CV
PERSONAL DETAILS
Date of Birth: 19 July 1956
Nationality: Danish
ACADEMIC RECORD
January 1978: Bachelor in Biology (1. Del)
January 1981: Bachelor in Mathematical Statistics (1. Del)
August 1984: Cand.Scient in Biology
January 1985: Masters Examination in Mathematics (no thesis report)
May 1985: Master Thesis in Molecular Biology, Aarhus University, Denmark
March 1990 Licentiat in Genetics, Aarhus University, Denmark
ACADEMIC APPOINTMENTS
Spring 1981 Graduate Assistant, Institute of Ecology and Genetics. Teaching Population Genetics
Spring 1982 Graduate Assistant, Institute of Ecology and Genetics. Teaching Population Genetics
February 1983-June 1984 Graduate Assistant, Institute of Mathematics. Teaching Calculus
November 1985-May 1987 Visiting Associate at NIEHS, Research Triangle Park, North Carolina under Norman Kaplan and Charles Langley
September 1987 Consultant at Harvard Medical School under T.F.Smith
Oktober-Januar 1988 Research Associate ved Institute of Mathematics, University of Southern California, LA under Michael Waterman
February 1988 - June 1989 Postdoctoral Fellow ved Center for Molecular Genetics, UCSD, La Jolla under Russell Doolittle
July-August 1989 Visiting Joseph Felsenstein at University of Washington, Seattle
August 1989- 15 Sept 90: Post Doc at Centre Recherche Mathematiquee under David Sankoff
October 90-April 91: Japanese Society for Promotion of Science
Fellow at National Institute of Genetics, Mishima, Japan. (Dr.T.Gojobori) and Japanese DNA Database
January 91-: Senior Stipend at Aarhus University funded by the Faculty of Sciences, Aarhus and by the Carlsberg Foundation
September 94-: Associate Professor, Aarhus University
July 98-December 98: Invited stay at The Newton Institute for Mathematical Sciences (Special Program: Biomolecular Function and Evolution in the Context of the Genome Project), Cambridge, UK
February 99 - April 99: Erskine Award to stay at Department of Mathematics, Massey University, Christchurch, NZ
2001 May-Aug Director of Bioinformatics Research Centre, Aarhus University
2001 Sept.- Professor of Bioinformatics, Dept. of Statistics, University of Oxford
Teaching Experience in Denmark (6 corresponds to full study activity in 12-13 weeks)
Spring 1992 Molecular Evolution (1)
Spring 1994 Molecular Evolution (2)
Autumn 1995 DNA & Population Genetical Problems (2)
Spring 1996 Molecular Evolution (3)
Spring 1997 Structural Sequence Analysis (2)
Spring 1998 Molecular Taxonomy (2)
Spring 1998 Evolutionary Sequence Analysis (3)
Autumn 1998 Evolutionary Virology (1) (Forsberg & Aagaard arranged and lectured)
Autumn 1999 Bioinformatics & Genome Analysis (2 + 1)
Autumn 2000 Evolutionary Virology (2)
Further Teaching
Bioinformatics and Computational Biology
DTC LS
DTC Sysbio
MSc Bioinformatics (Molecular Evolution & Comparative Genomics)
A one week course at Gulbenkian Institute (Lisbon, Portugal)
A two week course at Stellenbosch (Cape Town, South Africa) (starting 2009).
I also taught at the Summer Institute in Statistical Genetics for 10 years with Jeff Thorne and Bruce Weir when held at NCSU, Raleigh, North Carolina, USA
PhD study groups
Statistical Problems in Sequence Analysis (1995)
Computational Problems in Sequence Analysis (1996)
Epidemiological Models (Anderson & May + others) (1998)
2001-2003 Associate Editor of Genetics
2002-: Member of Danish Royal Society of Science
Master & Graduate Student Supervision
Jon Blandfort, master student (biology) (finished 1996) (Evolution of Heat Shock Proteins)
Rasmus Nielsen, master student (biology) co-supervised with Peter Arctander. (finished 1994)
Carsten Wiuf, graduate student (statistician) (finished 1997) (Coalescent Theory)
Kim Fisker, master student (computer science) (finished 1994) with Ole Caprani
Ivan Høi, master student (computer science) (finished 1995) with Ole Caprani
Klaus Lassen, master student (computer science) (finished 1997) with Ole Caprani
Morten Lauritsen, master student (computer science) (finished 1997) with Ole Caprani
Brian Carlsen, master student (computer science) (finished 1997) with Ole Caprani
Morten Møller (complexity of statistical alignment) - comp. sci. (master student) (finished 1999)
Rune Lyngsø (RNA structure prediction) - comp.sci. (graduate student) (finished 2000)
Christian Storm (string algorithms) - comp.sci. (graduate student) (finished 2000)
Lars Aagaard (evolutionary virology) - biologist (finished 2002)
Roald Forsberg (molecular epidemiolgy) - biologist (finished 2002)
Bjarne Knudsen (stochastic grammars and biology) - mathematical biologist (finished 2002)
Jacob Skou Pedersen (gene finding algorithms) graduate student (finished 2004)
Stephen McCauley (DPhil, Oxford) (annotating viruses) (finished 2008)
Lizhong Wei (DPhil, Oxford) (finished 2007) joint supervision with William Cookson (Wellcome Centre for Human Genetics) Functional Genetics of Asthma
Ben Holtom (DPhil, Oxford) (finished 2008) joint supervision with John Hancock (Harwell MRC)
Saskia de Groot (DPhil, Oxford) (finished 2008) (annotating viruses)
Naila Mimouni (DPhil, Oxford) (finished 2008) Measuring Selection on RNA Molecules
Joanna Davies (DPhil, Oxford) (started October 2006) Integrative Genomics
Rahul Satija (DPhil, Oxford) (started October 2006) Statistical Alignment and Footprinting
Aziz Mithani (DPhil, Oxford) (finished October 2009) Evolution of Networks
Marton Munz (DPhil, Oxford) (started October 2008) Evolution of Molecular Movements
Funded Grants (grants smaller than 30K£ not listed)
Professorship in Bioinformatics (MRC) G0100502. 1/9/2001-31/8/2005. £763,560
A comparative method for locating human conserved DNA (BBSRC) BB/D005418/1. 1/10/2005-31/3/2007. Grant extended for 6 months. £60,480
Practical statistical alignment (BBSRC) BB/C509566/1. Start date revised. Grant extended to 16/6/2008. £356,116
Evolutionary analysis of non-coding RNA genes and gene families (BBSRC) BB/D012139/1. 1/1/2006-31/12/2008. £201,998
Association mapping of breast and prostate cancer related genes (EU) POLYGENE LSHC-CT-2005-018827 1/12/2005-30/9/2009 £159,375
From population genomes to global pedigrees (EPSRC) EO5885X/1. End date extended to 31/7/2010. £194,456
PUBLICATIONS
Taylor, J., Street, T., Hao, L., Copley, R., Taylor, M., Hayden, P., Stolper, G., Mott, R., Hein, J., Moffatt, M. & Cookson, W. (2009) Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes. PLoS One, Oct 30, 4(10), e7651
Satija, R., Novak, A., Miklos, A., Lyngsø, R. & Hein, J. (2009) BiGFoot: Baysian alignment and phylogenetic footprinting for multiple sequences with MCMC. Evolutionary Biology 9, 217
Miklos, I., Novak, A., Satija, R., Lyngsø, R. & Hein J. (2009) Stochastic models of sequence evolution including insertion-deletion events. Statistical Methods in Medical Research 18(5), 453-485
Mithani, A., Preston, G. & Hein, J (2009) Rahnuma: hypergraph based tool for metabolic pathway prediction and network comparison Bioinformatics 25(14), 1831-1832
Mithani, A., Preston, G. & Hein, J (2009) A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinformatics
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)
Mimouni, N., Lyngsoe, R., Griffiths-Jones, S. & Hein, J. (2009) An analysis of Structural Influences on Selection in RNA Genes. Mol Biol Evol 26, 209-216
Davies, J., Rafnar, T., Hellenthal, G. & Hein, J. (2008) Integrative Genomics and Functional Explanation (manuscript)
de Groot, S., Mailund, T. Lunter, G. & Hein, J. (2008) Investigating selection on viruses: a statistical alignment approach. BMC Bioinformatics 9, 304
Lyngsø, R.B, Satija, R., Miklos, I., Novak, A. & Hein, J. (2008) Statistical alignment of very large number of sequences by k-restricted Steiner Tree Approximation2. Submitted to BMC Bioinformatics
Novak, A., Miklos, I., Lyngsø, R. & Hein, J. (2008) StatAlign: an extendable software package for join Bayesian estimation of alignments and evolutionary trees. Bioinformatics 24, 2403-2404`
Satija, R.,Pachter, L. & Hein, J. (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 24,1236-1242
Miklos, I., Novak, A., Dombai, B. & Hein, J. (2008) How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics 9,137
Mimouni, N., Lyngsø, R.B., Griffiths-Jones, S. & Hein, J. (2008) An Analysis of Structural Influences on Selection in RNA Genes. Submitted to Molecular Biology and Evolution
Lyngsø, R.B., Song, Y.S. & Hein, J. (2008) Accurate computation of likelihoods in the coalescent with recombination via parsimony. Lecture Notes in Bioinformatics: Proceedings of RECOMB 2008 463–477
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., František Simančík, Lyngsø, R.B., Mailund, T. & Hein, J. (2007) On recombination induced multiple and simultaneous coalescent events. Genetics 177, 2151–2160
Lunter, G., Rocco, A., Mimouni, N., Caldeira, A. & Hein, J. (2007) Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Research 18(2), 298-309
de Groot, S., Mailund, T. & Hein, J. (2007) Comparative annotation of viral genomes with non-conserved gene structure. 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 transcripts does it take to reconstruct the splice graph? Lecture Notes in Bioinformatics: Proceedings of WABI 2006. 4175, 103–114
Song, Y.S., Lyngsø, R.B. & Hein, J. (2006) Counting all possible ancestral configurations of sample sequences in population genetics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3), 239–251
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 functional 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
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. (2005) A Gibbs sampler for statistical multiple alignment. Statistica Sinica, 15(4), 889-908
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
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
Miklós, I., Ittzés, P. & Hein, J. (2005) ParIS genome rearrangement server. Bioinformatics, 21, 817–820
Song, Y.S. & Hein, J. (2005) Constructing minimal ancestral recombination graphs. J. Comp. Biol., 12, 147–169
Jensen, J.L. & Hein, J. (2005) Gibbs sampler for statistical multiple alignment. Statistica Sinica, 15(4), 889–908
Miklós, I. & Hein, J. (2004) Genome rearrangement in mitochondria and its computation biology. RECOMB Workshop on Comparative Genomics, 85–96
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
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.
Hein, J., Schierup, M.H. & Wiuf, C. (2004) Gene genealogies, variation and evolution, Oxford University Press (publ.)
Lunter, G.A. & Hein, J. (2004) A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics, special issue for ISMB 2004, 20, i216–i223
Lunter, G.A., Drummond, A.J., Miklos, I. & Hein, J. (2004) Statistical alignment: Recent progress, new applications and challenges. In Statistical Methods in Molecular Evolution. (Nielsen, R., ed.)
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
Hein, J. (2004) Pedigrees for all humanity. Nature 431, 518-519
Hein, J., Jensen, J. L. & Pedersen, C. N. S. (2003) Recursions for statistical multiple alignment. PNAS 100(25), 14960–14965
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.
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
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
Lunter, G.A., Miklós, I., Drummond, A., Jensen, J.L. & Hein, J. (2003) Bayesian phylogenetic inference under a statistical indel model. Lecture Notes in Bioinformatics, Proceedings of WABI'03, 2812, 228–244
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
Knudsen, B. & Hein, J. (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
Forsberg, R. , T. Storgaard, H. S. Nielsen, M. B. Oleksiewicz, P. Cordioli, G. Sala, Hein, J. & Bøtner, A. (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
Wiuf, C., Christensen, T. & Hein, J. (2001). A simulation study of the reliability of recombination detection methods. Journal of Molecular Biology and Evolution, 18, 1929-1939
Schierup, M.H., Mikkelsen, A. & Hein, J. (2001). Recombination and the analysis of sequence diversity in mhc and self-incompatibility systems. Genetics. 2001 (Dec) 159(4), 1833-44
Forsberg, R., Oleksiewicz, M., Petersen, K., Hein, J., 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
Steel, M. & Hein, J. (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)
Hein, J. (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.)
Hein, J., Wiuf, C., Knudsen, B., Møller, M., and Wibling, G. (2000) Statistical alignment: computational properties, homology testing and goodness-of-fit. J. Molecular Biology 302, 265-279
Schierup, M. & Hein, J. (2000) Recombination and the molecular clock. Letter Molecular Biology and Evolution 17(10), 1579-80
Schierup, M. & Hein, J. (2000) Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 897-91
Wiuf, C. & Hein, J. (2000) The coalescent with gene conversion. Genetics 155,451-462
Wiuf, C. & Hein, J. (1999) A contribution to the discussion of J. Chang's paper ‘Recent Common Ancestor of All Present Human Individuals’. Adv. Appl. Prob. 31(4)
Wiuf, C & Hein, J. (1999) The coalescent with recombination as a point process moving along sequences. Theoretical Population Biology 55, 248-259
Knudsen, B. & Hein, J. (1999) Using stochastic context free grammars and molecular evolution to predict RNA secondary structure. Bioinformatics Vol 15.5 15.6, 446-454
Bucka-Lassen,K., Caprani, O. & Hein, J. (1999) A method to combine a set of alignments in one better alignment. Bioinformatics Vol 15.2.122-30
Wiuf, C & Hein, J. (1999) The ancestry of a sample of sequences subject to recombination. Genetics 151, 1217-1228
Pedersen, C., Lyngsø, R. & Hein, J. Comparison of Coding DNA (1998) pp153-173 in (ed. Martin Farach-Colton) "Combinatorial Pattern Matching" Springer Lecture Notes in Computer Science Vol. 1448
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
Apostolico, A & Hein, J. (1997) (eds): "Combinatorial Pattern Matching" Springer Lecture Notes in Computer Science Vol. 1264
Wiuf, C. & Hein, J. (1997) On the number of ancestors to a DNA Sequence. Genetics 147, 1459-68
Hein, J & Støvlbæk, J. (1996) Combining DNA and Protein Alignment. Methods of Enzymology 266, 402-415
Hein, J., Jiang, T., Wang, L. & Zhang, K. (1996) On the complexity of comparing evolutionary trees. Discrete Applied Mathematics 71, 153-169
Hein, J. & Støvlbæk, J. (1994) A maximum likelihood approach to the evolution of overlapping reading frames. J. Mol. Evol. 40, 181-190
Hein, J. & Støvlbæk, J. (1994) Genomic Alignment. J. Mol. Evol. 38, 310-316
Hein, J. (1994) An algorithm combining DNA and protein alignment. J. Theor. Biol. 167, 169-174
Sankoff, D., Abel, Y. & Hein, J. (1994) A Tree, a window and a hill. Journal of Classification 11(2)
Hein, J. (1993) "TreeAlign" in Computer Analysis of Sequence Data (eds. Griffin & Griffin) Humana Press
Hein, J. (1993) A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 20, 402-411
Hein, J. (1990) A unified approach to phylogenies and alignments. Methods in Enzymology 183, 625-644
Hein, J. (1990) Reconstructing the history of sequences subject to gene conversion and recombination. Mathematical Biosciences 98, 185-200
Hein, J. (1989) An optimal algorithm to reconstruct trees from additive data. Bull. Math. Biol. 51(5), 597-603
Hein, J. (1989) A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Eviol.Biol. 6(6), 669-684
Hein, J. (1989) 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
Jensen, E., 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
Book
“Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory” Hein, J., Schierup, M. and Wiuf, C. (2005) Oxford University Press, 300 pages
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