Articles
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.
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)
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 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.
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.
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.
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. 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
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
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) '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 (May 2000): The Coalescent with Gene Conversion (Genetics 155.451-462). **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
Schierup, M. and J.Hein (2000 October): Consequences of Recombination on Traditional Phylogenetic Analysis. (Genetics 156.897-91). **PDF
Schierup, M. and J.Hein (2000 October): Recombination and the Molecular Clock (Letter Molecular Biology and Evolution 17.10.1579-80).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
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
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.
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
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
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
Pedersen, J.S. & J. Hein (2003) "Gene Finding with a Hidden Markov Model of Genome Structure and Evolution" Bioinformatics 19.2.219-227. PDF
Song, Y and J.J. Hein (2002) On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences PDF
Knudsen, B. and J.J.Hein (2002) "Practical RNA Folding"
Jensen, J. and J.Hein (2003) "A Gibbs Sampler for Multiple Statistical Alignment" PDF In Press
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
Lunter G, Hein J. A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics. 2004 Aug 4;20 Suppl 1:I216-I223. 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
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
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
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
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
Miklos, I, P.Ittzes and J.hein "ParIS Genome Rearrangement Server" In PressPDF
Book Reviews
Hein, J.J. “Biological Sequence Analysis” Durbin, Eddy, Krogh and Mitchison Cambridge University Press.(1998) Theoretical Population Biology vol 58.1.77-78 (August 2000) PDF
Hein, J.J. and C. Wiuf “Statistical Methods in Bioinformatics” by Warren Ewens and G.Grant Springer (2001) Briefings in Bioinformatics (August 2002) PDF
Schnell, S. and Hein, J.J. “Computational Cell Biology” by Fall, Marland,Wagner, Tyson (eds.) Springer (2002) PDF
Song, Y.S. and J.J.Hein (2004) "Phylogenetics" by C. Semple and M.Steel (2002) Oxford University Press - In Press PDF
Forthcoming Book
Hein, Schierup and Wiuf: "Genealogies, Variation and Evolution. PDF
