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.PDF
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)PDF
J.J.Hein: Reconstructing the history of sequences subject to Gene
Conversion and Recombination. Mathematical Biosciences. (1990)
98.185-200.PDF
J.J.Hein: A Unified Approach to Phylogenies and Alignments. Methods in
Enzymology. January 1990 vol 183. 625-644.PDF
J.J.Hein: A Heuristic Method to Reconstruct the History of Sequences
Subject to Recombination. J.Mol.Evol. 20.402-411. 1993PDF
J.J.Hein: "TreeAlign" (1993) in Computer Analysis of Sequence Data
(eds. Grffin & Griffin) Humana Press.PDF
Sankoff,D., Y.Abel and J.J.Hein: A Tree, A Window and a Hill. Journal
of Classification. (1994).PDF
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.PDF
Hein, J. J. and J. Støvlbæk. (1994). "A Maximum Likelihood Approach to
the Evolution of Overlapping Reading Frames." J.Mol.Evol. 40.181-190.PDF
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.PDF
Wiuf, C and J.J.Hein (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).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.PDF
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)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
Wiuf, C and J.J.Hein (1999): 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)PDF
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.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
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
Knudsen, B. and J.J.Hein (2002) "Practical RNA Folding" (submitted to
Bioinformatics)PDF
J.Hein, J.Jensen and C.Storm "Algorithms for Multiple Statistical
Alignment" (submitted to J. Computational Biology)PDF
Jensen, J. and J.Hein (2003) "A Gibbs Sampler for Multiple Statistical
Alignment" (submitted)PDF
Song, Y and J.J. Hein (2002) On the Minimum Number of Recombination
Events in the Evolutionary History of DNA Sequences (submitted to
J.Math.Biol.) **PDF
Lunter, Song, Miklos & Hein (2003) "A one-state recursion for multiple
statistical alignment" (submitted to J.Com.Biol.)
PDF