secondary structure space using information entropy.  14 (Suppl 2), S22
• Anderson, J., Novak, A., Sukosd, Z., Anuparam, P., Edvardsson, I., Golden, M. & Hein, J. (2013)  Quantifying the variances in RNA secondary structure prediction.  BMC Bioinformatics 14, 149
• Anderson, J., Sukosd, Z., Pedersen, C. & Hein, J. (2013)  An N-free-passes CYK algorithm for error-correction and the prediction of non-canonical base-pairs in RNA secondary structure.  Technical Report.
• Anderson, J. (2013)  Stochastic context-free grammars and RNA secondar structure prediction. Genome Analysis: Current Procedures and Applications
• Anderson, J., Lake, C., Teufel, A., Weir, W., Lyngsø,  R. & Hein. J. (2013). Frnakenstein 1.0: Inverse folding of RNA secondary structures with pseudoknots. Submitted.

2012

• Sukosd, Z., Andersen, E. and Lyngsø, R. (2012)  SCFGs in RNA secondary structure prediction: a hands-on approach.  In preparation
• Münz, M., Hein J. & Biggin P (2012)  The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains. PLoS Comput Biol 8(11): e1002749. doi:10.1371/journal.pcbi.1002749
• Lyngsø, R., Anderson, J.W.J., Sizikova, E., Badugu, A., Hyland, T. & Hein, J. (2012)  Frnakenstein: multiple target inverse RNA folding.  BMC Bioinformatics, 13, 260
• Anderson, J.W.J., Staines, J., Tataru, P., Hein, J. &  Lyngsø, R. (2012)  Evolving Stochastic Context-Free Grammars for RNA Secondary Structure Prediction. BMC Bioinformatics, 13, 78
• Cartey, L, Lyngsø, R & de Moor, O. (2012)  Synthesising graphics card programs from DSLs.  In Proceedings of the 33rd ACM SIGPLAN conference on Programming Language Design and Implementation. Pages 121–132. New York‚ NY‚ USA. 2012. ACM

2011

• Anderson, J.W.J., Staines, J., Tataru, P., Hein, J., Lyngsø, R. (2011)  An evolutionary algorithm for stochastic context-free grammar design, with application to RNA secondary structure prediction. Proceedings of the 30th Leeds Annual Statistical Research Workshop, 137-140
• Gan, X et al. (2011)  Mutliple reference genomes and transcriptomes for Arabidopsis thaliana. Nature  477, 419-423
• Thatte, B. (2011)  Reconstructing pedigrees: some identifiability questions for a recombination-mutation model.  J Math Biol. DOI 10.1007/s00285-011-0503-8
• Feuerbach, L., Lyngsø, R.,  Lengauer, T. & Hein, J. (2011)  Reconstructing the ancestral germ line methylation state of young repeats.  Mol Evol Biol 28(6), 1777-1784
• Herman, J.L., Lyngsø, R. & Hein, J. (2011) Statistical alignment of multiple protein structures under a dynamics-based model of structural evolution. In Next Generation Statistics in Biosciences (LASR 2011). Leeds University Press
• Jackson, H., Raharinirina N.A., Rusaitis, L., Anderson, J.W.J., Cartalano, M, Jones, N., Tsiantis, M., Hein, J. (2011)  Modelling leaf shape evolution with gaussian processes.  Student Report

2010

• Satija, R., Hein, J. & Lunter, G. A.  (2010)  Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.  Bioinformatics 26(17), 2116-2120
• Szabo, A., Novak, A., Miklos, I. & Hein, J. (2010) Reticular Alignment:  A progressive corner-cutting method for multiple sequence alignment. BMC Bioinformatics 11, 570
• Mithani, A., Hein, J. & Preston, G.  (2010)  Comparative analysis of metabolic networks provides insight into the evolution of plant pathogenic and non-pathogenic lifestyles in Psuedomonas.  Mol Biol Evol 28(1), 483-499
• Friedman, E., Miklós, I. & Hein, J. (2010)  MCMC Network: Graphical Interface for Bayesian Analysis of Metabolic Networks.  ERCIM News  82, 31-32
• Hordijk, W., Hein, J. & Steel, M. (2010)  Autocatalytic sets and the origin of life.  Entropy  12(7), 1733-1744
• Thatte, B. (2010)  Reconstructing pedigrees: some identifiability questions for a recombination-mutation model
• Mithani, A., Preston, G. & Hein, J. (2010)  A Bayesian approach to the evolution of metabolic networks on a phylogeny.  PLoS Computational Biology 6(8)
• Munz, M., Lyngsø, R., Hein, J. & Biggin, C. (2010)  Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity.  BMC Bioinformatics 11, 188
• Davies, J., Hein, J. & Holmes, C. (2010)  Detecting interacting genetic loci with effects on quantitative traits where nature and order of the interaction are unknown.  Genetic Epidemiology, 34, 299-308

2009

• Fischer, M. & Thatte, B.D.  (2009)  Revisiting an equivalence between maximum parismony and maximum likelihood methods in phylogenetics.  J Math Biol  72(1), 208-220
• Fischer, M. & Thatte, B.D. (2009)  Maximum parsimony on subsets of taxa.  J Theor Biol  260, 290-293
• Taylor, J., Street, T., Hao, L., Copley, R., Taylor, M., Hayden, P., Stolper, G., Mott, R., Hein, J., Moffatt, M. & Cookson, W. (2009)   Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes.  PLoS One, Oct 30, 4(10), e7651
• Kim, H., Toroczkai, Z., Erdõs, P., Miklós, I. & Székely, L. (2009) Degree-based graph construction. J. Phys. A., (accepted)
• Satija, R., Novák, Á., Miklós, I., Lyngsoe, R. & Hein, J. (2009)  BigFoot: Bayesian Alignment and Phylogenetic Footprinting with MCMC. BMC Evolutionary Biology 9, 217
• Miklós, I. & Darling, A. (2009) Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia.  Genome Biology and Evolution 1(1), 153-164
• Csürös, M., Miklós, I. (2009) Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol 26(9), 2087-2095
• Miklós, I., Mélykúti, B., Swenson, K. (2009) The Metropolized Partial Importance Sampling MCMC mixes slowly on minimum reversal rearrangement paths ACM/IEEE Transactions on Computational Biology and Bioinformatics, accepted
• Miklós, I., Novák, Á., Satija, R., Lyngsoe, R. & Hein, J. (2009) Stochastic Models of Sequence Evolution including Insertion-Deletion events  Statistical Methods in Medical Research 18(5) 453-485
• Mithani, A., Preston, G. & Hein, J. (2009)  Rahnuma: hypergraph based tool for metabolic pathway prediction and network comparison  Bioinformatics 25(14), 1831-1832
• Mithani, A., Preston, G. & Hein, J. (2009) A stochastic model for the evolution of metabolic networks with neighbor dependence.  Bioinformatics 25(12), 1528-1535
• Emily, M., Mailund, T., Hein, J., Schauser, L., Schierup, M. (2009)  Using biological networks to search for interacting loci in genome-wide association studies.  European Journal of Human Genetics (advance online publication)
• Mimouni, N., Lyngsoe, R., Griffiths-Jones, S., Hein, J. (2009)  An analysis of Structural Influences on Selection in RNA Genes.  Mol Biol Evol  26, 209-216

2008

• Thatte, B.  (2008)  Combinatorics of pedigrees I: counter examples to a reconstruction problem.  SIAM Journal of Discrete Mathematics  22(3), 961-970
• Thatte, B. & Steel, M.  (2008) Reconstructing pedigrees: a stochastic perspective.  J Theo Biol  251(3), 240-249
• Novák, Á., Miklós, I., Lyngsoe, R., Hein, J. (2008) StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees. Bioinformatics, 24(20), 2403-2404
• Darling, A., Miklós, I., Ragan, M. (2008) Dynamics of genome rearrangement in bacterial populations. PLoS Genetics, 4(7): e1000128
• Miklós, I., Novák, Á., Dombai, B. & Hein, J. (2008) How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics 9, 137
• Davies, J., Rafnar, T., Hellenthal, G. & Hein, J. (2008)  Integrative Genomics and Functional Explanation (manuscript)
• de Groot, S., Mailund, T. Lunter, G. & Hein, J. (2008) Investigating selection on viruses: a statistical alignment approach.  BMC Bioinformatics, 9,304
• Hellenthal, G., Auton, A. & Falush, D. (2008) Inferring Human Colonization History Using a Copying Model. PLoS Genetics, 4(5), e1000078
• Griffiths, R. C., Jenkins, P.A., Song, Y.S. (2008) Importance sampling and the two-locus model with subdivided population structure. Adv.Appl.Prob., 40, 473-500
• Satija, R.,Pachter, L. & Hein, J. (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 24,1236-1242
• Darling, A., Miklos, I. & Ragan, M. (2008) Dynamics of genome rearrangement in bacterial populations. PLoS Genetics  4(7), e1000128
• Lyngsø, R.B., Song, Y.S. & Hein, J. (2008) Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. Lecture Notes Comput Sci 4955 (LNBI), 463–477

2007

• McCauley, S., de Groot, S., Mailund, T. & Hein, J. (2007) Annotation of Selection Strengths in Viral Genomes. Bioinformatics, 23(22), 2978–2986
• Davies, J.L., František Simanèík, Lyngsø, R.B., Mailund, T. & Hein, J. (2007) On Recombination Induced Multiple and Simultaneous Coalescent Events. Genetics, 177(4), 2151–2160.
• Lunter, G., Rocco, A., Mimouni, N., Caldeira, A. & Hein, J. (2007) Uncertainty in Homology Inferences: Assessing and Improving Genomic Sequence Alignment. Genome Research, 18(2), 298-309
• Levy, D. & Pachter, L. (2007) The Neighbor-Net Algorithm. Advances in Applied Mathematics (in press)
• Lyngsø, R.B. RNA Secondary Structure Prediction by Minimum Free Energy (2007) In Encyclopedia of Algorithms (Kao, M.Y., ed.) (in press)
• Lyngsø, R.B. RNA Secondary Structure Boltzmann Distribution (2007) In Encyclopedia of Algorithms (Kao, M.Y., ed.) (in press).
• Lyngsø, R.B. RNA Secondary Structure Including Pseudoknots (2007) Encyclopedia of Algorithms (Kao, M.Y., ed.) (in press)
• Hellenthal, G. & Stephens, M. (2007) msHOT: modifying Hudson’s ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics, 23(4), 520–521
• de Groot, S., Mailund, T. & Hein, J. (2007) Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure. Bioinformatics, 23(9), 1080–1089
• Hobolth, A., Christensen, O.F., Mailund, T. & Schierup, M.H. (2007) Genomic relationships and speciation times of human, chimpanzee and gorilla inferred from a coalescent hidden Markov model. PLoS Genetics, 3(2), e7
• Mailund, T., Pedersen, C.N.S., Bardino, J., Vinter, B. & Karlsen, H.H. (2007) Experiences with GeneRecon on MiG. Future Generation Computer Systems, 23, 580–586

2006

• Song, Y.S (2006)  A sufficient condition for reducing recursions in hidden Markov models. Bulletin of Mathematical Biology 68, 361-384
• Hellenthal, G. & Stephens, M. (2006) Insights into recombination from population genetic variation. Current Opinion in Genetics & Development, 16(6), 565–572
• Mailund, T., Besenbacher, S. & Schierup, M.H. (2006) Whole genome association mapping by incompatibilities and local perfect phylogenies. BMC Bioinformatics, 7(454)
• Christensen, C., Mailund, T., Pedersen, C.N.S., Randers, M. & Stissing, M. (2006) Fast Calculation of the Quartet Distance Between Trees of Arbitrary Degrees. Algorithms for Molecular Biology, 1(16)
• Mailund, T., Schierup, M.H., Pedersen, C.N.S., Madsen, J.N., Hein, J. & Schauser, L. (2006) GeneRecon.A coalescent based tool for fine-scale association mapping. Bioinformatics, 22(18), 2317–2318
• Bataillon, T., Mailund, T., Thorlacius, S., Steingrimsson, E., Rafnar, T., Halldorsson, M.M., Calian, V. & Schierup, M.H. (2006) The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers. European Journal of Human Genetics, 14, 1044–53
• Mailund, T., Brodal, G.S., Fagerberg, R., Pedersen, C.N.S. & Phillips, D. (2006) Recrafting the Neighbor-Joining Method. BMC Bioinformatics 7(29)
• Jenkins, P., Lyngsø, R.B. & Hein, J. (2006) How Many Transcripts Does It Take to Reconstruct the Splice Graph?. Lecture Notes in Bioinformatics: Proceedings of WABI 2006 4175, 103–114
• Song, Y.S., Lyngsø, R.B. & Hein, J. (2006) Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3), 239–251
• McCauley, S. & Hein, J. (2006) Using Hidden Markov Models (HMM) and Observed Evolution to Annotate ssRNA Viral Genomes. Bioinformatics, 22(11), 1308–1316.
• Lunter, G., Ponting, C.P. & Hein, J. (2006) Genome-wide identification of human functional DNA using a neutral indel model. PLoS Computational Biology, 2(1), e5
• Steel, M. & Hein, J. (2006) Reconstructing pedigrees: a combinatorial perspective. Journal of Theoretical Biology, 240(3), 360–367

2005

• Forsberg, R., Drummond, A.J. & Hein, J. (2005) Tree measures and the number of segregating sites in Time-structured population samples. BMC Genetics, 6, 35
• Jensen, J.L. & Hein, J. (2005)  A Gibbs sampler for statistical multiple alignment.  Statistica Sinica, 15(4), 889-908
• Lyngsø, R.B., Song, Y.S. & Hein, J. (2005) Minimum Recombination Histories by Branch and Bound. Lecture Notes in Bioinformatics: Proceedings of WABI 2005 3692, 239–250
• Catts, V.S., Catts, S.V., Fernandez, H.R., Taylor, J.M., Coulson, E.J. & Lutze-Mann, L.H. (2005) A microarray study of post-mortem mRNA degradation in mouse brain tissue. Molecular Brain Research, 138(2), 164–77
• Lunter, G.A., Miklós, I., Drummond, A.J., Jensen, J.L. & Hein, J. (2005) Bayesian Coestimation of Phylogeny and Sequence Alignment. BMC Bioinformatics, 6, 83
• Vincent, A.J.,Taylor, J.M., Choi–Lundberg, D.L., West, A.K. & Chuah, M.I. (2005) Genetic expression profile of olfactory ensheathing cells is distinct from that of Schwann cells and astrocytes. Glia, 51(2), 132–147
• Havgaard, J.H., Lyngsø, R.B. & Gorodkin, J. (2005) The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Research, 33, W650–W653.
• Havgaard, J.H., Lyngsø, R.B., Stormo, G.D. & Gorodkin, J. (2005) Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics, 21, 1815–1824
• Miklós, I., Ittzés, P. & Hein, J. (2005) ParIS Genome Rearrangement Server. Bioinformatics, 21(6), 817–820
• Song, Y.S. & Hein, J. (2005) Constructing Minimal Ancestral Recombination Graphs. J. Comp. Biol., 12, 147–169
• Miklós, I., Meyer, I.M. & Nagy, B. (2005) Moments of the Boltzmann distribution for RNA secondary structures Bul. Math. Biol., 67(5), 1031–1047

2004

• Miklós, I. & Hein, J. (2004) Genome rearrangement in mitochondria and its computational biology. RECOMB Workshop on Comparative Genomics, 85–96
• Pedersen, J.S., Meyer, I.M., Forsberg, R., Simmonds, P., & Hein, J. (2004) A comparative method for finding and folding RNA secondary structures in protein-coding regions. Nucleic Acids Research, 32(6), 4925–4936
• Meyer, I.M. & Miklós, I. (2004) Co-transcriptional folding is encoded within RNA genes. BMC Molecular Biology, 5, 10
• Pedersen, J.S., Forsberg, R., Meyer, I.M. & Hein, J. (2004) An evolutionary model for protein-coding regions with conserved RNA structure. Mol. Biol. Evol, 21(10), 1913–1922.
• Pavey, S., Johansson, P., Packer, L., Taylor, J., Stark, M., Pollock, P.M., Walker, G.J., Boyle, G.M., Harper, U., Cozzi, S.J., Hansen, K., Yudt, L., Schmidt, C., Hersey, P., Ellem, K.A., O’Rourke, M.G., Parsons, P.G., Meltzer, P., Ringner, M. & Hayward, N.K. (2004) Microarray expression profiling in melanoma reveals a BRAF mutation signature. Oncogene, 23(23), 4060–4067.
• Hein, J., Schierup, M.H. & Wiuf, C. (2004) Gene Genealogies, Variation and Evolution, Oxford University Press (publ.)
• Lyngsø, R.B. (2004) Complexity of Pseudoknot Prediction in Simple Models. Lecture Notes in Computer Science, Proceedings of ICALP’04, 3142, 919–931
• Lunter, G.A. & Hein, J. (2004) A nucleotide substitution model with nearest–neighbour interactions. Bioinformatics 20, i216–i223
• Lunter, G.A., Drummond, A.J., Miklos, I. & Hein, J. (2004) Statistical Alignment: Recent Progress, New Applications and Challenges. In Statistical Methods in Molecular Evolution (Nielsen, R., ed.)
• Song, Y.S. & Hein, J. (2004) On the minimum number of recombination events in the evolutionary history of DNA sequences. J. Math. Biol., 48, 160–186
• Miklós, I., Lunter, G.A. & Holmes, I. (2004) A ‘long indel’ model for evolutionary sequence alignment. Mol. Biol. Evol. 21(3), 529–540
• Meyer, I.M. (2004) Entry in Dictionary of Bioinformatics (Hancock, J.M. & Zvelebil, M.J., eds.).
• Meyer, I.M. & Durbin, R. (2004) Gene structure conservation aids similarity based gene prediction. Nucleic Acids Research, 32(2), 776–783
• Jensen, J.L. & Hein, J. (2004) Gibbs sampler for statistical multiple alignment. Statistica Sinica, 15(4), 889–908
• Miklós, I. & Podani, J. (2004) Randomization of presence/absence matrices: comments and new algorithms. Ecology, 85, 86–92
• Hein, J. (2004)  Pedigrees for all humanity.  Nature  431, 518-519

2003

• Mori, Y., Selaru, F., Sato, F., Yin, J., Simms, L., Xu, Y., Olaru, A., Deacu, E., Wang, S., Taylor, J., Young, J., Leggett, B., Jass, J., Abraham, J., Shibata, D. & Meltzer, S. (2003) The impact of microsatellite instability on the molecular phenotype of colorectal tumors. Cancer Res., 63(15), 4577–82
• Drummond A, Pybus, O.G. & Rambaut, A. (2003) Inference of viral evolutionary rates from molecular sequences. Adv. Parasitology, 54, 331–358
• Song, Y.S. (2003) On the combinatorics of rooted binary phylogenetic trees. Annals of Combinatorics, 7, 365–379
• Hein, J., Jensen, J. L. & Pedersen, C. N. S. (2003) Recursions for statistical multiple alignment. PNAS 100(25), 14960–14965
• Lunter, G.A., Miklós, I., Song, Y.S. & Hein, J. (2003) An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. J. Comp. Biol., 10(6), 869–889.
• Miklós, I. (2003) MCMC Genome Rearrangement. Bioinformatics, special issue for ECCB2003, 19, ii130–ii137
• Rodrigo, A.G., Goode,M., Forsberg, R., Ross,H.A. & Drummond, A. (2003) Inferring evolutionary rates using serially sampled sequences from several populations. Mol. Biol. Evol., 20, 2010–2018
• Fredslund, J., Hein, J. & Scharling, T. (2003) A large version of the small parsimony problem. Lecture Notes in Bioinformatics, Proceedings of WABI’03, 2812, 417–432
• Song, Y.S. & Hein, J. (2003) Parsimonious reconstruction of sequence evolution and haplotype blocks: finding the minimum number of recombination events. Lecture Notes in Bioinformatics, Proceedings of WABI’03, 2812, 287–302
• Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L. & Hein, J. (2003) Bayesian phylogenetic inference under a statistical indel model. Lecture Notes in Bioinformatics, Proceedings of WABI’03, 2812, 228–244
• Drummond, A., Pybus, O.G., Rambaut, A., Forsberg, R. & Rodrigo, A. (2003) Measurably evolving populations. Trends in Ecology and Evolution, 18(9), 481–488
• Schnell, S. & Hein, J.J. (2003) Computational Cell Biology by Fall, Marland,Wagner, Tyson (eds.) Springer (2002), review. Briefings in Bioinformatics 4(1), 87–90
• Forsberg, R. & Christiansen, F.B. (2003) A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol. Biol. Evol., 20, 1252–1259
• Holmes, I. (2003) Using Guide Trees to Construct Multiple-Sequence Evolutionary HMMs. Bioinformatics, special issue for ISMB2003, 19, 147i–157i
• Knudsen, B. & Hein, J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Research, 31(13), 3423–3428
• Bunce, M., T.H. Worthy, T. Ford, W. Hoppitt, E. Willeslev, A. Drummond & A. Cooper. (2003) Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425, 172–175
• Pybus, O.G., Drummond, A.J., Nakano, T., Robertson, B.H. & Rambaut, A. (2003) The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol. Biol. Evol., 20, 381–387
• Pedersen, J.S. & Hein, J. (2003) Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics, 19, 219–227

2002

• Lyngsø, R.B. & Pedersen, C.N.S. (2002) The consensus string problem and the complexity of comparing hidden Markov models. J. Comput. Syst. Sci. 65(3), 545–569
• Brodal, G.S., Lyngsø, R.B., Östlin, A. & Pedersen, C.N.S. (2002) Solving the String Statistics Problem in Time O(n log n). Lecture Notes on Computer Science, Prooceedings of the 29th International Colloquium on Automata, Languages, and Programming, 2380, 728–739
• Holmes, I. (2002) Transcendent elements: Whole-genome transposon screens and open evolutionary questions. Genome Research, 12(8), 1152–1155

Posters

• Mithani, A., Rico, A., Jones, R., Preston, G., & Hein, J. Rahnuma: Hypergraph based Tool for Analysis and Comparison of Metabolic Pathways. Nitrogen2007
• Mimouni, N., Lyngsø, R., & Hein, J. An Analysis of Structural Influences on Selection in RNA Genes. The International Conference on Intelligent Systems for Molecular Biology and The European Conference on Computational Biology 2007
• de Groot, S. & Hein, J. Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure. 14th International Conference on Intelligent Systems for Molecular Biology
• Ryder, R., Hein, J. & Mailund, T. Reconstructing language evolution using syntactical features
• Giannoulatou, E. & Hein, J. Evolution of Metabolic Networks
• Mimouni, N., Lyngsø, R., & Hein, J. Measuring Selection in RNA molecules. European Conference on Computational Biology 2005.
• Miklós, I., Lunter, G., Drummond, A., Jensen, J.L. & Hein, J. Cosampling alignments and trees in a Bayesian evolutionary model
• McCauley, S. & Hein, J. Gene Finding in Viral Genomes
• Song, Y. & Hein, J. Constructing Minimal Ancestral Recombination Graphs
• Jenkins, P. & Hein, J. (2005) How many transcripts does it take to reconstruct the splice graph?
• Mimouni, N., Lunter, G. & Hein, J. (2005) The hunt for genomic dark matter: Aligning non-coding functional DNA. Mathematical and Statistical Aspects of Molecular Biology
• Lyngsø, R.B., Jagota, A., Nielsen, H. & Pedersen, C.N.S. (2002) Analysing Stochastic Language Models. Mathematics and Molecular Biology VII: Modeling Across the Scales – Atoms to Organisms