Publications

Münz, M., Hein J. and 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

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) 
Miklos, I., Novak, A., Dombai, B., Hein, J. (2008)  How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics 9,137

Satija, R., Pachter,L & Hein, J. (2008)  Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 24, 1236-1242
Mimouni, N., Lyngsø, R.B. & Hein, J.  An analysis of structural influences on selection in RNA genes (2008)  Molecular Biology and Evolution (in press)
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., Simancik, F., Lyngsø, R.B., Mailund, T. & Hein, J.  (2007) On recombinatiion induced multiple and simultaneous coalescent events. Genetics 177, 2151-2160
Lunter, G., Rocco, A., Mimouni, A., Caldeira, A., & Hein, J.  (2007) Uncertainty in homology inferences: assessing and improving genomic sequences alignment Genome Research 18(2), 298-309
de Groot, S., Mailund, T. & Hein, J.  Comparative annotation of viral genomes with non-conserved gene structure (2007) Bioinformatics 23(9), 1080-1089
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
Jenkins, P., Lyngsø, R.B. & Hein, J. (2006)  How many trancsripts does it take to reconstruct the splice graph?  Lecture Notes in Bioinformatics: Proceedings of WABI 2006 4175, 103-114
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 unctional 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
Jensen, J & Hein J (2005)  Gibbs sampler for multiple sttistical alignment.  Statistica Sinica, 2005. 15 (4), 889-907
Miklós, I & Hein, J. (2005) Genome rearrangement in mitochondria and its computational biology. Lecture Notes in Bioinformatics 3388, 85-96
Song, Y.S. & Hein, J. (2005) Constructing Minimal Ancestral Recombination Graphs. J. Comp. Biol., 12:147–169
Miklós, I., Ittzés, P. & Hein, J. (2005) ParIS Genome Rearrangement Server. Bioinformatics, 21:817–820
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
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.
Song, Y.S., Lyngsø, R.B. & Hein, J. (2005) Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
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. (2004) Gibbs sampler for statistical multiple alignment. Statistica Sinica, 15(4):889–907.
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.
Lunter, G.A., Drummond, A.J., Miklos, I. & Hein, J. (2004) Statistical Alignment: Recent Progress, New Applications and Challenges, chapter in: Rasmus Nielsen (ed), Statistical Methods in Molecular Evolution.
Lunter, G.A. & Hein, J. (2004) A nucleotide substitution model with nearest–neighbour interactions Bioinformatics, special issue for ISMB2004, 20: i216–i223.
Hein, J., Schierup, M. & Wiuf, C. (2004) Gene Genealogies, Variation and Evolution, Oxford University Press (publ.).
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., 21:1913–1922.
Pedersen, J.S., Meyer, I.M., Forsberg, R., P. Simmonds, & J. Hein (2004) A comparative method for finding and folding RNA secondary structures in protein-coding regions. Nucleic Acids Research, 32:4925–4936
Rafnar T, Thorlacius S, Steingrimsson E, Schierup MH, Madsen JN, Calian V, Eldon BJ, Jonsson T, Hein J, Thorgeirsson SS. The Icelandic Cancer Project--a population-wide approach to studying cancer. Nat Rev Cancer. 2004 Jun;4(6):488-92. PDF
Pedersen JS, Forsberg R, Meyer IM, Hein J. An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol. 2004 Oct;21(10):1913-22. PDF
Lunter G, Hein J. A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics. 2004 Aug 4;20 Suppl 1:I216-I223. PDF
Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 2004 Sep 24;32(16):4925-36. PDF
Knudsen, B. and J.J.Hein (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars.  Nucleic Acids Research, 31(13) 3423-3428
Pedersen, J.S. & Hein, J. (2003) Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics, 19:219–227..
Knudsen, B. & Hein, J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Research, 31(13):3423–3428.
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.
Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L. & Hein, J. (2003) Bayesian phylogenetic inference under a statistical indel model. ps pdf Lecture Notes in Bioinformatics, Proceedings of WABI'03, 2812:228–244.
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.
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.
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.
Hein, J., Jensen, J. L., Pedersen, C. S. N. (2003) Recursions for statistical multiple alignment. PNAS 100(25):14960–14965.
Miklos, I, P.Ittzes and J.hein "ParIS Genome Rearrangement Server" In PressPDF
Lunter GA, Miklos I, Song YS, Hein J. An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. J Comput Biol. 2003;10(6):869-89. PDF
Knudsen B, Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 2003 Jul 1;31(13):3423-8. PDF
Hein J, Jensen JL, Pedersen CN. Recursions for statistical multiple alignment. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14960-5 PDF
Song, Y and J.J. Hein (2002) On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences PDF
Pedersen, J.S. & J. Hein (2003) "Gene Finding with a Hidden Markov Model of Genome Structure and Evolution" Bioinformatics 19.2.219-227. PDF
Forsberg, R. , T. Storgaard, H. S. Nielsen, M. B. Oleksiewicz, P. Cordioli, G. Sala, J. Hein and A. Bøtner (2002). The genetic diversity of european type prrsv is similar to that of the north american type but is geographically skewed within europe. Virology, 299,38-47.PDF
Wiuf, C. , T. Christensen and J. J. Hein (2001). A simulation study of the reliability of recombination detection methods. Journal of molecular biology and evolution, 18: 1929-1939. ** PDF
Schierup, M. H. , A. M. Mikkelsen and J. Hein (2001). Recombination and the analysis of sequence diversity in mhc and self-incompatibility systems. Genetics. 2001 Dec;159(4):1833-44. **PDF
Forsberg, R. , M. B. Oleksiewicz, A. K. Petersen, J. Hein, A. B. r and T. Storgaard (2001). A molecular clock dates the common ancestor of european-type porcine reproductive and respiratory syndr ome virus at more than 10 years before the emergence of disease. Virology, 289 (2): 174-179.
J.J.Hein (2001): A generalisation of the Thorne-Kishino-Felsenstein model of Statistical Alignment to k sequences related by a binary tree. (Pac.Symp.Biocompu. 2001 p179-190 (eds RB Altman et al.)PDF
Hein,J., C.Wiuf, B.Knudsen, Møller, M., and G.Wibling (2000): Statistical Alignment: Computational Properties, Homology Testing and Goodness-of-Fit. (J. Molecular Biology 302.265-279)PDF
Schierup, M. and J.Hein (2000 October): Recombination and the Molecular Clock (Letter Molecular Biology and Evolution 17.10.1579-80).PDF
Schierup, M. and J.Hein (2000 October): Consequences of Recombination on Traditional Phylogenetic Analysis. (Genetics 156.897-91). **PDF
Steel, M. & J.J.Hein (2001): A generalisation of the Thorne-Kishino-Felsenstein model of Statistical Alignment to k sequences related by a star tree. (Letters in Applied Mathematics vol. 14.679-684)PDF
Wiuf,C. and J.J.Hein (May 2000): The Coalescent with Gene Conversion (Genetics 155.451-462). **PDF
Wiuf,C. and J.J.Hein (1999) 'A contribution to the discussion of J. Chang's paper "Recent Common Ancestor of All Present Human Individuals" ' ( Adv. Appl. Prob. vol. 31.4) PostScript
Wiuf, C and J.J.Hein (1998): The Coalescent with Recombination as a point process moving along sequences. Theoretical Population Biology (55.248-259). PDF
Wiuf, C and J.J.Hein (1999): The Ancestry of a Sample of Sequences Subject to Recombination. (Genetics 151.1217-1228 March 1999). **PDF
Bucka-Lassen,K., O.Caprani and J.J.Hein (1999): "A Method to Combine a Set of Alignments in one better Alignment". (Bioinformatics vol 15.2.122-30.).PDF
Knudsen, B. and J.J.Hein (1999) "Using stochastic context free grammars and molecular evolution to predict RNA secondary structure" (Bioinformatics vol 15.5 15.6.446-454) PDF
Hein, J. 1998. "Multiple alignment."- Pp. 334-340 in Karp, A., Isaac, P. G., & Ingram, D.S. Molecular Tools for Screening Biodiversity. Plants and Animals.- Chapman & Hall, London.
C.S.N.Pedersen, R.Lyngsø & J. Hein : "Comparison of Coding DNA" pp153-173 in (ed. Martin Farach-Colton): "Combinatorial Pattern Matching" Springer Lecture Notes in Computer Science vol. 1448. (1998) PostScript
Hein, J. J. and C. Wiuf. (1997). "On the Number of Ancestors to a DNA Sequence." Genetics 147.1459-68. PDF
Apostolico,A and J. Hein (eds): "Combinatorial Pattern Matching" Springer Lecture Notes in Computer Science vol. 1264. (1997).
Hein,J.J., T.Jiang, L.Wang & K.Zhang (1996): "On the complexity of comparing evolutionary trees" Discrete Applied Mathematics 71.153-169.PDF
Hein, J. J. and J. Støvlbæk. (1996). "Combining DNA and Protein Alignment." Methods of Enzymology 266: 402-415.
Sankoff,D., Y.Abel and J.J.Hein: A Tree, A Window and a Hill. Journal of Classification. (1994).
Hein, J. (1994). "An Algorithm Combining DNA and Protein Alignment." J. Theor. Biol. 167: 169-174.PDF
Hein, J. and J. Støvlbæk. (1994). "Genomic Alignment." J. Mol. Evol. 38: 310-316.
Hein, J. J. and J. Støvlbæk. (1994). "A Maximum Likelihood Approach to the Evolution of Overlapping Reading Frames." J.Mol.Evol. 40.181-190.
J.J.Hein: A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. J.Mol.Evol. 20.402-411. 1993
J.J.Hein: "TreeAlign" (1993) in Computer Analysis of Sequence Data (eds. Grffin & Griffin) Humana Press.
J.J.Hein: Reconstructing the history of sequences subject to Gene Conversion and Recombination. Mathematical Biosciences. (1990) 98.185-200.
J.J.Hein: A Unified Approach to Phylogenies and Alignments. Methods in Enzymology. January 1990 vol 183. 625-644.
J.J.Hein: A method that simultaneously aligns, finds the phylogeny and reconstructs ancestral sequences for any number of ancestral sequences. Mol.Biol.Evol. 6.6.649-668.(1989)PDF
J.J.Hein: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol.Eviol.Biol.6.6.669-684 (1989)PDF
J.J.Hein: An Optimal Algorithm to Reconstruct Trees from Additive Data. Bull.Math.Biol. 51.5.597-603. (1989)
E.O.Jensen,Hein,J.,Paludan,K.,Marcker,K. (1983): The Soy Bean Leghemoglobin Gene Family in Goldberg,R. (ed.): Plant Molecular Biology. Alan Liss Inc. NY.pp.367-379.