PUBLICATIONS
Papers
- 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).
- 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 .
- A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol.Biol.Evol. (1989), 6.6, 669-684.
- An Optimal Algorithm to Reconstruct Trees from Additive Data. Bull.Math.Biol. (1989), 51.5, 597-603.
- Reconstructing the history of sequences subject to Gene Conversion and Recombination. Mathematical Biosciences. (1990), 98, 185-200.
- A Unified Approach to Phylogenies and Alignments. Methods in Enzymology. Methods in Enzymology. (1990), 183, 625-644.
- A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. J.Mol.Evol. (1993), 20, 402-411.
- "TreeAlign" in Computer Analysis of Sequence Data (eds. Grffin & Griffin) Humana Press (1993).
- A Tree, A Window and a Hill. Journal of Classification. (1994),(with D.Sankoff and Y.Abel).
- An Algorithm Combining DNA and Protein Alignment. J. Theor. Biol. (1994), 167, 169-174.
- Genomic Alignment. J.Mol.Evol. (1994), 38, 310-316 (with J. Støvlbæk).
- "A Maximum Likelihood Approach to the Evolution of Overlapping Reading Frames." J.Mol.Evol. (1994), 40, 181-190, (with J. Støvlbæk).
- On the complexity of comparing evolutionary trees Discrete Applied Mathematics (1996), 71, 153-169 (with T.Jiang, L.Wang and K.Zhang).
- Combining DNA and Protein Alignment. Methods of Enzymology (1996), 266, 402-415, (with J. Støvlbæk).
- On the Number of Ancestors to a DNA Sequence Genetics (1997), 147, 1459-68 (with C.Wiuf).
- Combinatorial Pattern Matching. Springer Lecture Notes in Computer Science vol. 1264 (ed, with A. Apostolico) (1997).
- 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.
- 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).
- The Ancestry of a Sample of Sequences Subject to Recombination. Genetics (1999), 151, 1217-1228, (with C.Wiuf).
- 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).
- Using stochastic context free grammars and molecular evolution to predict RNA secondary structure Bioinformatics (1999), 15.5, 446-454, (with B.Knudsen).
- The Coalescent with Recombination as a point process moving along sequences. Theoretical Population Biology Theoretical Population Biology (1999), 55, 248-259.
- 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).
- The Coalescent with Gene Conversion. Genetics (2000), 155, 451-462, (with C.Wiuf).
- Consequences of Recombination on Traditional Phylogenetic Analysis. (Genetics 156.897-91). Schierup, M. and J.Hein (2000 October)
- 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).
- Consequences of Recombination on Traditional Phylogenetic Analysis. (Genetics 156.897-91). Schierup, M. and J.Hein (2000 October)
- A simulation study of the reliability of recombination reconstructing methods Mol.Biol.Evol. (2000),submitted (with C.Wiuf and T.Christensen).
- Artifacts caused by ignoring recombination in phylogenetic analyses, when recombination is present. Genetics (2000), 156, 879-891, (with M.Schierup).
- Recombination and the Molecular Clock. Letter to Mol.Biol.Evol. (2000), 17(10), 1578-79 (with M.Schierup).
- 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).
- 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.
- 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.
- 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)
- 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)
- 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)
- 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)
- 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
- Algorithms for Multiple Statistical Alignment. (PNAS 100(25):14960-14965.) J.Hein, J.Jensen and C.Storm (2003) 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)
- A one-state recursion for multiple statistical alignment. (J.Compu.Biol. J. Comp. Biol., 10(6):869-889.) Lunter, Song, Miklos & Hein (2003)
- Parsimoneous Reconstruction of Evolution and Haplotype Blocks (WABI03, Hungary. Lecture Notes in Bioinformatics vol.2812. p287-302) Song, Y and J.J. Hein (2003)
- 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)
- 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)
- A Gibbs sampler for statistical multiple alignment. Statistica Sinica, in press. Jensen, J.L. & Hein, J. (2004)
- Alignment, Statistics and Evolution (in .Statistical Methods in Molecular Evolution. ed. Rasmus Nielsen, in Press) Lunter, Miklos, Drummond, & Hein (2004)
- A substitution model with nearest neighbour interactions accepted in ISMB2004 Lunter,G and JJ Hein
- A comparative method for predicting and folding RNA structures within protein coding regions submitted to Molecular Biology Evolution Pedersen, JS, IM Meyer, R Forsberg, P. Simmonds and JJ Hein (2004)
- A stochastic model for the evolution of nucleotides subject to selective constraints from coding and RNA folding criteria In press Molecular Biology Evolution Pedersen, JS, IM Meyer, R Forsberg, P. Simmonds and JJ Hein (2004)
- Robust Invariant Set Methods for Normalization submitted to Bioinformatics Lyngsoe, Miklos,I, C. Sugnet, P.Underhill, S. Webb and JJ Hein (2004)
- Constructing minimal ancestral recombination graphs (in press J. Compu.Biol.) Song and Hein (2004)
- ParIS Genome Rearrangement Server Bioinformatics, accepted Miklós, I., Ittzés, P. & Hein, J. (2004)
Reviews
- Biological Sequence Analysis (Durbin, Eddy, Krogh and Mitchison) Cambridge University Press.(1998) to Appear in Theoretical Popu lation Biology (2000), 58.
- 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.
- Schnell, S. and Hein, J.J. .Computational Cell Biology. by Fall, Marland,Wagner, Tyson (eds.) Springer (2002) Briefings in Bioinformatics (2000), 58.
