Mikkel H. Schierup, Professor of Bioinformatics

 

Contact details

 

                        

Email:

mheide@birc.au.dk

Phone:

+45 8715 6535

Dept Web:

http://www.birc.au.dk

Postal Address:

Bioinformatics Research Centre (BiRC)

Map (red building)

Aarhus University

C. F. Mollers Alle 8, Building 1110

DK-8000 Aarhus C

Denmark


Research interests

 

I am interested in applications of population genetics to evolutionary genomics and association mapping. Sequencing of the genomes of many closely related species allows us to infer population genetics processes in the ancestral species. My group works on producing methods based on Hidden Markov models that estimate the genomics relationships of related species along genome alignments.

 

List of publications

 

Journals

 

58.       Stukenbrock EH, Bataillon T, Dutheil JY, Hansen TT, Li R, Zala M, McDonald BA, Wang J, Schierup MH: The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Res 2011, 21(12):2157-2166.

57.       Slotte T, Bataillon T, Hansen TT, St Onge K, Wright SI, Schierup MH: Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol 2011, 3:1210-1219.

56.       Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH: Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet 2011, 7(3):e1001319.

55.       Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al: Comparative and demographic analysis of orang-utan genomes. Nature 2011, 469(7331):529-533.

54.       Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T: Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res 2011, 21(3):349-356.

53.       Stukenbrock EH, Jorgensen FG, Zala M, Hansen TT, McDonald BA, Schierup MH: Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet 2010, 6(12):e1001189.

52.       Sjodin P, Bataillon T, Schierup MH: Insertion and deletion processes in recent human history. PLoS One 2010, 5(1):e8650.

51.       Castric V, Bechsgaard JS, Grenier S, Noureddine R, Schierup MH, Vekemans X: Molecular evolution within and between self-incompatibility specificities. Mol Biol Evol 2010, 27(1):11-20.

50.       Schierup MH, Mailund T, Li H, Wang J, Tjonneland A, Vogel U, Bolund L, Nexo BA: Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups. BMC Med Genet 2009, 10:20.

49.       Preker P, Nielsen J, Schierup MH, Jensen TH: RNA polymerase plays both sides: vivid and bidirectional transcription around and upstream of active promoters. Cell Cycle 2009, 8(8):1106-1107.

48.       Jorgensen FG, Schierup MH: Increased rate of human mutations where DNA and RNA polymerases collide. Trends Genet 2009, 25(12):523-527.

47.       Guo YL, Bechsgaard JS, Slotte T, Neuffer B, Lascoux M, Weigel D, Schierup MH: Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proc Natl Acad Sci U S A 2009, 106(13):5246-5251.

46.       Emily M, Mailund T, Hein J, Schauser L, Schierup MH: Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet 2009, 17(10):1231-1240.

45.       Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH: Ancestral population genomics: the coalescent hidden Markov model approach. Genetics 2009, 183(1):259-274.

44.       Boggs NA, Dwyer KG, Shah P, McCulloch AA, Bechsgaard J, Schierup MH, Nasrallah ME, Nasrallah JB: Expression of distinct self-incompatibility specificities in Arabidopsis thaliana. Genetics 2009, 182(4):1313-1321.

43.       Besenbacher S, Mailund T, Schierup MH: Local phylogeny mapping of quantitative traits: higher accuracy and better ranking than single-marker association in genomewide scans. Genetics 2009, 181(2):747-753.

42.       Schierup MH, Vekemans X: Genomic consequences of selection on self-incompatibility genes. Curr Opin Plant Biol 2008, 11(2):116-122.

41.       Schierup MH, Bechsgaard JS, Christiansen FB: Selection at work in self-incompatible Arabidopsis lyrata. II. Spatial distribution of S haplotypes in Iceland. Genetics 2008, 180(2):1051-1059.

40.       Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH: RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008, 322(5909):1851-1854.

39.       Leppala J, Bechsgaard JS, Schierup MH, Savolainen O: Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus. Heredity 2008, 100(1):71-78.

38.       Ehlers BK, Schierup MH: When gametophytic self-incompatibility meets gynodioecy. Genet Res (Camb) 2008, 90(1):27-35.

37.       Castric V, Bechsgaard J, Schierup MH, Vekemans X: Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genet 2008, 4(8):e1000168.

36.       Jorgensen FG, Schierup MH, Clark AG: Heterogeneity in regional GC content and differential usage of codons and amino acids in GC-poor and GC-rich regions of the genome of Apis mellifera. Mol Biol Evol 2007, 24(2):611-619.

35.       Hobolth A, Christensen OF, Mailund T, Schierup MH: Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet 2007, 3(2):e7.

34.       Schierup MH, Bechsgaard JS, Nielsen LH, Christiansen FB: Selection at work in self-incompatible Arabidopsis lyrata: mating patterns in a natural population. Genetics 2006, 172(1):477-484.

33.       Poulsen NA, Nielsen EE, Schierup MH, Loeschcke V, Gronkjaer P: Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Mol Ecol 2006, 15(2):321-331.

32.       Mailund T, Schierup MH, Pedersen CN, Madsen JN, Hein J, Schauser L: GeneRecon--a coalescent based tool for fine-scale association mapping. Bioinformatics 2006, 22(18):2317-2318.

31.       Mailund T, Besenbacher S, Schierup MH: Whole genome association mapping by incompatibilities and local perfect phylogenies. BMC Bioinformatics 2006, 7:454.

30.       Bechsgaard JS, Castric V, Charlesworth D, Vekemans X, Schierup MH: The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr. Mol Biol Evol 2006, 23(9):1741-1750.

29.       Bataillon T, Mailund T, Thorlacius S, Steingrimsson E, Rafnar T, Halldorsson MM, Calian V, Schierup MH: The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers. Eur J Hum Genet 2006, 14(9):1044-1053.

28.       Wernersson R, Schierup MH, Jorgensen FG, Gorodkin J, Panitz F, Staerfeldt HH, Christensen OF, Mailund T, Hornshoj H, Klein A et al: Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 2005, 6:70.

27.       Schierup MH, Mordhorst CH, Muller CP, Christensen LS: Evidence of recombination among early-vaccination era measles virus strains. BMC Evol Biol 2005, 5:52.

26.       Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L: CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005, 6:252.

25.       Jorgensen FG, Hobolth A, Hornshoj H, Bendixen C, Fredholm M, Schierup MH: Comparative analysis of protein coding sequences from human, mouse and the domesticated pig. BMC Biol 2005, 3:2.

24.       Fredsted T, Pertoldi C, Schierup MH, Kappeler PM: Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus). Mol Ecol 2005, 14(8):2363-2372.

23.       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, 4(6):488-492.

22.       Bechsgaard J, Bataillon T, Schierup MH: Uneven segregation of sporophytic self-incompatibility alleles in Arabidopsis lyrata. J Evol Biol 2004, 17(3):554-561.

21.       Richman AD, Herrera LG, Nash D, Schierup MH: Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus. Genet Res 2003, 82(2):89-99.

20.       Mable BK, Schierup MH, Charlesworth D: Estimating the number, frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata(Brassicaceae) with sporophytic control of self-incompatibility. Heredity 2003, 90(6):422-431.

19.       Eskildsen S, Justesen J, Schierup MH, Hartmann R: Characterization of the 2'-5'-oligoadenylate synthetase ubiquitin-like family. Nucleic Acids Res 2003, 31(12):3166-3173.

18.       Charlesworth D, Mable BK, Schierup MH, Bartolome C, Awadalla P: Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata. Genetics 2003, 164(4):1519-1535.

17.       Charlesworth D, Bartolome C, Schierup MH, Mable BK: Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol Biol Evol 2003, 20(11):1741-1753.

16.       Sogaard IZ, Boesen T, Mygind T, Melkova R, Birkelund S, Christiansen G, Schierup MH: Recombination in Mycoplasma hominis. Infect Genet Evol 2002, 1(4):277-285.

15.       Christensen LS, Scholler S, Schierup MH, Vestergaard BF, Mordhorst CH: Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains. APMIS 2002, 110(2):113-122.

14.       Schierup MH, Mikkelsen AM, Hein J: Recombination, balancing selection and phylogenies in MHC and self-incompatibility genes. Genetics 2001, 159(4):1833-1844.

13.       Schierup MH, Mable BK, Awadalla P, Charlesworth D: Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata. Genetics 2001, 158(1):387-399.

12.       Miege C, Ruffio-Chable V, Schierup MH, Cabrillac D, Dumas C, Gaude T, Cock JM: Intrahaplotype polymorphism at the Brassica S locus. Genetics 2001, 159(2):811-822.

11.       Schierup MH, Vekemans X, Charlesworth D: The effect of subdivision on variation at multi-allelic loci under balancing selection. Genet Res 2000, 76(1):51-62.

10.       Schierup MH, Hein J: Consequences of recombination on traditional phylogenetic analysis. Genetics 2000, 156(2):879-891.

9.         Schierup MH, Hein J: Recombination and the molecular clock. Mol Biol Evol 2000, 17(10):1578-1579.

8.         Schierup MH, Charlesworth D, Vekemans X: The effect of hitch-hiking on genes linked to a balanced polymorphism in a subdivided population. Genet Res 2000, 76(1):63-73.

7.         Charlesworth D, Awadalla P, Mable BK, Schierup MH: Population-level studies of multiallelic self-incompatibility loci, with particular reference to Brassicaceae. Annals of Botany 2000, 85:227-239.

6.         Vekemans X, Schierup MH, Christiansen FB: Mate availability and fecundity selection in multi-allelic self-incompatibility systems in plants. Evolution 1998, 52(1):19-29.

5.         Schierup MH, Vekemans X, Christiansen FB: Allelic genealogies in sporophytic self-incompatibility systems in plants. Genetics 1998, 150(3):1187-1198.

4.         Schierup MH: The effect of enzyme heterozygosity on growth in a strictly outcrossing species, the self-incompatible Arabis petraea (Brassicaceae). Hereditas 1998, 128(1):21-31.

3.         Schierup MH: The number of self-incompatibility alleles in a finite, subdivided population. Genetics 1998, 149(2):1153-1162.

2.         Schierup MH, Vekemans X, Christiansen FB: Evolutionary dynamics of sporophytic self-incompatibility alleles in plants. Genetics 1997, 147(2):835-846.

1.         Schierup MH, Christiansen FB: Inbreeding depression and outbreeding depression in plants. Heredity 1996, 77:461-468.

 

Books/book chapters

 

1.         S¿ren Besenbacher, Thomas Mailund, and Mikkel H. Schierup 2011. Association mapping: Evolutionary perspectives, Evolutionary Genomics: statistical and computational methods", Springer-Humana

2.         Schierup, M. H. (1997a): Methods of Risk Assessment of Transgenic Plants II: Pollination, Gene-Transfer and Population Impacts, edited by Kjellsson, G., V. Simonsen and K. Ammann, BirkhŠuser Verlag, Basel. Contribution 50 pages.

3.         M. H. Schierup and C. Wiuf. 2010. The Coalescent of Bacterial Populations. In Bacterial population genetics in infectious disease? edited by Ashley Robinson, Dan Falush and Ed Feil, Wiley

4.         Jotun Hein, Mikkel H. Schierup and Carsten Wiuf. 2005. Gene genealogies, sequences and evolution, A primer in coalescent theory, Oxford University Press, 320 pp. (equal authors contribution)

 

 

Other publications

1.     Christiansen, F. B., C. N. S. Pedersen, L. Schauser and M. H. Schierup (2002). Bioinformatik ved Aarhus Universitet: Etablering af center for bioinformatik og en 2 aarig kandidatuddannelse. Biozoom,5 (3): 12-16.

2.     Mikkel H. Schierup. 2006. Book review of Cavalli-Sforza, Moroni and Zei: Consanguinity, inbreeding and genetic drift in Italy, Heredity, in press

3.     Mikkel H. Schierup, Asger Hobolth, Thomas Mailund and Arne Vollertsen. 2007. DNA-statistik g¿r mennesket yngre, Aktuel Naturvidenskab no 3, 2007