Publications

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Sand, A., Brask, A. T., Pedersen, C. N. S., Mailund, T. & Brask, A. T. (2010). HMMlib: A C++ Library for General Hidden Markov Models Exploiting Modern CPUs. In 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification and Second International Workshop on High Performance Computational Systems Biology (pp. 126 - 134 ). IEEE.

Duch, M. R., Pedersen, F. S., Bahrami, S., Villesen, P., Wiuf, C. H., Østergaard, L. J. & Tolstrup, M. (2010). HIV-1 envelope polypeptides for HIV vaccine. (Patent No. WO2010022740).

Ahdidan, J., Foldager, L., Rosenberg, R., Rodell, A., Videbech, P. & Mors, O. (2013). Hippocampal volume and serotonin transporter polymorphism in major depressive disorder. Acta Neuropsychiatrica, 25(4), 206-214. https://doi.org/10.1017/neu.2013.3

Wiechec, E., Wiuf, C., Overgaard, J. & Hansen, L. L. (2011). High-resolution melting analysis for mutation screening of RGSL1, RGS16, and RGS8 in breast cancer. Cancer Epidemiology, Biomarkers & Prevention, 20(2), 397-407. https://doi.org/10.1158/1055-9965.EPI-10-0514

Shah, N., Hirakawa, H., Kusakabe, S., Sandal, N., Stougaard, J., Schierup, M. H., Sato, S. & Andersen, S. U. (2016). High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. D N A Research, 23(5), 487-494. https://doi.org/10.1093/dnares/dsw033

Martins, H. & Villesen, P. (2009). Highly improved dating of primate ERV integrations. Poster session presented at Frontiers of Retrovirology: Complex retroviruses, retroelements and their hosts, Montpellier, France. https://doi.org/10.1186/1742-4690-6-S2-P54

Meier, S. M., Agerbo, E., Maier, R., Pedersen, C. B., Lang, M., Grove, J., Hollegaard, M. V., Demontis, D., Trabjerg, B. B., Hjorthøj, C., Ripke, S., Degenhardt, F., Nöthen, M. M., Rujescu, D., Maier, W., Werge, T., Mors, O., Hougaard, D. M., Børglum, A. D. ... MooDS SCZ Consortium (2015). High loading of polygenic risk in cases with chronic schizophrenia. Molecular Psychiatry, 1-6. https://doi.org/10.1038/mp.2015.130

Thomsen, P. T., Capion, N. & Foldager, L. (2020). Higher odds of abortion in dairy cows hoof trimmed late in gestation. Research in Veterinary Science, 133, 1-3. https://doi.org/10.1016/j.rvsc.2020.08.016

Luo, Y., Li, J., Liu, Y., Lin, L., Du, Y., Li, S., Yang, H., Vajta, G., Callesen, H., Bolund, L. & Sørensen, C. B. (2011). High efficiency of BRCA1 knockout using rAAV-mediated gene targeting: developing a pig model for breast cancer. Transgenic Research, 20, 975-988. https://doi.org/10.1007/s11248-010-9472-8

Koed, K., Wiuf, C., Christensen, L. L., Wikman, F., Zieger, K., Jensen, K. M.-E., Maase, H. V. D. & Ørntoft, T. F. (2005). High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Research, 65(1), 34-45.

Radel, D., Sand, A. & Steel, M. (2013). Hide and seek: placing and finding an optimal tree for thousands of homoplasy-rich sequences. Molecular Phylogenetics and Evolution, 69(3), 1186–1189. https://doi.org/10.1016/j.ympev.2013.08.001

Jimenez Mena, B., Hospital, F. & Bataillon, T. (2016). Heterogeneity of effective population size and its implications in conservation genetics and animal breeding. Conservation Genetics Resources, 8(1), 35-41. https://doi.org/10.1007/s12686-015-0508-5

Jørgensen, F. G., Schierup, M. H. & Clark, A. G. (2006). 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. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msl190

Jørgensen, F. G., Schierup, M. H. & Clark, A. G. (2007). 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. Molecular Biology and Evolution, 24(2), 611-619. https://doi.org/10.1093/molbev/msl190

Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P.-R., Lareau, C., Shoresh, N., Genovese, G., Saunders, A., Macosko, E., Pollack, S., Brainstorm Consortium, Perry, J. R. B., Buenrostro, J. D., Bernstein, B. E., Raychaudhuri, S. ... Price, A. L. (2018). Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature Genetics, 50(4), 621-629. https://doi.org/10.1038/s41588-018-0081-4

Cheng, Z., Ferris, C., Crowe, M. A., Ingvartsen, K. L., Grelet, C., Vanlierde, A., Foldager, L., Becker, F., Wathes, D. C. & GplusE Consortium (2023). Hepatic global transcriptomic profiles of Holstein cows according to parity reveal age-related changes in early lactation. International Journal of Molecular Sciences , 24(12), Article 9906. https://doi.org/10.3390/ijms24129906

Polekhina, G., Thirup, S., Kjeldgaard, M., Nissen, P., Lippmann, C. & Nyborg, J. (1996). Helix unwinding in the effector region of elongation factor EF-Tu-GDP. Structure, 4(10), 1141-51.

Kaiser, M., Foldager, L. & Herskin, M. S. (2023). Height relative to body weight in nursery pigs. Journal of Animal Science, 101, 1-9. Article skad123. https://doi.org/10.1093/jas/skad123

Jespersen, A., Yilmaz, Z. & Vilhjálmsson, B. J. (2022). Harnessing the Power of Population Cohorts to Study the Relationship Between Endocrine-Metabolic Disorders and Depression. The American Journal of Psychiatry (Spanish Edition), 179(11), 788-790. https://doi.org/10.1176/appi.ajp.20220798

Fechete, L. I., Larking, A. C., Heslop, A., Hannaford, R., Anderson, C. B., Hong, W., Prakash, S., Mace, W., Alikhani, S., Hofmann, R. W., Tausen, M., Schierup, M. H., Andersen, S. U. & Griffiths, A. G. (2024). Harnessing cold adaptation for postglacial colonisation: Galactinol synthase expression and raffinose accumulation in a polyploid and its progenitors. Plant, Cell & Environment, 47(10), 4014-4030. https://doi.org/10.1111/pce.15009

Charlesworth, D., Bartolomé, C., Schierup, M. H. & Mable, B. K. (2003). Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol. Biol. Evol., 20(11), 1741-1753.

Schierup, M. H., Mailund, T., Li, H., Wang, J., Tjønneland, A., Vogel, U., Bolund, L. & Nexø, B. A. (2009). Haplotype frequencies in a sub-region of chromosome 19q13.3, related to risk and prognosis of cancer, differ dramatically between ethnic groups. BMC Medical Genetics, 10, 20. https://doi.org/10.1186/1471-2350-10-20

Foldager, L., Lindgren, S. D., Gebreyesus, G. & Thodberg, K. (2026). Halevækst for ukuperede og kuperede svin fra fødsel til slagt: var den kuperet kortere end lovgivningen tillader? In P. Linde (Ed.), Symposium i Anvendt Statistik 2026 (pp. 184-193). Fødevare- og Ressourceøkonomisk Institut, Københavns Universitet & Symposium i Anvendt Statistik.

Grove, J., Børglum, A. & Pearce, B. D. (2014). GWAS, Cytomegalovirus Infection, and Schizophrenia. Current Behavioral Neuroscience Reports, 1(4), 215-223. https://doi.org/10.1007/s40473-014-0022-1

Thomsen, A. H., Leth, P. M., Hougen, H. P. & Villesen, P. (2021). Gunshot homicides in Denmark 1992-2016. International Journal of Legal Medicine (Online), 135(4), 1507-1514. https://doi.org/10.1007/s00414-021-02548-5

Swenson, M. S., Anderson, J., Ash, A., Gaurav, P., Sükösd, Z., Bader, D. A., Harvey, S. C. & Heitsch, C. E. (2012). GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops. BMC Research Notes, 5(341). https://doi.org/10.1186/1756-0500-5-341

Haudry, A., Cenci, A., Ravel, C., Bataillon, T., Brunel, D., Poncet, C., Hochu, I., Poirier, S., Santoni, S., Glemin, S. & David, J. (2007). Grinding up Wheat: a Massive Loss of Nucleotide Diversity Since Domestication. Molecular Biology and Evolution, 24(7), 1506-1517. https://doi.org/10.1093/molbev/msm077

Tausen, M., Clausen, M. M., Moeskjær, S., Shihavuddin, ASM., Dahl, A. B., Janss, L. & Andersen, S. U. (2020). Greenotyper: Image-based plant phenotyping using distributed computing and deep learning. Frontiers in Plant Science, 11, Article 1181. https://doi.org/10.3389/fpls.2020.01181

Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O'Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J. ... Marques-Bonet, T. (2013). Great ape genetic diversity and population history. Nature, 499, 471–475. https://doi.org/10.1038/nature12228

Røikjer, T., Hobolth, A. & Munch, K. (2022). Graph-based algorithms for phase-type distributions. Statistics and Computing, 32(6), Article 103. https://doi.org/10.1007/s11222-022-10174-3

Ernst, E. H., Franks, S., Hardy, K., Villesen, P. & Lykke-Hartmann, K. (2018). Granulosa cells from human primordial and primary follicles show differential global gene expression profiles. Human Reproduction, 33(4), 666-679. https://doi.org/10.1093/humrep/dey011

Simonsen, M., Thomsen, R., Christensen, M. H. & Pedersen, C. N. S. (2011). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In GECCO'11 Proceedings of the 13th annual conference on Genetic and evolutionary computation (pp. 1803-1810). Association for Computing Machinery. https://doi.org/10.1145/2001576.2001818

Simonsen, M., Christensen, M. H., Thomsen, R. & Pedersen, C. N. S. (2013). GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution. In S. tsutsui & P. Collet (Eds.), Massively Parallel Evolutionary Computation on GPGPUs Springer Publishing Company.

Gengler, N., Grelet, C., Soyeurt, H., Dehareng, F. & GplusE Consortium (2019). GplusE: Mid-infrared milk analysis based technologies adding value to gene banks. In Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science (Vol. 25, pp. 443). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-890-2

Cheng, Z., Buggiotti, L., Salavati, M., Marchitelli, C., Palma-Vera, S., Wylie, A., Takeda, H., Tang, L., Crowe, M. A., Wathes, D. C. & GplusE Consortium (2021). Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis. Molecular Biology Reports, 48, 4611-4623. https://doi.org/10.1007/s11033-021-06494-8

Mailund, T. (2006). Getting Started with HapCluster: An introduction to the HapCluster association mapping tool.

Mailund, T. & Schauser, L. (2006). Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon.

Mailund, T. (2005). Getting Started with CoaSim — An Introduction to the Simulator CoaSim.

Mailund, T. (2006). Getting Started with Blossoc. http://www.daimi.au.dk/~mailund/Blossoc/download/getting-started-1.1.pdf

Ernst, M., Rogers, S., Lausten-Thomsen, U., Bjorkbom, A., Laursen, S. S., Courraud, J., Borglum, A., Nordentoft, M., Werge, T., Mortensen, P. B., Hougaard, D. M. & Cohen, A. S. (2021). Gestational age-dependent development of the neonatal metabolome. Pediatric Research, 89(6), 1396-1404. https://doi.org/10.1038/s41390-020-01149-z

Madsen, B. E., Ramos, E. M., Boulard, M., Duda, K., Overgaard, J., Nordsmark, M., Wiuf, C. & Hansen, L. L. (2008). Germline mutation in RNASEL predicts increased risk of head and neck, uterine cervix and breast cancer. PLoS One, 3(6), e2492. https://doi.org/10.1371/journal.pone.0002492

Lamy, P., Andersen, C. L. & Wiuf, C. (2007). Genotyping and Annotation of Affymetrix SNP Probe Sets, presented at PhD Annual Day, Graduate School of Health, University of Aarhus.. Poster session presented at Genotyping and Annotation of Affymetrix SNP Probe Sets, presented at PhD Annual Day, Graduate School of Health, University of Aarhus..

Lamy, P., Andersen, C. L., Wikman, F. & Wiuf, C. (2006). Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Research, 34(14). https://doi.org/10.1093/nar/gkl475

Martínez-Ruiz, C., Black, J. R. M., Puttick, C., Hill, M. S., Demeulemeester, J., Larose Cadieux, E., Thol, K., Jones, T. P., Veeriah, S., Naceur-Lombardelli, C., Toncheva, A., Prymas, P., Rowan, A., Ward, S., Cubitt, L., Athanasopoulou, F., Pich, O., Karasaki, T., Moore, D. A. ... TRACERx Consortium (2023). Genomic-transcriptomic evolution in lung cancer and metastasis. Nature, 616(7957), 543-552. https://doi.org/10.1038/s41586-023-05706-4

Hübel, C., Gaspar, H. A., Coleman, J. R. I., Finucane, H., Purves, K. L., Hanscombe, K. B., Prokopenko, I., Graff, M., Ngwa, J. S., Workalemahu, T., O'Reilly, P. F., Bulik, C. M., Breen, G., Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Tourette Syndrome/Obsessive-Compulsive Disorder Working Group of the Psychiatric Genomics Consortium, MAGIC Investigators & Eating Disorders Working Group of the Psychiatric Genomics Consortium (2019). Genomics of body fat percentage may contribute to sex bias in anorexia nervosa. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 180(6), 428-438. https://doi.org/10.1002/ajmg.b.32709

Ma, J. (2024). Genomic Responses to Evolution of Sociality in Stegodyphus Spiders. [PhD dissertation, Aarhus University]. Aarhus Universitet.

Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. (2007). Genomic Relationships and Speciation Times of Human, Chimpanzee and Gorilla inferred from a Coalescent Hidden Markov Model. Poster session presented at Beyond the HapMap, Boston, United States.

Hobolth, A., Christensen, O. F., Mailund, T. & Schierup, M. H. (2007). Genomic relationships and speciation times of human, chimpanzee and gorilla inferred from a coalescent hidden Markov model. PLoS Genetics, 3(2). https://doi.org/10.1371/journal.pgen.0030007

Jacobsen, L. M. W., Pujolar, J. M., Bernatchez, L., Munch, K., Jian, J., Niu, Y. & Hansen, M. M. (2014). Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. Rostrata). Molecular Ecology, 23(19), 4785-4798. https://doi.org/10.1111/mec.12896

Slotte, T., Bataillon, T., Hansen, T. T., St Onge, K., Wright, S. I. & Schierup, M. H. (2011). Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biology and Evolution, 3, 1210-1219. https://doi.org/10.1093/gbe/evr094

Displaying results 751 to 800 out of 1417

Revised 13.01.2026

Palle Villesen