Publications

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Wiuf, C., Laidlaw, Z. & Stumpf, MPH. (2003). Some notes on the combinatorial properties of haplotype tagging. Math. Biosci., 185, 205-216.

Brodal, G. S., Lyngsø, R. B., Östlin, A. & Pedersen, C. N. S. (2002). Solving the String Statistics Problem in Time O(n log n). In P. Widmayer, S. Eidenbenz, F. Triguero, R. Morales, R. Conejo & M. Hennessy (Eds.), Automata, Languages and Programming: 29th International Colloquium, ICALP 2002 Málaga, Spain, July 8–13, 2002 Proceedings (pp. 728-739). Springer. Lecture Notes in Computer Science Vol. 2380 https://doi.org/10.1007/3-540-45465-9_62

Holmstrup, M., Sørensen, J. G., Schmidt, I. K., Nielsen, P. L., Mason, S., Tietema, A., Smith, A. R., Bataillon, T., Beier, C. & Ehlers, B. K. (2013). Soil microarthropods are only weakly impacted after 13 years of repeated drought treatment in wet and dry heathland soils. Soil Biology & Biochemistry, 66, 110-118. https://doi.org/10.1016/j.soilbio.2013.06.023

Warrier, V., Toro, R., Won, H., Leblond, C. S., Cliquet, F., Delorme, R., De Witte, W., Bralten, J., Chakrabarti, B., Børglum, A. D., Grove, J., Poelmans, G., Hinds, D. A., Bourgeron, T. & Baron-Cohen, S. (2019). Social and non-social autism symptoms and trait domains are genetically dissociable. Communications Biology, 2(1), [328]. https://doi.org/10.1038/s42003-019-0558-4

Li, S., Ma, L., Li, H., Vang, S., Hu, Y., Bolund, L. & Wang, J. (2007). Snap: An Integrated SNP Annotation Platform. Nucleic Acids Research, 35, D707-D710. https://doi.org/10.1093/nar/gkl969

Mørup, N., Stakaitis, R., Golubickaite, I., Riera, M., Dalgaard, M. D., Schierup, M. H., Jørgensen, N., Daugaard, G., Juul, A. & Almstrup, K. (2021). Small RNAs in Seminal Plasma as Novel Biomarkers for Germ Cell Tumors. Cancers, 13(10), [2346]. https://doi.org/10.3390/cancers13102346

Hobolth, A. & Stone, E. (2009). Simulation from endpoint-conditioned, continuous-time Markov chains on a finite state space, with applications to molecular evolution. Annals of Applied Statistics, 3(3), 1204-1231. https://doi.org/10.1214/09-AOAS247

Posada, D. & Wiuf, C. (2003). Simulating haplotype blocks in the human genome. Bioinformatics, 19(2), 289-290.

Christiansen, F. (1990). Simplified models for viability selection at multiple loci. Theoretical Population Biology, 37, 39-54.

Madsen, T., Hobolth, A., Jensen, J. L. & Pedersen, J. S. (2017). Significance evaluation in factor graphs. BMC Bioinformatics , 18, 199. https://doi.org/10.1186/s12859-017-1614-z

De, T., Goncalves, A., Speed, D., Froguel, P., NFBC consortium, Gaffney, D. J., Johnson, M. R., Jarvelin, M-R. & Coin, L. J. (2021). Signatures of TSPAN8 variants associated with human metabolic regulation and diseases. iScience, 24(8), [102893]. https://doi.org/10.1016/j.isci.2021.102893

Feliu, E., Knudsen, M. & Wiuf, C. H. (2012). Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels. Advances in Experimental Medicine and Biology, 736, 81-94. https://doi.org/10.1007/978-1-4419-7210-1_4

Madsen, B. E., Villesen, P. & Wiuf, C. (2008). Short tandem repeats in human exons: a target for disease mutations. B M C Genomics, 9, 410. https://doi.org/10.1186/1471-2164-9-410

Madsen, B. E., Villesen, P. & Wiuf, C. (2010). Short tandem repeats and genetic variation. Methods in Molecular Biology, 628, 297-306. https://doi.org/10.1007/978-1-60327-367-1_16

Villesen, P., Madsen, B. E. & Wiuf, C. H. (2008). Short Tandem Repeats in Human Exons: A Target for Disease Mutations. Poster session presented at Frontiers in genomics, Denmark.

Thomsen, A. H., Hougen, H. P., Villesen, P., Brink, O. & Leth, P. M. (2020). Sharp Force Homicide in Denmark 1992-2016. Journal of Forensic Sciences, 65(3), 833-839. https://doi.org/10.1111/1556-4029.14244

Munn-Chernoff, M. A., Johnson, E. C., Chou, Y-L., Coleman, J. R. I., Thornton, L. M., Walters, R. K., Yilmaz, Z., Baker, J. H., Hübel, C., Gordon, S., Medland, S. E., Watson, H. J., Gaspar, H. A., Bryois, J., Hinney, A., Leppä, V. M., Mattheisen, M., Ripke, S., Yao, S. ... Agrawal, A. (2021). Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies. Addiction Biology, 26(1), [e12880]. https://doi.org/10.1111/adb.12880

Donelly, P. & Wiuf, C. (1999). Shared chromosomal segments and genome-wide association mapping.

Blokland, G. A. M., Grove, J., Chen, C. Y., Cotsapas, C., Tobet, S., Handa, R., Schizophrenia Working Group of the Psychiatric Genomics Consortium, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Sex Differences Cross-Disorder Analysis Group of the Psychiatric Genomics Consortium & iPSYCH (2022). Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders. Biological Psychiatry, 91(1), 102-117. https://doi.org/10.1016/j.biopsych.2021.02.972

Ehlers, B., Maurice, S. & Bataillon, T. (2005). Sex inheritance in gynodioecious species: a polygenic view. Royal Society of London. Proceedings. Biological Sciences, 272, 1795 - 1802.

Li, C. H., Prokopec, S. D., Sun, R. X., Yousif, F., Schmitz, N., PCAWG Tumour Subtypes and Clinical Translation, Boutros, P. C. & PCAWG Consortium (2020). Sex differences in oncogenic mutational processes. Nature Communications, 11, [4330]. https://doi.org/10.1038/s41467-020-17359-2

Maretty, L., Jensen, J. M., Petersen, B., Sibbesen, J. A., Liu, S., Villesen, P., Skov, L., Belling, K. C., Theil Have, C., Izarzugaza, J. M. G., Grosjean, M., Bork-Jensen, J., Grove, J., Als, T. D., Huang, S., Chang, Y., Xu, R., Ye, W., Rao, J. ... Schierup, M. H. (2017). Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature, 548, 87-91. https://doi.org/10.1038/nature23264

Christensen, S., Schöller, S., Schierup, M. H., Vestergaard, B. F. & Mordhorst, C. H. (2002). Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains. Acta Pathologica Microbiologica et Immunologica Scandinavica, 110, 113-122.

Mailund (2000). Separation of style and content with XML in an interchange format for high-level Petri nets. In Proceedings on the XML/SGML based interchange formats for Petri nets (pp. 7-12)

Østergaard, S. D., Dinesen, P. T. & Foldager, L. (2011). Sensitivity x PPV is a recognized test called the clinical utility index (CUI+). The Authors Reply. European Journal of Epidemiology, 26, 252-252. https://doi.org/10.1007/s10654-011-9561-x

Jakobsen, H. J., Brorson, M., Bildsøe, H. K., Skibsted, J. & Hansen, M. R. (2008). Sensitivity Enhancement in Natural-Abundance Solid-State ³³S MAS NMR Spectroscopy Employing Adiabatic Inversion Pulses to the Satellite Transitions. Poster session presented at 49th Experimental NMR Conference (ENC), Asilomar, California, United States.

Jakobsen, H. J., Brorson, M., Bildsøe, H. K., Skibsted, J. & Hansen, M. R. (2008). Sensitivity Enhancement in Natural Abundance Solid-State ³³S MAS NMR Spectroscopy Employing Adiabatic Inversion Pulses to the Satellite Transitions. Abstract from 49^th Experimental NMR Conference, Asilomar, Pacific Grove, California, United States.

Munch, K., Nam, K., Schierup, M. H. & Mailund, T. (2016). Selective sweeps across twenty millions years of primate evolution. Molecular Biology and Evolution, 33(12), 3065-3074. https://doi.org/10.1093/molbev/msw199

Kuderna, L. F. K., Lizano, E., Julia, E., Gomez-Garrido, J., Serres-Armero, A., Kuhlwilm, M., Alandes, R. A., Alvarez-Estape, M., Juan, D., Simon, H., Alioto, T., Gut, M., Gut, I., Schierup, M. H., Fornas, O. & Marques-Bonet, T. (2019). Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nature Communications, 10(1), [4]. https://doi.org/10.1038/s41467-018-07885-5

Hartfield, M. & Bataillon, T. (2020). Selective Sweeps Under Dominance and Inbreeding. G3 (Bethesda, Md.), 10(3), 1063-1075. https://doi.org/10.1534/g3.119.400919

Paape, T., Bataillon, T., Zhou, P., J Y Kono, T., Briskine, R., Young, N. D. & Tiffin, P. (2013). Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Molecular Ecology, 22(13), 3525-3538. https://doi.org/10.1111/mec.12329

Christiansen, F. (1990). Selection in natural populations. In S. Lessard (Ed.), Mathematical and Statistical Developments of Evolutionary Theory (pp. 121-176). Kluwer Academic Publishers. NATO ASI Series

Christiansen, F. & Feldman, M. W. (1983). Selection in complex genetic systems V. Some properties of mixed selfing and random mating with two loci. Theoretical Population Biology, 23, 257-272.

Siegismund, H. & Christiansen, F. (1985). Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, III. Theoretical Population Biology, 27, 268–297.

Østergaard, H. & Christiansen, F. (1981). Selection component analysis of natural polymorphisms using population samples including mother-offspring combinations, II. Theoretical Population Biology, 19, 378-419.

Schierup, M. H., Bechsgaard, J. S., Nielsen, L. H. & Christiansen, F. B. (2006). Selection at work in self-incompatible Arabidopsis lyrata: Mating patterns in a natural population. Genetics, 172, 477-484.

Schierup, M. H., Bechsgaard, J. S. & Christiansen, F. B. (2008). Selection at work in self-incompatible Arabidopsis lyrata. II. Spatial distribution of S haplotypes in Iceland. Genetics, 180(2), 1051-9. https://doi.org/10.1534/genetics.108.088799

Christiansen, F. (1985). Selection and population regulation with habitat variation. American Naturalist, 126.

Christiansen, F. (1985). Selection and population regulation with habitat variation. American Naturalist, 126, 418-429.

Hauberg, M. E., Holm-Nielsen, M. H., Mattheisen, M., Askou, A. L., Grove, J., Børglum, A. D. & Corydon, T. J. (2016). Schizophrenia risk variants affecting microRNA function and site-specific regulation of NT5C2 by miR-206. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology, 26(9), 1522-6. https://doi.org/10.1016/j.euroneuro.2016.06.014

Foldager, L., Steffensen, R. N., Thiel, S., Als, T. D., Kristensen, A. S., Straarup, S., Nielsen, H. J., Nordentoft, M., Mortensen, P. B., Rosenberg, R., Mors, O. & Jensenius, J. C. (2008). Schizophrenia and innate immune defense: association study of mannan-bindinglectin (MBL) and MBL-associated serine proteases-2 (MASP-2) deficiency. In WCPG 2008 Abstract Book (pp. 225)

Christensen, O. F., Roberts, G. & Rosenthal, J. (2005). Scaling limits for the transient phase of local Metropolis-Hastings algorithms. Journal of the Royal Statistical Society, Series B, 67, 253-268.

Møllegaard Friborg, R., Bjørndalen, J. M. & Vinter, B. (2013). Scaling PyCSP. Paper presented at Communicating Process Architectures 2013, Edinburgh, United Kingdom.

Stumpf, MPH. & Wiuf, C. (2005). Sampling properties of random graphs: The degree distribution. Physical Review E, 72(036118), 1-7.

Hobolth, A. & Jeff, T. (2014). Sampling and summary statistics of endpoint-conditioned paths in DNA sequence evolution. In M-H. Chen, L. Kuo & P. O. Lewis (Eds.), Bayesian Phylogenetics: Methods, Algorithms, and Applications (1 ed., Vol. 1). CRC Press.

Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M. H. & Wang, J. (2013). SOAPindel: efficient identiﬁcation of indels from short paired reads. Genome Research, 23(1), 195-200. https://doi.org/10.1101/gr.132480.111

Lindgreen, S., Krogh, A. & Pedersen, J. S. (2014). SNPest: a probabilistic graphical model for estimating genotypes. BMC Research Notes, 7, 698. https://doi.org/10.1186/1756-0500-7-698

Nielsen, J. & Mailund, T. (2008). SNPFile - A software library and file format for large scale association mapping and population genetics studies. B M C Bioinformatics, 9(526), 1-11. https://doi.org/10.1186/1471-2105-9-526

Sükösd, Z., Andersen, E. S. & Lyngsø, R. (2014). SCFGs in RNA secondary structure prediction: a hands-on approach. Methods in Molecular Biology, 1097, 143-62. https://doi.org/10.1007/978-1-62703-709-9__8, https://doi.org/10.1007/978-1-62703-709-9_8

Bolvig, A. K., Nørskov, N., van Vliet, S., Foldager, L., Curtasu, M. V., Hedemann, M. S., Sørensen, J. F., Lærke, H. N. & Knudsen, K. E. B. (2017). Rye bran modified with cell wall-degrading enzymes influences the kinetics of plant lignans but not of enterolignans in multicatheterized pigs. Journal of Nutrition, 147(12), 2220-2227 . https://doi.org/10.3945/jn.117.258483

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Palle Villesen