Publications

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W. Abdallah, M., Larsen, N., Grove, J., Bonefeld-Jørgensen, E. C., Nørgaard-Pedersen, B., M. Hougaard , D. & L. Mortensen, E. (2013). Neonatal chemokine levels and risk of autism spectrum disorders: Findings from a Danish historic birth cohort follow-up study. Cytokine, 61(2), 370–376. https://doi.org/10.1016/j.cyto.2012.11.015

Castellano, D., James, J. & Eyre-Walker, A. (2018). Nearly Neutral Evolution across the Drosophila melanogaster Genome. Molecular Biology and Evolution, 35(11), 2685-2694. https://doi.org/10.1093/molbev/msy164

Juul, M., Madsen, T., Guo, Q., Bertl, J., Hobolth, A., Kellis, M. & Pedersen, J. S. (2019). ncdDetect2: Improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. Bioinformatics, 35(2), 189-199. https://doi.org/10.1093/bioinformatics/bty511

Christiansen, F. B. (2016). Naturlig selektion. In K. Finster, T. Wang, F. Borchsenius & F. B. Christiansen (Eds.), Evolutionsbiologiske milepæle (pp. 20-39). Aarhus Universitetsforlag.

Hansen, M. C., Nyvold, C. G., Roug, A. S., Kjeldsen, E., Villesen, P., Nederby, L. & Hokland, P. (2015). Nature and nurture: a case of transcending haematological pre-malignancies in a pair of monozygotic twins adding possible clues on the pathogenesis of B-cell proliferations. British Journal of Haematology, 169(3), 391–400. https://doi.org/10.1111/bjh.13305

Subrahmaniam, H. J., Pico, X., Bataillon, T., Salomonsen, C. L., Glasius, M. & Ehlers, B. (2025). Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula. New Phytologist, 245(4), 1437-1449. https://doi.org/10.1111/nph.20314

Christiansen, F. (1984). Natural selection related to the biotic environment. In S. D. Jayakar & L. Zonta (Eds.), Evolution and the Genetics of Populations (Vol. XXIX, pp. 85–102).

Christiansen, F. (1990). Natural selection: Measures and modes. In Population Biology (pp. 27-74). Springer.

Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G. & Przeworski, M. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360(6389), 656-660. https://doi.org/10.1126/science.aar3684

Athanasiadis, G., Cheng, J. Y., Vilhjálmsson, B. J., Jørgensen, F. G., Als, T. D., Le Hellard, S., Espeseth, T., Sullivan, P. F., Hultman, C. M., Kjærgaard, P. C., Schierup, M. H. & Mailund, T. (2016). Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity. Genetics, 204(2), 711-722. https://doi.org/10.1534/genetics.116.189241

Sonntag, Y., Musgaard, M., Olesen, C., Schiøtt, B., Møller, J. V., Nissen, P. & Thøgersen, L. (2011). Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes. Nature Communications, 2, 304. https://doi.org/10.1038/ncomms1307

Rafnar, T., Gudbjartsson, D. F., Sulem, P., Jonasdottir, A., Sigurdsson, A., Jonasdottir, A., Besenbacher, S., Lundin, P., Stacey, S. N., Gudmundsson, J., Magnusson, O. T., le Roux, L., Orlygsdottir, G., Helgadottir, H. T., Johannsdottir, H., Gylfason, A., Tryggvadottir, L., Jonasson, J. G., de Juan, A. ... Stefansson, K. (2011). Mutations in BRIP1 confer high risk of ovarian cancer. Nature Genetics, 43(11), 1104-7. https://doi.org/10.1038/ng.955

Nordentoft, I. K., Lamy, P., Birkenkamp-Demtröder, K., Shumansky, K., Vang, S., Hornshøj, H., Juul, M., Villesen, P., Hedegaard, J., Roth, A., Thorsen, K., Høyer, S., Borre, M., Reinert, T., Fristrup, N., Dyrskjøt, L., Shah, S., Pedersen, J. S. & Ørntoft, T. F. (2014). Mutational context and diverse clonal development in early and late bladder cancer: Genomic changes in bladder cancer. Cell Reports, 7(5), 1649–1663. https://doi.org/10.1016/j.celrep.2014.04.038

Julienne, H., Laville, V., McCaw, Z. R., He, Z., Guillemot, V., Lasry, C., Ziyatdinov, A., Nerin, C., Vaysse, A., Lechat, P., Ménager, H., Le Goff, W., Dube, M.-P., Kraft, P., Ionita-Laza, I., Vilhjálmsson, B. J. & Aschard, H. (2021). Multitrait GWAS to connect disease variants and biological mechanisms. PLoS Genetics, 17(8), Article e1009713. https://doi.org/10.1371/journal.pgen.1009713

Goleva, S. B., Leu, C., Anne Feng, Y. C., Burstein, D., Venkatesh, S., Birnbaum, R., Rajagopal, V. M., Straub, P., Christensen, J., Bautista, J. F., Busch, R. M., Najm, I. M., Grove, J., Børglum, A. D., Voloudakis, G., Roussos, P., Smoller, J., Lal, D. & Davis, L. K. (2026). Multisite, Multiancestry Genome-Wide Association Study Meta-Analysis of Functional Seizure Disorder in a Hospital Sample of 675,680 Patients. Biological Psychiatry Global Open Science, 6(1), Article 100604. https://doi.org/10.1016/j.bpsgos.2025.100604

Albiñana, C., Zhu, Z., Schork, A. J., Ingason, A., Aschard, H., Brikell, I., Bulik, C. M., Petersen, L. V., Agerbo, E., Grove, J., Nordentoft, M., Hougaard, D. M., Werge, T., Børglum, A. D., Mortensen, P. B., McGrath, J. J., Neale, B. M., Privé, F. & Vilhjálmsson, B. J. (2023). Multi-PGS enhances polygenic prediction by combining 937 polygenic scores. Nature Communications, 14(1), Article 4702. https://doi.org/10.1038/s41467-023-40330-w

Justesen, P. & Ursem, R. K. (2009). Multiobjective Distinct Candidates Optimization (MODCO): A Cluster-Forming Differential Evolution Algorithm. In M. Ehrgott, C. Fonseca, X. Gandibleux, J.-K. Hao & M. Sevaux (Eds.), Evolutionary Multi-Criterion Optimization: 5th International Conference, EMO 2009. Nantes, France, April 2009. Proceedings (Vol. 5, pp. 525-539). Springer. https://doi.org/10.1007/978-3-642-01020-0_41

Keightley, P. D. & Bataillon, T. (2000). Multigeneration maximum-likelihood analysis applied to mutation-accumulation experiments in Caenorhabditis elegans. Genetics, 154(3), 1193-201.

Gouesnard, B., Bataillon, T., Decoux, G., Rozale, C., Schoen, D. J. & David, J. L. (2001). MSTRAT: an algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness. Journal of Heredity, 92(1), 93-4. https://doi.org/10.1093/jhered/92.1.93

Nielsen, M. M., Tataru, P., Madsen, T., Hobolth, A. & Pedersen, J. S. (2016). Motif discovery in ranked lists of sequences. (pp. 1-4). http://biorxiv.org/content/biorxiv/suppl/2016/01/11/035956.DC2/035956-1.pdf

Rydder, P. M., Andreasen, L., Thomsen, S. H., Jensen, U. B., Becher, N., Dunø, M. & Vogel, I. (2025). Mosaic STS gene deletions in chorionic villus samples are often confined to the placenta, and they differ in size from STS gene deletions in patients with X-linked Ichthyosis. Placenta, 165, 16-22. https://doi.org/10.1016/j.placenta.2025.03.016

Birkenkamp-Demtröder, K., Christensen, E., Nordentoft, I. K., Knudsen, M., Taber, A., Høyer, S., Lamy, P., Agerbæk, M., Jensen, J. B. & Dyrskjøt, L. (2018). Monitoring treatment response and metastatic relapse in advanced bladder cancer by liquid biopsy analysis. European Urology, 73(4), 535-540. https://doi.org/10.1016/j.eururo.2017.09.011

Thomsen, P. F., Kielgast, J., Iversen, L. L., Wiuf, C. H., Rasmussen, M., Gilbert, M. T. P., Orlando, L. A. A. & Willerslev, E. (2012). Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21(11), 2565-2573. https://doi.org/10.1111/j.1365-294X.2011.05418.x

Grivet, D., Sebastiani, F., Alía, R., Bataillon, T., Torre, S., Zabal-Aguirre, M., Vendramin, G. G. & González-Martínez, S. C. (2011). Molecular footprints of local adaptation in two Mediterranean conifers. Molecular Biology and Evolution, 28(1), 101-16. https://doi.org/10.1093/molbev/msq190

Castric, V., Bechsgaard, J. S., Grenier, S., Noureddine, R., Schierup, M. H. & Vekemans, X. (2010). Molecular evolution within and between self-incompatibility specificities. Molecular Biology and Evolution, 27(1), 11-20. https://doi.org/10.1093/molbev/msp224

De Mita, S., Santoni, S., Hochu, I., Ronfort, J. & Bataillon, T. (2006). Molecular evolution and positive selection of the symbiotic gene NORK in Medicago truncatula. Journal of Molecular Evolution, 62(2), 234-244.

Musgaard, M., Thøgersen, L. & Schiøtt, H. B. (2008). Molecular Dynamics Simulations of the E2 Form of the Ca²⁺-ATPase: Preliminary Results. Poster session presented at 12^th International ATPase Conference. Na,K-ATPase and Related Transport ATPases of P-type: Structures, Mechanisms, and Roles in Health and Disease, Aarhus, Denmark.

Lie, M. A., Thomsen, R., Pedersen, C. N. S., Schiøtt, B. & Christensen, M. H. (2011). Molecular Docking with Ligand Attached Water Molecules. Journal of Chemical Information and Modeling, 51(4), 909-917. https://doi.org/10.1021/ci100510m

Kraft, J. F., Lie, M. A. & Schiøtt, H. B. (2009). Molecular Docking Simulations: Improvement of methodologies for membrane proteins. Poster session presented at iNANO autumn school 2007.

De Mita, S., Chantret, N., Loridon, K., Ronfort, J. & Bataillon, T. (2011). Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula. BMC Evolutionary Biology, 11(1), 229-241. https://doi.org/10.1186/1471-2148-11-229

Tuni, C., Goodacre, S., Bechsgaard, J. S. & Bilde, T. (2012). Moderate multiple parentage and low genetic variation reduces the potential for genetic incompatibility avoidance despite high risk of inbreeding. PLoS One, 7(1), e29636. https://doi.org/10.1371/journal.pone.0029636

Agerbo, E., Mortensen, P. B., Wiuf, C., Pedersen, M. S., McGrath, J., Hollegaard, M. V., Nørgaard-Pedersen, B., Hougaard, D. M., Mors, O. & Pedersen, C. B. (2012). Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: A Danish national birth cohort-based study. Schizophrenia Research, 134(2-3), 246-52. https://doi.org/10.1016/j.schres.2011.10.025

Siuda, I. A. (2012). Modelling Protein Dynamics on the Microsecond Time Scale: Problems and Solutions. Aarhus University, Faculty of Science and Technology.

Kraft, J. F., Vestergaard, M., Schiøtt, B. & Thøgersen, L. (2012). Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations. Journal of Chemical Theory and Computation, 8(5), 1556–1569. https://doi.org/10.1021/ct200921u

Vilhjálmsson, B. J., Yang, J., Finucane, H. K., Gusev, A., Lindström, S., Ripke, S., Genovese, G., Loh, P.-R., Bhatia, G., Do, R., Hayeck, T., Won, H.-H., Kathiresan, S., Pato, M., Pato, C., Tamimi, R., Stahl, E., Zaitlen, N., Pasaniuc, B. ... Børglum, A. (2015). Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores. American Journal of Human Genetics, 97(4), 576-92. https://doi.org/10.1016/j.ajhg.2015.09.001

Knudsen, M. & Nielsen, R. (2009). Modeling cis- and trans-regulation in Drosophila species. In Tampere International Center for Signal Processing, TICSP Series 48 Tampere International Center for Signal Processing.

Ratmann, O., Andrieu, C., Wiuf, C. H. & Richardson, S. (2009). Model criticism based on likelihood-free inference: with an application to protein network evolution. Proceedings of the National Academy of Sciences (PNAS), 106, 10576-10581. https://doi.org/10.1073/pnas.0807882106

Hobor, S., Al Bakir, M., Hiley, C. T., Skrzypski, M., Frankell, A. M., Bakker, B., Watkins, T. B. K., Markovets, A., Dry, J. R., Brown, A. P., van der Aart, J., van den Bos, H., Spierings, D., Oukrif, D., Novelli, M., Chakrabarti, T., Rabinowitz, A. H., Ait Hassou, L., Litière, S. ... TRACERx Consortium (2024). Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nature Communications, 15(1), Article 4871. https://doi.org/10.1038/s41467-024-47606-9

Nielsen, M. M. & Pedersen, J. S. (2021). miRNA activity inferred from single cell mRNA expression. Scientific Reports, 11(1), Article 9170. https://doi.org/10.1038/s41598-021-88480-5

Rani, S., Sørensen, M. T., Noel, S. J., Nørskov, N., Krogh, U., Foldager, L. & Hojberg, O. (2022). Minor influence of feed glyphosate on gut microbial ecology of weaned piglets. In Book of Abstracts of the 73rd Annual Meeting of the European Federation of Animal Science (pp. 286-286). Wageningen Academic Publishers. https://doi.org/10.3920/978-90-8686-937-4

Buggiotti, L., Cheng, Z., Wathes, D. C., GplusE Consortium & Ingvartsen, K. L. (2020). Mining the unmapped reads in bovine RNA-Seq data reveals the prevalence of bovine herpes virus-6 in European dairy cows and the associated changes in their phenotype and leucocyte transcriptome. Viruses, 12(12), Article 1451. https://doi.org/10.3390/v12121451

Villesen, P., Eickhardt, E., Knudsen, B., Knudsen, B. R., Wiuf, C. H. & Andersen, F. F. (2010). Minimizing oligo sequence similarities for three dimensional DNA nanostructure assembly. Paper presented at Foundations of Nanosciences: Self-assembled Architectures and Devices, Snowbird, United States.

Gengler, N., Mineur, A., Vanderick, S., Hammami, H. & GplusE Consortium (2018). Milk mid-infrared spectra based biomarkers contributing to genetic improvement for udder health, fertility and longevity. In J. Bryant, M. Burke, R. Cook, B. Harris, C. Mosconi & B. Wickham (Eds.), Proceedings of the ICAR Conference (Vol. 23, pp. 221-227) https://www.icar.org/wp-content/uploads/2018/07/ICAR-Technical-Series-23-Auckland-2018-Proceedings.pdf

Villesen, P., Gertsch, P. J. & Boomsma, JJ. (2002). Microsatellite primers for fungus-growing ants. Molecular Ecology Resources, 2(3), 320-322.

Ronfort, J., Bataillon, T., Santoni, S., Delalande, M., David, J. & Prosperi, J.-M. (2006). Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. BMC Plant Biology, 6(28). https://doi.org/10.1186/1471-2229-6-28

Fredsted, T., Schierup, M. H., Pertoldi, C. & Kappeler, M. (2005). Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus). Molecular Ecology, 14, 2363-2372.

Starnawski, P., Bataillon, T., Ettema, T. J. G., Jochum, L. M., Schreiber, L., Chen, X., Lever, M. A., Polz, M. F., Jørgensen, B. B., Schramm, A. & Kjeldsen, K. U. (2017). Microbial community assembly and evolution in subseafloor sediment. Proceedings of the National Academy of Sciences (PNAS), 114(11), 2940-2945. https://doi.org/10.1073/pnas.1614190114

Damsgaard, E. M., Frøland, A., Jørgensen, O. D. & Mogensen, C. E. (1990). Microalbuminuria as predictor of increased mortality in elderly people. BMJ, 300(6720), 297-300.

Saetre, P., Grove, J., Børglum, A., Mors, O., Werge, T. M., Andreassen, O. A., Vares, M., Agartz, I., Terenius, L. & Jönsson, E. G. (2012). Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age at onset of schizophrenia: no consistent evidence for an association in the Nordic population. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 159B(8).

Kristensen, T. G., Nielsen, J. & Pedersen, C. N. S. (2013). Methods for Similarity-Based Virtual Screening. Computational and Structural Biotechnology Journal, 5(6). https://doi.org/10.5936/csbj.201302009

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Palle Villesen