Publications

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Anciaux, Y., Lambert, A., Ronce, O., Roques, L. & Martin, G. (2019). Population persistence under high mutation rate: From evolutionary rescue to lethal mutagenesis. Evolution, 73(8), 1517-1532. https://doi.org/10.1111/evo.13771

Castellano, D. & Munch, K. (2020). Population Genomics in the Great Apes. In J. Y. Dutheil (Ed.), Methods in Molecular Biology (pp. 453-463). Springer. https://doi.org/10.1007/978-1-0716-0199-0_19

Feldman, M. & Christiansen, F. (1984). Population genetic theory of the cost of inbreeding. American Naturalist, 123, 642–653.

Christiansen, FB. (2006). Population Genetics with a view towards Bioinformatics. Lecture Notes in Population Genetics. Eget.

Christiansen, F. B. (2005). Population Genetics with a view towards Bioinformatics. Lecture Notes in Molecular Population Genetics. Eget.

Feldman, M. W., Otto, S. P. & Christiansen, F. (1996). Population genetic perspectives on the evolution of recombination. Annual Review of Genetics, 49, 261-295.

Christiansen, F. (1990). Population consequences of genetic design in sexually reproducing organisms. In H. Mooney & G. Bernardi (Eds.), Introduction of Genetically Modified Organisms into the Environment (pp. 43-55). John Wiley & Sons Ltd.

Chalmer, M. A., Kogelman, L. J. A., Ullum, H., Sørensen, E., Didriksen, M., Mikkelsen, S., Dinh, K. M., Brodersen, T., Nielsen, K. R., Bruun, M. T., Banasik, K., Brunak, S., Erikstrup, C., Pedersen, O. B., Ostrowski, S. R., Olesen, J. & Hansen, T. F. (2023). Population-Based Characterization of Menstrual Migraine and Proposed Diagnostic Criteria. JAMA Network Open, 6(5), e2313235. Article e2313235. https://doi.org/10.1001/jamanetworkopen.2023.13235

Qian, Y., Kehr, B. & Halldorsson, B. V. (2015). PopAlu: population-scale detection of Alu polymorphisms. PeerJ, 3, Article 1269. https://doi.org/10.7717/peerj.1269

Weiner, D. J., Wigdor, E. M., Ripke, S., Walters, R. K., Kosmicki, J. A., Grove, J., Samocha, K. E., Goldstein, J. I., Okbay, A., Bybjerg-Grauholm, J., Werge, T., Hougaard, D. M., Taylor, J., Skuse, D., Devlin, B., Anney, R., Sanders, S. J., Bishop, S., Mortensen, P. B. ... iPSYCH-Broad Autism Group (2017). Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nature Genetics, 49(7), 978-985. https://doi.org/10.1038/ng.3863

Ding, Y., Hou, K., Xu, Z., Pimplaskar, A., Petter, E., Boulier, K., Privé, F., Vilhjálmsson, B. J., Olde Loohuis, L. M. & Pasaniuc, B. (2023). Polygenic scoring accuracy varies across the genetic ancestry continuum. Nature, 618, 774-781. https://doi.org/10.1038/s41586-023-06079-4

Gholipourshahraki, T., Ejlskov, L., Semark, B. D., Maseras, G. T., Steinbach, J., Hansen, O. S., Pedersen, C. B., Bulik, C. M., Benros, M. E., Mortensen, P. B., Agerbo, E., Petersen, L. V. & Vilhjálmsson, B. J. (2025). Polygenic Scores and Environmental Factors in Psychiatric Disorders: Gene-Environment Interaction Analyses Using the iPSYCH Study. Research Square. https://doi.org/10.21203/rs.3.rs-8201911/v1

Hayeck, T. J., Busby, G. B., Chun, S., Lewis, A. C. F., Roberts, M. C. & Vilhjálmsson, B. J. (2023). Polygenic Risk Scores: Genomes to Risk Prediction. Clinical Chemistry, 69(6), 551–557. https://doi.org/10.1093/clinchem/hvad049

Henches, L., Kim, J., Yang, Z., Rubinacci, S., Pires, G., Albiñana, C., Boetto, C., Julienne, H., Frouin, A., Auvergne, A., Suzuki, Y., Djebali, S., Delaneau, O., Ganna, A., Vilhjálmsson, B., Privé, F. & Aschard, H. (2025). Polygenic risk score prediction accuracy convergence. Human Genetics and Genomics Advances, 6(3), Article 100457. https://doi.org/10.1016/j.xhgg.2025.100457

Agerbo, E., Sullivan, P. F., Vilhjálmsson, B. J., Pedersen, C. B., Mors, O., Børglum, A. D., Hougaard, D. M., Hollegaard, M. V., Meier, S., Mattheisen, M., Ripke, S., Wray, N. R. & Mortensen, P. B. (2015). Polygenic Risk Score, Parental Socioeconomic Status, Family History of Psychiatric Disorders, and the Risk for Schizophrenia: A Danish Population-Based Study and Meta-analysis. JAMA Psychiatry. https://doi.org/10.1001/jamapsychiatry.2015.0346

Wang, X., Walker, A., Revez, J. A., Ni, G., Adams, M. J., McIntosh, A. M. & Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2023). Polygenic risk prediction: why and when out-of-sample prediction R² can exceed SNP-based heritability. American Journal of Human Genetics, 110(7), 1207-1215. https://doi.org/10.1016/j.ajhg.2023.06.006

Jefsen, O. H., Holde, K., McGrath, J. J., Rajagopal, V. M., Albiñana, C., Vilhjálmsson, B. J., Grove, J., Agerbo, E., Yilmaz, Z., Plana-Ripoll, O., Munk-Olsen, T., Demontis, D., Børglum, A., Mors, O., Bulik, C. M., Mortensen, P. B. & Petersen, L. V. (2024). Polygenic risk of mental disorders and subject-specific school grades. Biological Psychiatry, 96(3), 222-229. https://doi.org/10.1016/j.biopsych.2023.11.020

Smit, R. A. J., Wade, K. H., Hui, Q., Arias, J. D., Yin, X., Christiansen, M. R., Yengo, L., Preuss, M. H., Nakabuye, M., Rocheleau, G., Graham, S. E., Buchanan, V. L., Chittoor, G., Graff, M., Guindo-Martínez, M., Lu, Y., Marouli, E., Sakaue, S., Spracklen, C. N. ... VA Million Veteran Program (2025). Polygenic prediction of body mass index and obesity through the life course and across ancestries. Nature Medicine, 31(9), 3151-3168. https://doi.org/10.1038/s41591-025-03827-z

Musliner, K. L., Andersen, K. K., Agerbo, E., Albiñana, C., Vilhjalmsson, B. J., Rajagopal, V. M., Bybjerg-Grauholm, J., Bækved-Hansen, M., Pedersen, C. B., Pedersen, M. G., Munk-Olsen, T., Benros, M. E., Als, T. D., Grove, J., Werge, T., Børglum, A. D., Hougaard, D. M., Mors, O., Nordentoft, M. ... Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (2023). Polygenic liability, stressful life events and risk for secondary-treated depression in early life: a nationwide register-based case-cohort study. Psychological Medicine, 53(1), 217-226. https://doi.org/10.1017/S0033291721001410

Mundy, J., Hall, A. S. M., Steinbach, J., Albinaña, C., Agerbo, E., Als, T. D., Thapar, A., McGrath, J. J., Vilhjálmsson, B. J., Nordentoft, M., Werge, T., Børglum, A., Mortensen, P. B. & Musliner, K. L. (2024). Polygenic liabilities and treatment trajectories in early-onset depression: a Danish register-based study. Psychological Medicine, 54(14), 3828-3837. https://doi.org/10.1017/S0033291724002186

Tataru, P. & Bataillon, T. (2019). polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species. Bioinformatics (Oxford, England), 35(16), 2868-2869. https://doi.org/10.1093/bioinformatics/bty1060

Tataru, P. & Bataillon, T. (2020). polyDFE: Inferring the distribution of fitness effects and properties of beneficial mutations from polymorphism data. In J. Y. Dutheil (Ed.), Statistical population genomics (pp. 125-146). Humana Press. https://doi.org/10.1007/978-1-0716-0199-0_6

Miller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., Kim, H. L., Burhans, R. C., Drautz, D. I., Wittekindt, N. E., Tomsho, L. P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G. K., Rode, K., Obbard, M., Montiel, R. ... Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proceedings of the National Academy of Sciences (PNAS). https://doi.org/10.1073/pnas.1210506109

Christiansen, F. (1987). Pleiotropy in dynamical parameters of models on the evolution of simple phenotypes. In V. Loeschcke (Ed.), Genetic Constraints on Adaptive Evolution (pp. 107-124). Springer.

Dalby, R. B., Elfving, B., Poulsen, P. H. P., Foldager, L., Frandsen, J., Videbech, P. & Rosenberg, R. (2013). Plasma brain-derived neurotrophic factor and prefrontal white matter integrity in late-onset depression and normal aging. Acta Psychiatrica Scandinavica, 128(5), 387-396. https://doi.org/10.1111/acps.12085

Świtnicki, M. P., Rasmussen, M. J., Madsen, T., Sørensen, K. D. & Pedersen, J. S. (2016). PINCAGE: Probabilistic integration of cancer genomics data for perturbed gene identification and sample classification. Bioinformatics, 32(9), 1353-1365. https://doi.org/10.1093/bioinformatics/btv758

Wernersson, R., Schierup, M. H., Jørgensen, F. G., Gorodkin, J., Panitz, F., Staerfeldt, HH., Christensen, O. F., Mailund, T., Hornshøj, H., Klein, A., Jun, W., Liu, B., Hu, S., Dong, W., Li, W., Wong, GK.-S., Yu, J., Wang, J., Bendixen, C. ... Bolund, L. (2005). Pigs in Sequence Space: A 0.66X Coverage Pig Genome Survey based on Shotgun Sequencing. BMC Genomics, 6(70). http://www.biomedcentral.com/1471-2164/6/70

Coutant, M. P., Malmkvist, J., Kaiser, M. Ø., Foldager, L. & Herskin, M. S. (2022). Piglets' acute responses to procaine-based local anesthetic injection and surgical castration: Effects of two volumes of anesthetic. Frontiers in Pain Research, 3, Article 943138. https://doi.org/10.3389/fpain.2022.943138

Coutant, M., Malmkvist, J., Kaiser, M., Foldager, L. & Herskin, M. S. (2022). Piglets' acute responses to local anesthetic injection and surgical castration: Effects of the injection method and interval between injection and castration. Frontiers in Veterinary Science, 9, Article 1009858. https://doi.org/10.3389/fvets.2022.1009858

Kobek-Kjeldager, C., Jensen, L. D., Foldager, L., Kaiser, M., Thodberg, K. & Herskin, M. S. (2025). Pig behaviour during transit – welfare hazards in assembly centres. In Proceedings of the 58th CONGRESS OF THE ISAE (pp. 137) https://isae2025utrecht.nl/wp-content/uploads/2025/08/ISAE_Proceedings_6aug.pdf

Mikalsen, S.-O., Tausen, M. & Kongsstovu, S. I. (2020). Phylogeny of teleost connexins reveals highly inconsistent intra- and interspecies use of nomenclature and misassemblies in recent teleost chromosome assemblies. BMC Genomics, 21(1), Article 223. https://doi.org/10.1186/s12864-020-6620-2

Shao, Y., Zhou, L., Li, F., Zhao, L., Zhang, B. L., Shao, F., Chen, J. W., Chen, C. Y., Bi, X., Zhuang, X. L., Zhu, H. L., Hu, J., Sun, Z., Li, X., Wang, D., Rivas-González, I., Wang, S., Wang, Y. M., Chen, W. ... Wu, D. D. (2023). Phylogenomic analyses provide insights into primate evolution. Science (New York, N.Y.), 380(6648), 913-924. https://doi.org/10.1126/science.abn6919

Fredslund, J. (2006). PHY∙FI: fast and easy online creation and manipulation of phylogeny color figures. BMC Bioinformatics, 7(315). https://doi.org/10.1186/1471-2105-7-315

Rolland, T., Cliquet, F., Anney, R. J. L., Moreau, C., Traut, N., Mathieu, A., Huguet, G., Duan, J., Warrier, V., Portalier, S., Dry, L., Leblond, C. S., Douard, E., Amsellem, F., Malesys, S., Maruani, A., Toro, R., Børglum, A. D., Grove, J. ... Bourgeron, T. (2023). Phenotypic effects of genetic variants associated with autism. Nature Medicine, 29(7), 1671-1680. https://doi.org/10.1038/s41591-023-02408-2

iPSYCH Consortium (2024). Phenotypic and ancestry-related assortative mating in autism. Molecular Autism, 15(1), 27. Article 27. https://doi.org/10.1186/s13229-024-00605-5

Zheng, J., Richardson, T. G., Millard, L. A. C., Hemani, G., Elsworth, B. L., Raistrick, C. A., Vilhjalmsson, B., Neale, B. M., Haycock, P. C., Smith, G. D. & Gaunt, T. R. (2018). PhenoSpD: an integrated toolkit for phenotypic correlation estimation and multiple testing correction using GWAS summary statistics. GigaScience, 7(8), 1-10. https://doi.org/10.1093/gigascience/giy090

Kresge, H. A., Blostein, F., Goleva, S., Albiñana, C., Revez, J. A., Wray, N. R., Vilhjálmsson, B. J., Zhu, Z., McGrath, J. J. & Davis, L. K. (2024). Phenomewide Association Study of Health Outcomes Associated With the Genetic Correlates of 25 Hydroxyvitamin D Concentration and Vitamin D Binding Protein Concentration. Twin Research and Human Genetics, 27(2), 69-79. https://doi.org/10.1017/thg.2024.19

Rivas-González, I., Andersen, L. N. & Hobolth, A. (2023). PhaseTypeR: an R package for phase-type distributions in population genetics. The Journal of Open Source Software, 8(82). https://doi.org/10.21105/joss.05054

Hobolth, A., Rivas-González, I., Bladt, M. & Futschik, A. (2024). Phase-type distributions in mathematical population genetics: An emerging framework. Theoretical Population Biology, 157, 14-32. https://doi.org/10.1016/j.tpb.2024.03.001

Sendrowski, J. & Hobolth, A. (2026). PhaseGen: exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies. Genetics, 232(1), Article iyaf135. https://doi.org/10.1093/genetics/iyaf135

Rivas-González, I., Rousselle, M., Li, F., Zhou, L., Dutheil, J. Y., Munch, K., Shao, Y., Wu, D., Schierup, M. H. & Zhang, G. (2023). Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science, 380(6648), eabn4409. Article eabn4409. https://doi.org/10.1126/science.abn4409

Watkins, T. B. K., Lim, E. L., Petkovic, M., Elizalde, S., Birkbak, N. J., Wilson, G. A., Moore, D. A., Grönroos, E., Rowan, A., Dewhurst, S. M., Demeulemeester, J., Dentro, S. C., Horswell, S., Au, L., Haase, K., Escudero, M., Rosenthal, R., Bakir, M. A., Xu, H. ... Swanton, C. (2020). Pervasive chromosomal instability and karyotype order in tumour evolution. Nature, 587, 126-132. https://doi.org/10.1038/s41586-020-2698-6

Andreasen, V. & Christiansen, F. (1989). Persistence of an infectious disease in a subdivided population. Mathematical Biosciences, 96, 239-253.

Krogh, U., Højberg, O., Foldager, L., Rani, S., Nørskov, N. P. & Sørensen, M. T. (2021). Performance and mineral status of weaning pigs fed diets with different levels of glyphosate and tryptophan. Livestock Science, 252, Article 104681. https://doi.org/10.1016/j.livsci.2021.104681

Carlsvig, A. D., Foldager, L., Steenfeldt, S., Højberg, O., Nørskov, N. & Sørensen, M. T. (2022). Performance and mineral status of laying hens fed diets with different levels of glyphosate. Livestock Science, 264, Article 105046. https://doi.org/10.1016/j.livsci.2022.105046

Thøgersen, L., Schiøtt, B., Vosegaard, T., Nielsen, N. C. & Tajkhorshid, E. (2008). Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study. Biophysical Journal, 95(9), 4337-4347. https://doi.org/10.1529/biophysj.108.133330

Jimenez Mena, B., Schad, K., Hanna, N. & Lacy, R. C. (2016). Pedigree analysis for the genetic management of group-living species. Ecology and Evolution, 6(10), 3067-3078. https://doi.org/10.1002/ece3.1831

Villesen, P. & Boomsma, JJ. (2003). Patterns of male parentage in the fungus-growing ants. Behavioral Ecology and Sociobiology, 53(4), 246-253.

Glémin, S., Ronfort, J. & Bataillon, T. (2003). Patterns of inbreeding depression and architecture of the load in subdivided populations. Genetics, 165(4), 2193-212.

Mollion, M., Ehlers, B., Figuet, E., Santoni, S., Lenormand, T., Maurice, S., Galtier, N. & Bataillon, T. (2018). Patterns of genome-wide nucleotide diversity in the gynodioecious plant Thymus vulgaris are compatible with recent sweeps of cytoplasmic genes. Genome Biology and Evolution, 10(1), 239-248. https://doi.org/10.1093/gbe/evx272

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Palle Villesen