cv.gif (3690 bytes) research.gif (4308 bytes) publications.gif (2986 bytes)


PUBLICATIONS

Papers

  1. The Soy Bean Leghemoglobin Gene Family in Goldberg,R. (ed.): Plant Molecular Biology. Alan Liss Inc. (1989), 367-379 (with E.O.Jensen, K.Paludan, K.Marcker) .
  2. A method that simultaneously aligns, finds the phylogeny and reconstructs ancestral sequences for any number of ancestral sequences. Mol.Biol.Evol. (1989), 6.6, 649-668 .
  3. A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol.Biol.Evol. (1989), 6.6, 669-684.
  4. An Optimal Algorithm to Reconstruct Trees from Additive Data. Bull.Math.Biol. (1989), 51.5, 597-603.
  5. Reconstructing the history of sequences subject to Gene Conversion and Recombination. Mathematical Biosciences. (1990), 98, 185-200.
  6. A Unified Approach to Phylogenies and Alignments. Methods in Enzymology. Methods in Enzymology. (1990), 183, 625-644.
  7. A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. J.Mol.Evol. (1993), 20, 402-411.
  8. "TreeAlign" in Computer Analysis of Sequence Data (eds. Grffin & Griffin) Humana Press (1993).
  9. A Tree, A Window and a Hill. Journal of Classification. (1994),(with D.Sankoff and Y.Abel).
  10. An Algorithm Combining DNA and Protein Alignment. J. Theor. Biol. (1994), 167, 169-174.
  11. Genomic Alignment. J.Mol.Evol. (1994), 38, 310-316 (with J. Støvlbæk).
  12. "A Maximum Likelihood Approach to the Evolution of Overlapping Reading Frames." J.Mol.Evol. (1994), 40, 181-190, (with J. Støvlbæk).
  13. On the complexity of comparing evolutionary trees Discrete Applied Mathematics (1996), 71, 153-169 (with T.Jiang, L.Wang and K.Zhang).
  14. Combining DNA and Protein Alignment. Methods of Enzymology (1996), 266, 402-415, (with J. Støvlbæk).
  15. On the Number of Ancestors to a DNA Sequence Genetics (1997), 147, 1459-68 (with C.Wiuf).
  16. Combinatorial Pattern Matching. Springer Lecture Notes in Computer Science vol. 1264 (ed, with A. Apostolico) (1997).
  17. Multiple alignment in Karp, A., Isaac, P. G., & Ingram, D.S. Molecular Tools for Screening Biodiversity. Plants and Animals.- Chapman & Hall, London. (1998), 334-340.
  18. Comparison of Coding DNA in Combinatorial Pattern Matching, Springer Lecture Notes in Computer Science vol. 1448, (ed. Martin Farach-Colton) (1998), (with C.S.N.Pedersen and R.Lyngsø).
  19. The Ancestry of a Sample of Sequences Subject to Recombination. Genetics (1999), 151, 1217-1228, (with C.Wiuf).
  20. A Method to Combine a Set of Alignments in one better Alignment. Bioinformatics (1999), 15.2, 122-30, (with K.Bucka-Lassen and O.Caprani).
  21. Using stochastic context free grammars and molecular evolution to predict RNA secondary structure Bioinformatics (1999), 15.5, 446-454, (with B.Knudsen).
  22. The Coalescent with Recombination as a point process moving along sequences. Theoretical Population Biology Theoretical Population Biology (1999), 55, 248-259.
  23. A contribution to the discussion of J. Chang's paper "Recent Common Ancestor of All Present Human Individuals" Adv. Appl. Prob (1999), 31, 4, (with C.Wiuf).
  24. The Coalescent with Gene Conversion. Genetics (2000), 155, 451-462, (with C.Wiuf).
  25. Consequences of Recombination on Traditional Phylogenetic Analysis. (Genetics 156.897-91). Schierup, M. and J.Hein (2000 October)
  26. A generalisation of the Thorne-Kishino-Felsenstein model of Statistical Alignment to k sequences related by a star tree. Letters in Applied Mathematics (2000), in press, (with M.Steel).
  27. Consequences of Recombination on Traditional Phylogenetic Analysis. (Genetics 156.897-91). Schierup, M. and J.Hein (2000 October)
  28. A simulation study of the reliability of recombination reconstructing methods Mol.Biol.Evol. (2000),submitted (with C.Wiuf and T.Christensen).
  29. Artifacts caused by ignoring recombination in phylogenetic analyses, when recombination is present. Genetics (2000), 156, 879-891, (with M.Schierup).
  30. Recombination and the Molecular Clock. Letter to Mol.Biol.Evol. (2000), 17(10), 1578-79 (with M.Schierup).
  31. Computational and Statistical Properties of The Thorne-Kishino-Felsenstein model of Statistical Alignment: Computational Properties, Homology Testing and Goodness-of-Fit. J.Mol.Biol. (2000), 302, 265-279, (with C.Wiuf, M.Møller, B.Knudsen and G.Wibling).
  32. A generalisation of the Thorne-Kishino-Felsenstein model of Statistical Alignment to k sequences related by a binary tree. Pac. Symp. Biocompu. (2000). In press.
  33. 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 syndrome virus at more than 10 years before the emergence of disease. Virology, 289 (2): 174-179. Pac. Symp. Biocompu. (2000). In press.
  34. Recombination and the analysis of sequence diversity in mhc and self-incompatibility systems Genetics. 2001 Dec;159(4):1833-44. Schierup, M. H. , A. M. Mikkelsen and J. Hein (2001)
  35. A simulation study of the reliability of recombination detection methods. Journal of molecular biology and evolution, 18: 1929-1939. Wiuf, C. , T. Christensen and J. J. Hein (2001)
  36. 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 Forsberg, R. , T. Storgaard, H. S. Nielsen, M. B. Oleksiewicz, P. Cordioli, G. Sala, J. Hein and A. Bøtner (2002)
  37. Gene finding with as hidden Markov model of genome structure and evolution. Bioinformatics 19.2.219-227. Pedersen, J.S. and J.J. Hein (2003)
  38. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res. 2003 Jul 1; 31(13): 3423-8. Knudsen,B. and J. Hein
  39. Algorithms for Multiple Statistical Alignment. (PNAS 100(25):14960-14965.) J.Hein, J.Jensen and C.Storm (2003)
    40. On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences (In Press, J. Math.Biol.) Song, Y and J.J. Hein (2003)
  40. A one-state recursion for multiple statistical alignment. (J.Compu.Biol. J. Comp. Biol., 10(6):869-889.) Lunter, Song, Miklos & Hein (2003)
  41. Parsimoneous Reconstruction of Evolution and Haplotype Blocks (WABI03, Hungary. Lecture Notes in Bioinformatics vol.2812. p287-302) Song, Y and J.J. Hein (2003)
  42. Bayesian Phylogenetic Inference under a statistical insertion-deletion model (WABI03, Hungary. Lecture Notes in Bioinformatics vol.2812. P228-244) Lunter, Miklos, Drummond, Jensen & Hein (2003)
  43. A Large Version of the Small Parsimony Problem (WABI03, Hungary. Lecture Notes in Bioinformatics vol.2812.p417-432) Fredslund,J, T.Scharling & J.Hein (2003)
  44. A Gibbs sampler for statistical multiple alignment. Statistica Sinica, in press. Jensen, J.L. & Hein, J. (2004)
  45. Alignment, Statistics and Evolution (in .Statistical Methods in Molecular Evolution. ed. Rasmus Nielsen, in Press) Lunter, Miklos, Drummond, & Hein (2004)
  46. A substitution model with nearest neighbour interactions accepted in ISMB2004 Lunter,G and JJ Hein
  47. Reviews
    1. Biological Sequence Analysis (Durbin, Eddy, Krogh and Mitchison) Cambridge University Press.(1998) to Appear in Theoretical Popu lation Biology (2000), 58.
    2. Hein, J.J. and C. Wiuf “Statistical Methods in Bioinformatics” by Warren Ewens and G.Grant Springer (2001) Briefings in Bioinformatics (August 2002) (2000), 58.
    3. Schnell, S. and Hein, J.J. “Computational Cell Biology” by Fall, Marland,Wagner, Tyson (eds.) Springer (2002) Briefings in Bioinformatics (2000), 58.

spires.gif (7312 bytes)

| department of statistics |